Podcasts about Chromatin

In this episode of the Epigenetics Podcast, we talked with Boyan Bonev from the HelmholtzZetrum in Munich about his work on neuroepigenetics, focusing on gene regulation, chromatin architecture, and primate epigenome evolution, This Episode focuses on Dr. Bonev's recent research, particularly focusing on how chromatin architecture and gene regulation influence neural cell identity and function. He discusses his work investigating transcriptional activity in relation to chromatin insulation, highlighting a critical finding that induced expression of genes does not necessarily lead to chromatin insulation—a point that complicates prior assumptions about the relationship between gene expression and chromatin organization. This study aimed to determine the causal versus correlative aspects of chromatin architecture in brain development and links it to developmental processes and neurodevelopmental disorders. Building on his findings in gene regulation, Dr. Bonev elaborates on a significant study he conducted in his own lab, where he mapped the regulatory landscape of neural differentiation in the mouse neocortex. Here, he employed cutting-edge single-cell sequencing methodologies to analyze intricate gene and enhancer interactions, revealing that selective enhancer-promoter interactions are primarily cell-type specific. This nuanced understanding aids in deciphering the complexities associated with gene expression as it relates to neural stem cells and differentiated neurons, emphasizing the importance of single-cell analyses over bulk sequencing methods. Moreover, Dr. Bonev reveals a novel methodology developed in his lab that allows for the simultaneous assessment of spatial genome organization, chromatin accessibility, and DNA methylation at high resolution. This advancement not only reduces costs but also enhances the potential to correlate higher-dimensional genomic data with specific biological questions, fostering a more integrative approach to understanding genetic regulation. The discussion then shifts focus towards Dr. Bonev's recent project profiling primate epigenome evolution, where he investigated the 3D genome organization, chromatin accessibility, and gene expression among iPSCs and neural stem cells from various species, including humans, chimpanzees, gorillas, and macaques. In this research, he identifies trends related to transcription factor evolution and chromatin modifications across species. The insights gleaned from this work underscore the evolutionary significance of structural variations in the 3D genome, pointing to a possible link between chromatin dynamics and the evolutionary development of the primate brain.   References Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L, Papadopoulos GL, Lubling Y, Xu X, Lv X, Hugnot JP, Tanay A, Cavalli G. Multiscale 3D Genome Rewiring during Mouse Neural Development. Cell. 2017 Oct 19;171(3):557-572.e24. doi: https://doi.org/10.1016/j.cell.2017.09.043. PMID: 29053968; PMCID: PMC5651218. Noack, F., Vangelisti, S., Raffl, G. et al. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler. Nat Neurosci 25, 154–167 (2022). https://doi.org/10.1038/s41593-021-01002-4 Noack F, Vangelisti S, Ditzer N, Chong F, Albert M, Bonev B. Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids. Nat Cell Biol. 2023 Dec;25(12):1873-1883. doi: 10.1038/s41556-023-01296-5. Epub 2023 Nov 23. PMID: 37996647; PMCID: PMC10709149.   Related Episodes Characterization of Epigenetic States in the Oligodendrocyte Lineage (Gonçalo Castelo-Branco) Polycomb Proteins, Gene Regulation, and Genome Organization in Drosophila (Giacomo Cavalli) The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn)   Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: podcast@activemotif.com

In this episode of the Epigenetics Podcast, we talked with Viviana Risca from Rockefeller University about her work on RICC-Seq and how it's used to probe DNA-DNA contacts in intact or fixed cells using ionizing radiation. This Interview covers Dr. Viviana Risca's cutting-edge methodologies, such as RICC-seq, which enables high-resolution analysis of chromatin structures without traditional cross-linking biases. We engage in a detailed discussion about how different techniques, such as RICC-seq and Micro-C, complement each other to provide robust insights into nucleosome interactions and chromatin dynamics. Dr. Risca articulates the challenges and innovations within her lab as it navigates through the complexities of chromatin mapping. The episode takes an exciting turn toward traversing the landscape of her future research directions, particularly studying the role of linker histones and other chromatin architectural proteins in regulating gene expression. Dr. Risca emphasizes the importance of understanding chromatin's mechanical properties and how these influence cellular processes like transcriptional regulation, DNA replication, and cellular responses to damage. We also explore her collaborative work that bridges the gap between basic research and clinical applications, particularly in cancer therapy. Dr. Risca shares insights into her investigations into how chromatin dynamics change during cell cycle arrest and their implications for cancer therapy resistance. Our discussion culminates in her reflections on the definition of epigenetics, framing it as the exploration of how cellular mechanisms encode and process information.   References Risca VI, Denny SK, Straight AF, Greenleaf WJ. Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. Nature. 2017 Jan 12;541(7636):237-241. doi: 10.1038/nature20781. Epub 2016 Dec 26. PMID: 28024297; PMCID: PMC5526328. Soroczynski J, Anderson LJ, Yeung JL, Rendleman JM, Oren DA, Konishi HA, Risca VI. OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization. bioRxiv [Preprint]. 2024 Jul 13:2024.07.11.602973. doi: 10.1101/2024.07.11.602973. PMID: 39026714; PMCID: PMC11257509. Prescott, N. A., Biaco, T., Mansisidor, A., Bram, Y., Rendleman, J., Faulkner, S. C., Lemmon, A. A., Lim, C., Tiersky, R., Salataj, E., Garcia-Martinez, L., Borges, R. L., Morey, L., Hamard, P.-J., Koche, R. P., Risca, V. I., Schwartz, R. E., & David, Y. (2025). A nucleosome switch primes hepatitis B virus infection. Cell, S0092867425001023. https://doi.org/10.1016/j.cell.2025.01.033   Related Episodes Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden) Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman) Effects of Non-Enzymatic Covalent Histone Modifications on Chromatin (Yael David)   Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: podcast@activemotif.com

References Guerra, DJ 2024. Biochemistry lectures de novo. Zevon, W. 1980. "Empty Handed Heart" https://open.spotify.com/track/2jqAdzGsLts2SPcDxNjqGJ?si=a3d0cf83804641c3 Manfred Mann [solo], Colin Pattenden, Peter Thomas .1976 "The Road to Babylon" https://open.spotify.com/track/7cUBAZwaFjPkdEkFMAGy7Y?si=210544d489544d29 Haydn, Michael. 1794. Excerpts from his Catholic Masses https://open.spotify.com/album/67v4gHJdnVWAn4erEtbuIc?si=3FHMYbRGQJaTHGbqYHHo8Q --- Support this podcast: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/support

TWiV notes the passing of virologist Diane Griffin, first H5N1 influenza virus in US pigs, Innate immune control of influenza virus interspecies adaptation via IFITM3, and antiviral trained innate immunity in alveolar macrophages after SARS-CoV-2 infection reduces secondary influenza A virus disease. Hosts: Vincent Racaniello, Alan Dove, Rich Condit, Kathy Spindler, and Brianne Barker Subscribe (free): Apple Podcasts, RSS, email Become a patron of TWiV! Links for this episode MicrobeTV Discord Server MicrobeTV Fundraiser Diane Griffin passes (Johns Hopkins) Diane Griffin on TWiV 453 First H5N1 influenza virus in US pigs (CIDRAP) IFITM3 controls interspecies influenza virus infection (Nat Comm) Trained innate immunity by alveolar macrophages (Immunity) Timestamps by Jolene. Thanks! Weekly Picks Angela – See a giant ‘ghost particle' detector and more — October's best science images Brianne – October 27 APoD: Bat nebula Dickson – Nikon Small World Contest 2024 winners Kathy – AAAS 150th anniversary video, celebrating scientists and Pew's 2024 annual Trust in Science survey findings Rich – Cats Basically Are a Liquid After All, Study Confirms Alan – HHMI's Beautiful Biology site Vincent – EcoHealth Alliance Fights Back Listener Picks Hunter – Don't stop me now: Queen's Brian May on saving badgers — and the scientific method Anne – Reasons to be cheerful Intro music is by Ronald Jenkees Send your virology questions and comments to twiv@microbe.tv Content in this podcast should not be construed as medical advice.

In this episode of the Epigenetics Podcast, we talked with Carl Wu from John's Hopkins University about his work on nucleosome remodeling, histone variants, and the role of single-molecule imaging in gene regulation. Our discussion starts with Carl Wu sharing his first significant milestones, a paper in "Cell" and the serendipitous discovery of DNA hypersensitive sites, which transformed our understanding of chromatin accessibility and its implications for gene regulation. As we delve into Dr. Wu's specific areas of research, he elaborates on the biochemistry of nucleosome remodeling and the intricate role of chromatin remodeling enzymes like NURF. We discuss how these enzymes employ ATP hydrolysis to reposition nucleosomes, making DNA accessible for transcription. He then explains the collaborative relationship between chromatin remodelers and transcription factors, showcasing the fascinating interplay that governs gene expression and regulatory mechanisms. The conversation takes a deeper turn as we explore Carl Wu's groundbreaking studies on histone variants, particularly H2AZ. He elucidates the role of SWR1 in facilitating the exchange between H2A and H2AZ in nucleosome arrays. The high-resolution structural insights garnered from recent studies reveal how the enzyme mediates histone eviction and insertion with remarkable precision, providing a clearer picture of chromatin dynamics at a molecular level.   References Wu, C., Bingham, P. M., Livak, K. J., Holmgren, R., & Elgin, S. C. (1979). The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell, 16(4), 797–806. https://doi.org/10.1016/0092-8674(79)90095-3 Wu, C., Wong, Y. C., & Elgin, S. C. (1979). The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell, 16(4), 807–814. https://doi.org/10.1016/0092-8674(79)90096-5 Wu C. (1980). The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature, 286(5776), 854–860. https://doi.org/10.1038/286854a0 Wu, C., Wilson, S., Walker, B., Dawid, I., Paisley, T., Zimarino, V., & Ueda, H. (1987). Purification and properties of Drosophila heat shock activator protein. Science (New York, N.Y.), 238(4831), 1247–1253. https://doi.org/10.1126/science.3685975 Mizuguchi, G., Shen, X., Landry, J., Wu, W. H., Sen, S., & Wu, C. (2004). ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science (New York, N.Y.), 303(5656), 343–348. https://doi.org/10.1126/science.1090701 Kim, J. M., Visanpattanasin, P., Jou, V., Liu, S., Tang, X., Zheng, Q., Li, K. Y., Snedeker, J., Lavis, L. D., Lionnet, T., & Wu, C. (2021). Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife, 10, e69387. https://doi.org/10.7554/eLife.69387   Related Episodes Multiple challenges of ATAC-Seq, Points to Consider (Yuan Xue) Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret) ATAC-Seq, scATAC-Seq and Chromatin Dynamics in Single-Cells (Jason Buenrostro)   Contact Epigenetics Podcast on X Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Epigenetics Podcast on Threads Active Motif on X Active Motif on LinkedIn Email: podcast@activemotif.com

BUFFALO, NY- October 23, 2024 – A new #editorial was #published in Oncotarget's Volume 15 on October 11, 2024, entitled, “Gene regulatory network and signalling pathway rewiring: How blood cancer cells shift their shapes to evade drug treatment.” As highlighted in the paper, Acute Myeloid Leukemia (AML) is a complex and diverse disease caused by multiple mutations in genes that regulate transcription and growth. These mutations lead to extensive rewiring of the gene regulatory network (GRN), which alters the identity of hematopoietic stem and progenitor cells, ultimately blocking normal myeloid differentiation. A key feature of AML is the presence of mutations in growth factor receptor and signaling genes, such as FLT3, KIT, and RAS. Notably, FLT3 is one of the most commonly mutated genes in AML, with around 25% of cases showing an internal tandem duplication (ITD) that causes the receptor to remain constantly active. In their paper, researchers Constanze Bonifer and Peter N. Cockerill from the Institute of Cancer and Genomic Sciences at the University of Birmingham, UK, and the Murdoch Children's Research Institute, Royal Children's Hospital in Melbourne, Australia, discuss recent publications from their group addressing this issue through a multi-omics study. The authors investigated how gene regulatory networks (GRNs) in FLT3-ITD patients were rewired compared to normal cells and in response to FLT3 inhibitor treatment. Several key findings stood out, including: 1) Mapping of open chromatin regions revealed that patients initially responsive to FLT3 inhibition showed significant rewiring of their GRNs, forming new connections between transcription factors (TFs) and target genes, while non-responsive patients did not; 2) Chromatin immunoprecipitation (ChIP) experiments showed that drug treatment led to the loss of binding of RUNX1, the master regulator of hematopoiesis, and the MAP-Kinase (MAPK)-inducible TF AP-1; 3) Disruption of AP-1 binding via a dominant-negative version of the TF (dnFOS) also abolished RUNX1 binding at hundreds of sites, indicating that RUNX1 binding is AP-1 dependent; and 4) Inhibition of both AP-1 and RUNX1 led to a pronounced cell cycle block. “In summary, drugs that target individual signalling pathways in AML often fail to stop proliferation malignant growth, due to the wide variety, redundancy and cross talk between multiple pathways regulating and differentiation.” DOI - https://doi.org/10.18632/oncotarget.28662 Correspondence to - Constanze Bonifer - constanze.bonifer@mcri.edu.au Video short - https://www.youtube.com/watch?v=5c_uT6aE36A Sign up for free Altmetric alerts about this article: https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28662 Subscribe for free publication alerts from Oncotarget: https://www.oncotarget.com/subscribe/ Keywords - cancer, acute myeloid leukemia, gene regulatory networks, aberrant growth factor signaling, transcription, RUNX1/AP-1 axis About Oncotarget Oncotarget (a primarily oncology-focused, peer-reviewed, open access journal) aims to maximize research impact through insightful peer-review; eliminate borders between specialties by linking different fields of oncology, cancer research and biomedical sciences; and foster application of basic and clinical science. Oncotarget is indexed and archived by PubMed/Medline, PubMed Central, Scopus, EMBASE, META (Chan Zuckerberg Initiative) (2018-2022), and Dimensions (Digital Science). To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us: Facebook - https://www.facebook.com/Oncotarget/ X - https://twitter.com/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/@OncotargetJournal LinkedIn - https://www.linkedin.com/company/oncotarget Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget/ Spotify - https://open.spotify.com/show/0gRwT6BqYWJzxzmjPJwtVh

In this episode of the Epigenetics Podcast, we talked with Karine Le Roch from the University of California at Riverside about her work on malaria chromatin structure and its transcriptional regulation. In this Interview Dr. Le Roch discusses her investigation of post-transcriptional controls and nucleosome positioning in Plasmodium falciparum, employing next-generation sequencing and chromatin profiling methods. Karin emphasizes how these methodologies contribute to a comprehensive understanding of gene regulation beyond mere transcription initiation, emphasizing the significance of mRNA binding proteins and their role in stabilizing gene transcripts for translation. This exploration of the interaction between chromatin structure, transcriptional dynamics, and post-transcriptional regulation reveals a multidimensional perspective of gene expression. Transitioning to her lab's focus on high-throughput genomic technologies, we discuss how Karin and her team are uncovering conserved and species-specific genomic organization principles within various Plasmodium species. By generating 3D genomic models through Hi-C experiments, she describes how they have identified patterns that underline the parasite's immune evasion strategies. In particular, we learn how genes involved in antigenic variation are controlled through intricate epigenetic mechanisms, illuminating the pathways that allow these parasites to elude host immune responses.   References Le Roch, K. G., Zhou, Y., Blair, P. L., Grainger, M., Moch, J. K., Haynes, J. D., De La Vega, P., Holder, A. A., Batalov, S., Carucci, D. J., & Winzeler, E. A. (2003). Discovery of gene function by expression profiling of the malaria parasite life cycle. Science (New York, N.Y.), 301(5639), 1503–1508. https://doi.org/10.1126/science.1087025 Ponts, N., Harris, E. Y., Prudhomme, J., Wick, I., Eckhardt-Ludka, C., Hicks, G. R., Hardiman, G., Lonardi, S., & Le Roch, K. G. (2010). Nucleosome landscape and control of transcription in the human malaria parasite. Genome research, 20(2), 228–238. https://doi.org/10.1101/gr.101063.109 Bunnik, E. M., Cook, K. B., Varoquaux, N., Batugedara, G., Prudhomme, J., Cort, A., Shi, L., Andolina, C., Ross, L. S., Brady, D., Fidock, D. A., Nosten, F., Tewari, R., Sinnis, P., Ay, F., Vert, J. P., Noble, W. S., & Le Roch, K. G. (2018). Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nature communications, 9(1), 1910. https://doi.org/10.1038/s41467-018-04295-5   Related Episodes Epigenetics in Human Malaria Parasites (Elena Gómez-Diaz)   Contact Epigenetics Podcast on X Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Epigenetics Podcast on Threads Active Motif on X Active Motif on LinkedIn Email: podcast@activemotif.com

In this episode of the Epigenetics Podcast, we talked with Bas van Steensel from the Netherlands Cancer Institute about his work on characterizing chromatin at the Nuclear Lamina. The Interview starts with discussing Bas van Steensel's significant contributions to understanding genome-nuclear lamina interactions. Bas detailed the development of the DAM-ID technique during his postdoctoral studies, which provided a novel way to map genome-wide occupancy and identify Lamina-Associated Domains (LADs). He elaborated on how LADs reveal a distinct domain architecture, often correlating with gene expression levels. This prompted an exploration of the dynamics of these domains during differentiation processes, allowing insights into how gene activation and repression are influenced by their positioning relative to the nuclear lamina. The conversation highlighted the intricate relationship between chromatin dynamics and gene regulation, with Bas sharing compelling findings on how LADs behave during cell differentiation. The research indicated that regions moving away from the lamina often correlated with increased gene expression, revealing a complex interplay of spatial genome organization and transcriptional activity. Additionally, we ventured into the significance of outreach and transparency in scientific research. Bas shared his philosophy regarding collaboration and the ethical responsibility of scientists to share knowledge and resources openly. He emphasized that making lab notebooks and research processes accessible can greatly enhance reproducibility and understanding in the scientific community.   References Open Science Policy of our lab Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M. B., Talhout, W., Eussen, B. H., de Klein, A., Wessels, L., de Laat, W., & van Steensel, B. (2008). Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature, 453(7197), 948–951. https://doi.org/10.1038/nature06947 Kind, J., Pagie, L., Ortabozkoyun, H., Boyle, S., de Vries, S. S., Janssen, H., Amendola, M., Nolen, L. D., Bickmore, W. A., & van Steensel, B. (2013). Single-cell dynamics of genome-nuclear lamina interactions. Cell, 153(1), 178–192. https://doi.org/10.1016/j.cell.2013.02.028 Kind, J., Pagie, L., de Vries, S. S., Nahidiazar, L., Dey, S. S., Bienko, M., Zhan, Y., Lajoie, B., de Graaf, C. A., Amendola, M., Fudenberg, G., Imakaev, M., Mirny, L. A., Jalink, K., Dekker, J., van Oudenaarden, A., & van Steensel, B. (2015). Genome-wide maps of nuclear lamina interactions in single human cells. Cell, 163(1), 134–147. https://doi.org/10.1016/j.cell.2015.08.040 Leemans, C., van der Zwalm, M. C. H., Brueckner, L., Comoglio, F., van Schaik, T., Pagie, L., van Arensbergen, J., & van Steensel, B. (2019). Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. Cell, 177(4), 852–864.e14. https://doi.org/10.1016/j.cell.2019.03.009 van Schaik, T., Liu, N. Q., Manzo, S. G., Peric-Hupkes, D., de Wit, E., & van Steensel, B. (2022). CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. Genome biology, 23(1), 185. https://doi.org/10.1186/s13059-022-02754-3 van Steensel B. (2018). Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results. EMBO reports, 19(10), e46866. https://doi.org/10.15252/embr.201846866   Related Episodes scDamID, EpiDamID and Lamina Associated Domains (Jop Kind) Identification of Functional Elements in the Genome (Bing Ren) Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff)   Contact Epigenetics Podcast on X Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Epigenetics Podcast on Threads Active Motif on X Active Motif on LinkedIn Email: podcast@activemotif.com

Guest: Dr. Erin Macdonald Dr. Erin Macdonald, the official science advisor for the Star Trek universe, joins us to discuss the science behind Season 5 of Star Trek: Discovery and Season 2 of Star Trek: Prodigy. "Chromatin remodeling in tribbles in Star Trek: Prodigy" by Prof. Mohamed Noor: https://www.youtube.com/watch?v=r2PePbR3FPk Erin's Nerd Nite talk, "Faster-Than-Light Travel in Science Fiction": https://www.youtube.com/watch?v=4Lw7JOgQ_MI Mike's Nerd Nite talk, "The Astrobiology of Star Trek": https://www.youtube.com/watch?v=JtgcaVg7puM Follow us on Twitter! Strange New Worlds: twitter.com/scienceoftrek Mike: twitter.com/miquai Erin: twitter.com/drerinmac

Send us a Text Message.About the guest: Giulia Santoni, PhD is a neuroscientist who obtained her PhD at the EPFL in Switzerland, where she studied epigenetic influences on memory formation.Episode summary: Nick and Dr. Santoni discuss: transcription & gene regulation; synaptic plasticity; learning & associative memory; epigenetics, histones, DNA methylation, and mechanisms of gene regulation; chromatin plasticity & the neural basis of memory formation; and more.Related episodes:Emotion, Cognition, Consciousness, Behavior & Brain Evolution | Joseph LeDoux | #73Cognitive Neuroscience, Cognitive Flexibility & Control, Attention, Working Memory, Multitasking & Behavior | Tobias Egner | #130*This content is never meant to serve as medical advice.Support the Show.All episodes (audio & video), show notes, transcripts, and more at the M&M Substack Try Athletic Greens: Comprehensive & convenient daily nutrition. Free 1-year supply of vitamin D with purchase.Try SiPhox Health—Affordable, at-home bloodwork w/ a comprehensive set of key health marker. Use code TRIKOMES for a 10% discount.Try the Lumen device to optimize your metabolism for weight loss or athletic performance. Use code MIND for 10% off.Learn all the ways you can support my efforts

Nels and Vincent discuss the genome sequence of an ancient wooly mammoth, which shows that the three-dimensional architecture of the DNA can persist after 50,000 years. Hosts: Nels Elde and Vincent Racaniello Subscribe (free): Apple Podcasts, Google Podcasts, RSS, email Become a patron of TWiEVO Links for this episode Join the MicrobeTV Discord server Three dimensional architecture of 50,000 year old wooly mammoth genome (Cell) Timestamps by Jolene Science Picks Nels – Mysterious SARS-CoV-2 variants showing up in sewer samples Vincent – ‘Cocaine sharks' found in waters off Brazil Music on TWiEVO is performed by Trampled by Turtles Send your evolution questions and comments to twievo@microbe.tv

Chromatin Accessibility: A new avenue for gene editingHello and welcome to the NanoLSI podcast. Thank you for joining us today. In this episode we feature the latest research by researchers from Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, led by Yusuke Miyanari.The research described in this podcast was published in Nature Genetics in February 2024Kanazawa University NanoLSI websitehttps://nanolsi.kanazawa-u.ac.jp/en/Chromatin Accessibility: A new avenue for gene editingIn a study recently published in Nature Genetics, researchers from Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University explore chromatin accessibility, that is, endogenous access pathways to the genomic DNA, and its use as a tool for gene editing.Our DNA is protected from unwanted external modifications by forming structures called nucleosomes that consist of threads of DNA wound around chunks of special proteins known as histones. This unique coiled shape prevents the access of undesirable molecules to a cell's DNA. However, for vital genetic functions—such as DNA repair—the right set of proteins require access to these DNA fragments. This phenomenon known as ‘chromatin accessibility' involves a privileged set of protein molecules, many of which are still unknown.Now, researchers from Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University, led by Yusuke Miyanari, have used advanced genetic screening methods to unravel chromatin accessibility and its pathways.So how did they go about it?For the investigation the team used a combination of two technologies—CRISPR screening and ATAC-see. While the former is a method to suppress the function of a desired set of genes, the latter is a means to identify which ones are essential for chromatin accessibility. Thus, using this method all genes playing a crucial role in chromatin accessibility could be pinned down.With the help of these assays, novel pathways and individual players involved in chromatin accessibility were uncovered—some playing a positive role and some negative. Of these, one particular protein, TFDP1, showed a negative effect on chromatin accessibility. When it was suppressed, a significant increase in chromatin accessibility was observed, accompanied by nucleosome reduction. A deeper dive into the mechanism of TFDP1 revealed that it functions by regulating the genes responsible for production of certain histone proteins.The team then focused their study towards exploring biotechnological applications of their findings. After suppressing TFDP1, two different approaches were tried. The first approach involved gene editing using the CRISPR/Cas9 tool. This revealed that deletion of TFDP1 made the gene editing process easier. Now, most chromatin accessibility occurs in nucleosome-depleted regions or NDRs. However, by suppressing TFDP1 chromatin accessibility occurred not only in NDRs but across other regions as well. Secondly, the depletion of TFDP1 aided the process of converting regular cells into stem cells, a massive step forward in cellular transformation.This study identified new chromatin accessibility pathways and channels for exploring its potential even further. “Our study shows the significant potential to manipulate chromatin accessibility as a novel strategy to enhance DNA-templated biological applications, including genome editing and cellular reprogramming,” conclude the researchers.ReferenceSatoko Ishii, Taishi Kakizuka, Sung-Joon Park, Ayako Tagawa, Chiaki Sanbo, Hideyuki Tanabe, Yasuyuki Ohkawa, Mahito Nakanishi, Kenta Nakai, Yusuke Miyanari. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nature Genetics, FebNanoLSI Podcast website

In this episode of the Epigenetics Podcast, we talked with Mark Parthun from Ohio State University about his work on the role of Hat1p in chromatin assembly. Mark Parthun shares insights into his pivotal paper in 2004 that explored the link between type B histone acetyltransferases and chromatin assembly, setting the stage for his current research interests in epigenetics. He highlights the role of HAT1 in acetylating lysines on newly synthesized histones, its involvement in double-strand break repair, and the search for phenotypes associated with HAT1 mutations. The discussion expands to a collaborative research project between two scientists uncovering the roles of HAT1 and NASP as chaperones in chromatin assembly. Transitioning from yeast to mouse models, the team investigated the effects of HAT1 knockout on mouse phenotypes, particularly in lung development and craniofacial morphogenesis. They also explored the impact of histone acetylation on chromatin dynamics and its influence on lifespan, aging processes, and longevity.   References Parthun, M. R., Widom, J., & Gottschling, D. E. (1996). The Major Cytoplasmic Histone Acetyltransferase in Yeast: Links to Chromatin Replication and Histone Metabolism. Cell, 87(1), 85–94. https://doi.org/10.1016/S0092-8674(00)81325-2 Kelly, T. J., Qin, S., Gottschling, D. E., & Parthun, M. R. (2000). Type B histone acetyltransferase Hat1p participates in telomeric silencing. Molecular and cellular biology, 20(19), 7051–7058. https://doi.org/10.1128/MCB.20.19.7051-7058.2000 Ai, X., & Parthun, M. R. (2004). The nuclear Hat1p/Hat2p complex: a molecular link between type B histone acetyltransferases and chromatin assembly. Molecular cell, 14(2), 195–205. https://doi.org/10.1016/s1097-2765(04)00184-4 Nagarajan, P., Ge, Z., Sirbu, B., Doughty, C., Agudelo Garcia, P. A., Schlederer, M., Annunziato, A. T., Cortez, D., Kenner, L., & Parthun, M. R. (2013). Histone acetyl transferase 1 is essential for mammalian development, genome stability, and the processing of newly synthesized histones H3 and H4. PLoS genetics, 9(6), e1003518. https://doi.org/10.1371/journal.pgen.1003518 Agudelo Garcia, P. A., Hoover, M. E., Zhang, P., Nagarajan, P., Freitas, M. A., & Parthun, M. R. (2017). Identification of multiple roles for histone acetyltransferase 1 in replication-coupled chromatin assembly. Nucleic Acids Research, 45(16), 9319–9335. https://doi.org/10.1093/nar/gkx545 Popova, L. V., Nagarajan, P., Lovejoy, C. M., Sunkel, B. D., Gardner, M. L., Wang, M., Freitas, M. A., Stanton, B. Z., & Parthun, M. R. (2021). Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones. Nucleic Acids Research, 49(21), 12136–12151. https://doi.org/10.1093/nar/gkab1044   Related Episodes Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni) Effects of Non-Enzymatic Covalent Histone Modifications on Chromatin (Yael David) scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)   Contact Epigenetics Podcast on X Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Epigenetics Podcast on Threads Active Motif on X Active Motif on LinkedIn Email: podcast@activemotif.com

Is aging a disease that can be cured? Neil deGrasse Tyson and cohosts Chuck Nice and Gary O'Reilly discover the field of epigenetics, the Information Theory of Aging, and curing blindness for mice with Professor of Genetics at Harvard Medical School, David Sinclair.NOTE: StarTalk+ Patrons can listen to this entire episode commercial-free here: https://startalkmedia.com/show/is-aging-a-disease-epigenetics-with-david-sinclair/Thanks to our Patrons Jason L, Daniel Holzmann, Anne P Vance, Unknown, Myles G Blanton, Paul A. Straus, and Gregory Dees for supporting us this week.

Dr. Peter Hotez is a veritable force. He has been the tip of the spear among physicians and scientists for taking on anti-science and has put himself and his family at serious risk.Along with Dr. Maria Bottazzi, he developed the Corbevax Covid vaccine —without a patent— that has already been given to over 10 million people, and was nominated for the Nobel Peace Prize. Here an uninhibited, casual and extended conversation about his career, tangling with the likes of RFK Jr, Joe Rogan, Tucker Carlson, Steve Bannon, and an organized, funded, anti-science mob, along with related topics.Today is publication day for his new book, The Deadly Rise of Anti-Science.Transcript (AI generated)Eric Topol (00:00):Hello, this is Eric Topol with Ground Truths, and I'm with my friend and colleague who's an extraordinary fellow, Dr. Peter Hotez. He's the founding dean of the National School of Tropical Medicine and University professor at Baylor, also at Texas Children's founding editor of the Public Library Science and Neglected Tropical Disease Journal. and I think this is Peter, your fifth book.Peter Hotez (00:28):That's my fifth single author book. That's right, that's right.Eric Topol (00:32):Fifth book. So that's pretty amazing. Peter's welcome and it's great to have a chance to have this conversation with you.Peter Hotez (00:39):Oh, it's great to be here and great to be with you, Eric, and you know, I've learned so much from you during this pandemic, and my only regret is not getting to know you before the pandemic. My life would've been far richer. AndPeter Hotez (00:53):I think, I think I first got to really know about you. You were are my medical school, Baylor College of Medicine, awarded you an honorary doctorate, and that's when I began reading about it. Oh. I said, holy cow. Why didn't, why haven't I been with this guy before? SoEric Topol (01:08):It's, oh my gosh. So you must have been there that year. And I came to the graduation.Peter Hotez (01:12):No, I actually was speaking at another graduation. That's why I couldn't be there, . Ah,Eric Topol (01:18):Right. As you typically do. Right. Well, you know, it's kind of amazing to track your career besides, you know, your baccalaureate at Yale and PhD at Rockefeller and MD at Cornell. But you started off, I, I think deep into hookworm. Is that where you kind of got your start?Peter Hotez (01:36):Yeah, and I'm still, and I'm still there actually, the hookworm vaccine that I started working on as an MD-PhD student at Rockefeller and Cornell is now in phase 2 clinical trials. Wow. So, which is, I tell people, is about the average timeframe --about 40 years-- is about a, not an unusual timeframe. These parasites are obviously very tough targets. oh man. And then we have AOIs vaccine and clinical trials and a Chagas disease vaccine. That's always been my lifelong passion is making vaccines for these neglected parasitic infections. And the story with Covid was I had a collaboration with Dr. Sarah Lustig at the New York Blood Center, who, when we were working on a river blindness vaccine, and she said, Hey, I want you to meet these two scientists, New York Blood Center. They're working on something called coronaviruses vaccines.(02:27):They were making vaccines for severe acute respiratory syndrome and SARS and ultimately MERS. And so we, we plugged their, their, some of their discoveries into our vaccine development machine. And they had found that if you were using the receptor binding domain of the, of the spike protein of SARS and ultimately MERS it produced an equivalent protective immune response neutralizing antibodies without the immune enhancement. And that's what we wrote to the NIT to do. And they supported us with a $6 million grant back in 2012 to make SARS and MERS vaccines. And, and then when Covid 19 hit, when the sequence came online and BioXriv in like early 2020, we just pivoted our program to Covid and, and we were able to hit the ground running and it worked. Everything just clicked and worked really well. And stars aligned and we were then transferred that technology.(03:26):We did it with no patent minimizing strings attached to India, Indonesia, Bangladesh. any place that we felt had the ability to scale up and produce it, India went the furthest. They developed it into Corbevax, which has reached 75 million kids in India. And another 10 million as their, for their primary immunization. Another 10 million is adult booster. And then Indonesia developed their own version of our, of our technology called IndoVac. And, and that's also reaching millions of, of people. And now they're using it as a, also as a booster for Pfizer, because I think it may be a superior booster. So it was really exciting to s you know, after working in parasitic disease vaccines, which are tough targets and decades to get it through the clinical trials because the pressure was on to move quickly goes to show you when people prioritize it. And also the fact that I think viruses are more straightforward targets than complex parasites. And well, so that in all about a hundred million doses have been administered andEric Topol (04:33):Yeah, no, it's just a spectacular story, Corbevax and these other named of the vaccine that, that you and Maria Bottazzi put together and without a patent at incredibly low cost and not in the us, which is so remarkable because as we exchanged recently, the us the companies, and that's three Moderna, Pfizer, and Novavax are going to charge well over $110 per booster of the, the new booster updated XBB.1.5. And you've got one that could be $2 or $4 that's,Peter Hotez (05:11):And it's getting, so we're making, we're making the XBB recombinant protein booster of ours. And part of it's the technology, you can, you know, it's done through microbial fermentation in yeast, and it's been in a big bioreactor. And it's an older technology that's been around a couple of decades, and there's no limit to the amount you could scale. The yields are really high. So we can do this for two to $3 a dose, and it'd even be less, it wasn't for the cost of the adjuvant. The C P G, the nucleotide is probably the most expensive component, but the antigen is, you know, probably pennies to, to, you know, when you're doing it at that scale. And, and so that, that's really meaningful. I'd like to get our XBB booster into the us It's,Eric Topol (05:55):Yeah, it's just no respect from,Peter Hotez (05:58):We're not a pharma company, so we don't, we didn't get support from Operation Warp Speed, and so we didn't get any US subsidies for that. And it's just very hard to get on the radar screen of BARDA and those agencies and, 'cause that's, they're all set up to work with pharma companies.Eric Topol (06:16):Yeah, I know. It's, it's just not right. And who pays for this is the people, the public, because they, you know, the affordability is going to have a big influence on who gets boosters and is drivingPeter Hotez (06:27):. Yeah. So, so what I say is we, we provide, you know, the anti-vaccine guys, like the call me a Shill for pharma, not knowing what they're talking about. We've done the opposite, right? We've provided a path that shows you don't need to go to big pharma all the time. And, and so they should be embracing what we're doing. So we, we've, you know, have this new model for how you can get low cost vaccines out there. Not, not to demonize the pharma companies either. They, they do what they do and they do a lot of important innovation. But, but there are other pathways, especially for resource coordination. So we'd love to get this vaccine in, in the us I think it's looking a little work just, just as well, it's, you know, butEric Topol (07:12):You, yeah, I mean, it's not, I don't want ot demonize the vaccine companies either, but to raise the price fivefold just because it's not getting governed subsidy and the billions that have been provided by the government through taxpayer monies. Yeah.Peter Hotez (07:28):Well, the Kaiser Family Foundation reported that they did an analysis that, that pharma, I think it was Pfizer and Moderna got 25 to 30 billion Yeah. Dollars in US subsidies, either for development costs for Moderna. I think Pfizer didn't accept development costs, but they both took advanced purchase money, so $30 billion. And you know, that's not how you show gratitude to the American people byEric Topol (07:55):JackingPeter Hotez (07:56):Up the price times for, I think I said, guys, you know, have some situational awareness. I mean, do you want people to hate you? Yeah.Eric Topol (08:04):That's what it looks like. Well, speaking of before I get to kind of the anti-science, the, THE DEADLY RISE OF ANTI-SCIENCE, your new book, I do want to set it up that, you know, you spent a lot of your career besides working on these tropical diseases, challenging diseases, you know, Leischmania, and you know, Chagas, and the ones you've mentioned. You've also stood up quite a bit for the low middle income countries with books that you've written previously about forgotten people, Blue Marble Health. And so, I, I, before I, I don't want to dismiss that 'cause it's really important and it ties in with what the work you've done with the, the Covax or Covid vaccine. Now, what I really want to get into is the book that you wrote that kind of ushered in your very deep personal in anti-science and anti-vax, which I'm going in a minute ask you to differentiate. But your daughter, Rachel, you wrote a book about her and about vaccines not causing autism. So can you tell us about that?Peter Hotez (09:11):Yeah. So as you point out, my first two books were about these, what I would call forgotten diseases of Forgotten people. In fact, that's what the first book was called, forgotten People, forgotten Diseases, which my kids used to call Dad's Forgotten book on Forgotten people, Forgotten Diseases, all the, all the, now it's in his third edition. So, but it talks about, you know, the, how important these conditions are. It's just that they're widely prevalent. It's just that they're occurring among people who live in extreme poverty, including people in poverty in the United States. That's why we set up our School of Tropical Medicine on the US Gulf Coast. I didn't do it for the summer weather which is these days in this heat dome. It's like, well, living on planet Mercury right now, in here, here in Texas.(09:58):But then, so that, that's what, that's how I started learning how to advocate, you know, for people and for diseases through neglected diseases. But, you know, when we came to Texas, we saw this very aggressive anti-vaccine movement, and they were making false claims that vaccines cause autism. And, and I said, look, I'm, you know, I'm a vaccine scientist here in Texas. I have a daughter with autism, Rachel, with an, an intellectual disabilities. And so if I don't say something who does, and, and then wrote the book, vaccines did not cause Rachel's Autism, which unfortunately made me public enemy number one or two with anti-vaccine groups. but you know, it, it, it does a deep dive explaining the science, showing there's absolutely no link between vaccines and autism, but also an absence of plausibility because what we know about autism, how it begins in early fetal brain development through the action of autism genes.(10:54):And we actually did whole exome genomic sequencing on, on Rachel and my wife Ann and I, and we found Rachel's autism gene, which is like many of them in, involved in early neuronal communication and connections. It was actually a neuronal cytoskeleton gene, as are many, in this case, a neuronal spectrum. And that one hadn't been reported before, but other neuronal cytoskeleton genes had been reported by the Broad Institute at Harvard, m i t and others. And, and that was important to have that alternative narrative because the refrain from always was, okay, doc, if vaccines don't do it, what does cause autism? And, and being able to have that other side of the story, I think is very compelling.Eric Topol (11:37):What was it, the, the fabricated paper by Andrew Wakefield and the Lancet that, that got all this started? Or did it really annotate the ? There wasPeter Hotez (11:47):Something before in the eighties about the DPT, the diptheria, pertussis tetanus vaccine claiming it caused, you know, seizures and then could lead to neurodevelopmental difficulties. But it really took off with the Wakefield paper in 1998, published in The Lancet. And that claimed that the MMR vaccine, a live virus vaccine, had the ability to replicate in the colon of kids. And somehow that led to pervasive developmental disorder. That was the term used back then. And I was Rachel's diagnosis. And it never made sense to me how something, 'cause the reason it's pervasive is it's, it's global in, in the central nervous system in, in the brain. And how, how could something postnatally do something like that? I mean, there is, there are epigenetic underpinnings of autism as well, and that's fun. Eric, you ever talk to, ever try to talk to lay audience about epigenetics? That's a tough one. That's, that's a tough one. You start talking about microRNAs and DNA methylation, histone modification. The, the lights go out pretty quickly, butEric Topol (12:46):Chromatin and histone modification. Right? Bye-bye. Yeah, you got that one.Peter Hotez (12:51):That, so that's,Eric Topol (12:52):But that, that was your really, you knowPeter Hotez (12:55):But that's when, you know, I started going up against Robert F. Kennedy Jr. And, and, and all that was, that was pre-pandemic.Eric Topol (13:03):That was in 2018, right?Peter Hotez (13:05):2017 Trump came out and said, you know, it was about to be inaugurated and, and RFK Jr said he was going be appointed to run a vaccine commission by the Trump administration. And, and I actually was sitting, you know, in my office and my assistant said Dr. Francis Collins and Dr. Anthony Fauci are on the phone. Do you have time to talk with us ? And I said, yeah, I think so. And they arranged, they had arranged for me to, because I have a daughter with autism could articulate why vaccines don't cause out arranged for me to speak with RFK Jr threw it through a mediator and, and, and it didn't go well. He was just really dug in and, and soEric Topol (13:49):He, he was just as bad then as now.Peter Hotez (13:52):Yeah. I mean, it was just, you know, kept on, you know, as I say, moving the goalposts, you couldn't pin him down. Was he talking about MMR? Was he talking about the am Marisol, was he talking about spacing vaccines too close together? He just, that always kept on moving around and, and then it was not even autism at times. You were talking about it was something called chronic illness, you know, you know, what do you do with that? Mm-hmm. . So I, and that's one when I was challenged by, you know, Joe Rogan and Elon to debate RFK Jr, one of the reasons I didn't want to do it, because I, I knew, you know, doing it in public would be no different from doing this in, in, in private, that it would not be a productive conversation.Eric Topol (14:39):Yeah, no, that I can, I do want to get into that, because that was the latest chapter of kind of vicious anti-science, which was taking on covid and vaccines and the whole ball of wax whereby you were challenged by Joe Rogan on his very big podcast, which apparently is, you know, bigger than CNN  various cable news networks,Peter Hotez (15:07):Which I had done, I had been on his show a couple of times. Yeah. And that was, and that was okay. I mean, I actually liked the experience quite a bit. AndEric Topol (15:15):And he challenged you to go on with RFK Jr. And then Elon Musk, you know, joined and, you know, basically Peter Hotez (15:21):Actually, he started before then, about the week before, or a few days before, Steve Bannon publicly declared me a criminal. And you know, which I said, wow, that's, that's something. And then Roger Stone weighed in. So it was this whole sort of frontal attack from, well, people with extremist viewpoints. And there'sEric Topol (15:41):Been a long history, and a Tucker Carlson in the book, you quote, he referring to Hotezis a misinformation machine constantly spewing insanity. Speaking of projecting things, my goodness. Yeah.Peter Hotez (15:54):Yeah. Well, he did that. You know, he, that was the, that was in 2022. It was, he went on his broadcast the evening after the evening of the, in the, during that day I, with Maria, I was, we were nominated for the Nobel Peace Prize. And I guess, and I don't know if the two are related or not, I think it may have driven him off the edge, and then he just went on this rant against me. And, you know, claimed I have no experience anything about Covid. I mean, we had made two covid vaccines, right. And transferred the technology nominated for the Nobel Peace Prize and just, you know, omitted all of that. But this is how these guys work. It's, it's all about asserting control. And, and it seems to come from an extremist element of the, of the far right.(16:39): and, and, and it's not that I'm a very political person at all. I mean, you know, I've been here in Texas now for 12 years, and I've gotten, you know, I've gotten to know people like Jim Bakker and his wife Susan Baker and, and you know, a lot of prominent Republicans here in Texas, that that wasn't an issue. This is something sort of weird and, and twisted. And, and the point that I make in the book is, and it's not just a theoretical concern or a construct, it's the fact that so many Americans lost their lives during the delta and BA.1 omicron waves in 2021 and 2022, after vaccines were widely and freely available because they refused a vaccine. so vaccines were rolled out in 2021. we started strong and then vaccination rates stalled. And then we didn't get very far by this after the spring because there was this launch of an, of, of a wave of what I call anti-vaccine or anti-science aggression, convinced that deliberately sought to convince Americans not to take a covid vaccine.Eric Topol (17:56):Chapter, yeah. Your chapter in the book Red Covid. Yeah, gets into it quantifies it, hundreds of thousands of lives lost. And I know you've seen some of the papers whereby studies in red states or states like Ohio and Florida showing the, the, the connection between this.Peter Hotez (18:15):Yeah, I, I relied heavily on this guy Charles Gaba, who has a, a website called ACA signups. And he did some really in, you know, strong analysis showing that the, that the people who were refusing covid vaccines and losing their lives were overwhelmingly in red states and could even show the redder the county as measured by voters, the lower the immunization rate and higher the death rates. And the term Red Covid came from David Leonhart of the New York Times wrote an article about Charles Gaba's work, and he called it Red Covid and did a lot of updates. And the data is so strong. I mean, so much so that one person at the Kaiser Family Foundation wrote, if you wanted to ask me whether or not a person was vaccinated, and I can only know one thing about them, you know, she said, the one thing I'd want to know is what political party they're affiliated with.(19:09):It was, it's, it's that strong. And it's, and it's not that I care about your politics, even your extreme views, but somehow we have to uncouple this one from it, right. Because somehow not getting vaccinated been added to the canon of stuff that you're supposed to believe in. If you are, if you're down that rabbit hole watching Fox News every night, or, or listening to Rogan Podcasts and that sort of stuff. And somehow we have to uncouple those two, and it's the hardest thing I've ever had to do. First of all, it's unpleasant to talk about, because all of, you know, your training, Eric mine as well is, you know, said you don't talk about politics and you're, you know, we're supposed to be above all that. But what do you do when the death and dying is so strong on, on one side?(19:58):And, and I, I was in east Texas not too long ago, giving grand rounds at a new medical school in East Texas and Tyler, Texas, and very conservative part of the state. And, you know, basically everyone you talked to has lost a loved one mm-hmm. because they refused a Covid vaccine and died. I mean, that's, that's where you really start to see that. And then, and these people are wonderful people. I gave you know Bob Harrington at oh yes, at at Stanford Medicine, now he's going be the Dean of Cornell. He, he invited me with Michelle Berry to, to give grand rounds, medical grand rounds at Stanford. And I said, look, if, if my car had broken down and the flat had a flat tire, and you, and I can't fix, I'm, I'm a disaster at fixing anything.(20:49):So if you said, okay, where you had the choice, where, where do you want your car broken down in Palo Alto, California, or Stanford is, or very wealthy enclave or East Texas, I'd say I'd pick East Texas in a second. 'cause in East Texas, they'd be fighting over who you know, is going to rush to help you change your tire. Right? And these are, you know, just incredible people. And they were victims. They were victims of this far right. Attacks from, from Fox News. And one of the things I do in the book is, you know, the documentation is really strong media matters. The Watchdog group has looked at the evening broadcast of Tucker Carlson, Laura Ingram, and, and Hannity, and, you know, can I, you know, actually identify the anti-vaccine content with each broadcast during the summer and fall. And then our a social science research group out of ETH Zurich, the Federal University of Technology of Zurich, where Einstein studied, actually, you know, one of the great universities did another analysis and showed that watching Fox News is one of the great predictors of refusing a vaccine.(21:52):And, and so that, those were the amplifiers, but those generating a lot of the messages were elected leaders coming out of the House Freedom Caucus, or Senator, you know, Johnson's conservative senate that, I don't even like to use the word conservative, because it's not really that they're conservative, they're extremists. And yeah, a Senator Johnson of Wisconsin, or Rand Paul, you know, of, of Kentucky, you know, all the physician know what Yeah. And know physician and the CPAC conference of conservatives in Dallas, in 2021, they said, first you're gonna, they're going to vaccinate you, and then they're going to take away your guns and your Bibles. And as ridiculous as that sounds to us, people in my state of Texas and elsewhere in the South accepted it and didn't take a covid vaccine and pay for it with their lives. And, and how do we, you know, begin walking that back?(22:45):And, and the point of writing the book said, well, the first step is to at least describe it so people can know what we're talking about. Because I think right now, when you look at the way people talk about anti-vaccine or anti-science stuff, they, they call it misinformation or the infodemic, like it's just some random junk that appears out of nowhere on the internet. And it's not any of those things. It's, it's organized, it's well financed. It's politically motivated, and it's killing Americans on, on a massive scale. So I said, look, you know, I, I went, I'm did my MD and PhD in New York at Rockefeller and Cornell. I devoted my life to becoming a vaccine scientist. You know, the motto of Rockefeller universities to be the Rockefeller Institute of Medical Research translates to science for the benefit of humanity. And, and I believe making vaccines is one of the high expressions. And I think most physician scientists believe, I think you believe that too. And that's why you're, you're in this as well, you know, not vaccines, but you know, other lifesaving interventions. And, and so I said, well, now making vaccines is not enough. 'cause now we have to counter all of this anti-vaccine stuff, and there's, there's nobody better, you know, in terms of my training and my background going up against anti-vaccine movements because of Rachel to do this. So I, I've done it and yeah.Eric Topol (24:11):Well, you've done it. All right. you,Peter Hotez (24:14):That's my wife. Ann says you've done it. Alright, .Eric Topol (24:17):Well, as I wrote in your, with your book of blurb about you are a new species, the physician scientist warrior, and you are Peter, because you're the only one of all the physicians. We're talking about a million docs almost in this country who has stood up and you've put your life at risk, your family at risk, you've had death threats, you've had the people you know, come right to your house. and so what you've described this kind of coalescence of political will of extremists, media, of course, amplification because it benefits them. They, they're selling more you know, they get more viewers, more the spots for commercials and more they can charge. And then you're even, as you described in the book, so well, is you even have outside interested parties like Russia as part of this organization, of this coalescence of forces that are taking on the truth, that are promoting anti-science, that are winding up, people are dying, or, yeah. Or having a, you know, serious morbidity,Peter Hotez (25:26):Right? Yeah. In the case of, in the case of Russia, , it's a slightly different motivation. What they're doing is they're filling the internet and social media with both anti-vaccine messages and pro-vaccine messages. Because they have a different agenda. Their agenda is destabilized democracies. So what they're doing is they're cherry picking certain issues that they can use as a wedge to sow discord. And so when they saw the stuff about vaccines, yeah, they'll flood it with both pro and anti-vaccine message. And you see the stuff on Twitter, so much of it is computer generated, and it's just repeats the same stuff over and over again. And, and a lot of that are, you know, some of that not only, only Russia, I think China's doing it, North Korea, Iran's doing it, but particularly Russia. And that was documented by a colleague of mine, David Broniatowski who's a computer scientist at George Washington University, has really done a deep dive in that. So so'sEric Topol (26:22):I think a lot of people are not aware that's what your book, book brings to light of how organized, how financed, you know, how this thing is a machine from coming from many different domains, you know, and for different interests as you, as you just summarized, it's, it's actually scary. And besides you standing up and facing, you know, the really ultimate bravery with the, all of the, these factions attacking you, literally ad hominem, you know, personally attacking you, then you have you know, this continues to get legs throughout the pandemic, and there's no counter as you've, as you've touched on what is going to be done. You can't stand up alone on this.Peter Hotez (27:09):Well, there's, there's a couple of things. First of all, it's not only attacking the science, it's attacking the scientists. Right, right,Eric Topol (27:15):Right.Peter Hotez (27:16):Exactly. It's, it's portraying and you get get it too, as well. I mean, it's basically portraying scientists as enemies of the state. which I think is so dangerous. I mean, as I like to say, you know, this is a nation that's built on science and technology, right? The, you know, the strengths of our research universities and institutions like Scripps, like Baylor, like Rockefeller, like MIT and Stanford, and University of Michigan and University of Chicago. This is what, you know, helped us defeat fascism in World War II as evidenced by the Oppenheimer movie, right. Or, and or allowed us to achieve so many things, why people so admire our nation. When I served as US Science Envoy and the Obama administration, the State Department, and the White House. I mean, that's where people loved our country, is they all wanna study at our research universities, or they want their kids to study at our research universities.(28:10):And, and by attacking not only science, but the scientists, I think it's weakening our stature globally. And, and, and, and I think that's, that, that's another aspect. I think the other problem is we, we don't get the backing that I think we should from the scientific societies in the Times, even the National Academies. I think they, they could be out there more. exactly why, you know, I think part of it is they see, they see how I get beat up and they say, well, what's that? Right? Yeah. And I, and I understand that, but I think also, you know, they, they depend on, oftentimes on government funding. And I think they're worried that, you know, if they're, again, it's this idea that you have to be politically neutral, even if it favors the torment or the aggressor to paraphrase Desmond Tutu, that's part of it as well.(29:09):I mean, it, I mean, I do find it meaningful. It's scary at times, and I, but I do find it meaningful to ha to have this role. But getting, getting more help and backing, I mean, we're our, our university, I mean, Baylor College of Medicine, Texas Children's Hospital has been pretty good. You know, Stan, you know, having my back, it's not that way at every, and I know Scripps has been really strong with what Kristian Anderson's had to deal with around you know, all the phony bologna around covid origins. But, but not all academic health centers are that way. And, and I think we need our university presidents to be more vocal on this issue. And, and too often they're not as well as our academies and our, our scientific societies, because this is, I believe, going to do irreparable harm to, to science. Well, yeah.Eric Topol (30:04):You know, in my experience too, we, we've actually seen, you know, academic physicians who have basically, you know, supported conspiracy theories who have detracted from evidence and science, you knowin a major way. Some of the leading universities here as you, as you mentioned. And when I've contacted and others, their leadership, they say, well, freedom of speech, freedom of speech. 'cause they're afraid to confront them because, you know, all the different things. We've, we, you've mentioned social media, but no, the universities don't want to get attacked on social media. They're afraid of that. They're afraid of, of calling out, you know, one of the people, faculty members who are deliberately, you know garnering a lot of, yeah. And,Peter Hotez (30:56):And the point is, is it's not just, you know, freedom of speech in the sense of espousing you know, crazy views. It's the fact that they're going on the attack against mm-hmm. . I mean, I don't attack these guys, but they attacked me with, with impunity and Yes. Say terrible thing, untrue things about me. I mean, where's there's, isn't there something called professionalism or, or ethics, yeah. Right. That don't, don't, don't, don't we, aren't we supposed to be in instilling that in our, in our faculty and, and that that doesn't seem to happen.Eric Topol (31:28):So that'sPeter Hotez (31:28):Troubling asEric Topol (31:29):Well. They're, they're making credible scientists who are doing the best they can into pinatas Right. And attacking them. And with, and it can't, it can't be reciprocated because that's, that's beneath professionalism. I mean, just as you say. So, you know, you just keep, they just keep going at it. So what you have is now we've added all these different entities and all add more. One more is ai, which is going to further blur the truth.Peter Hotez (31:59):Yeah, Renee DiResta at the Stanford Internet Observatory, I don't if you know Renee, she does fabulous work. And she's written about, you know, what happens when, you know, all of the anti-science, anti-vaccine stuff is now imbued with ai, and, you know, it's going become even more sophisticated and more difficultEric Topol (32:17):To No, there's, there's gonna be a video of you saying that, you know, these vaccines are killing people but don't get a booster and it'll be just like you with your voice. Yeah.Peter Hotez (32:28):Well, they already, they already have. Now these, there's these few things on YouTube that, that claim, I'm secretly Jack Black, the actor . And that the CIA has arranged it so that Jack Black plays this fictional character named Dr. Peter Hotez. And they do all these things like, you know, focus in on my eyes and do like eye identification. It's just, it's just nuts. I mean, what, what's out there?Eric Topol (32:54):Well, has there been a time in these months where you were very scared you, you're for yourself or your family because of all the incredible density and, and what appears to be very serious threats and duringPeter Hotez (33:08):, during, during the day, during the day, I'm okay. I mean, in, you know, when the, when the, when the Steve Bannon in stuff and Joe Rogan stuff, then I had the stalking at the house, and, you know, I had to have a Houston Police Department officer parked in front of my house or a Harris County Sheriff that, that was troublesome. But it, it's more of during the day, I am fine. I'm working, I'm talking, you know, to people like you and in lab meetings, doing what scientists do, writing grants and throwing pencils at the wall when you get a paper with a major review or, or a major revision or rejection. But, but it's, I think at night, you know, wake up in the middle of the night and the, it's, the stuff does start to mess with your head at times. And it'sEric Topol (33:54):Well, and you travel a lot and you, you've, I think expressed that, hey, you could be given a talk in an innocent place and somebody could come, you know, attack youPeter Hotez (34:04):There. Yeah. So I have to, I have, I have security now at, in major venues when I speak. and, you know, I had an, there was an incident at the World Vaccine Congress in Washington. There were protesters out in front of the, out in front of the convention center waiting for me that that wasn't fun. And so, even, you know, we've got, we'll see what happens with the, when the, you know, I'm doing a number of events around the book in Washington DC and New York and elsewhere. We'll, we'll see how that goes. soEric Topol (34:38):Well take it. You, you're, I know you well enough to know that you're an optimistic person. I mean, you've been smiling and we've been laughing during this and discussing some very heavy, serious stuff. What gives you still optimism that this can someday get on track?Peter Hotez (34:57):Well, I think it could get worse before it gets better, first of all. And, and two fronts. One, you know, I had the opportunity to meet with Dr. Tedros, the World Health Organization Director, general of World Health Organization towards the end of last year. And to say this could be the warmup act in the sense that now it's globalizing. I'm anticipating spillover all childhood immunization rates. And, you know, you're starting to see the same US style of anti-vaccine rhetoric now, you know, even in low and middle income countries on the African continent in South Asia. So I worry about, you know, measles and polio, both in the US and, and globally. I think that's, that's, I'm worried about that. The other is, you know, a lot of this is heating up, I think because of the 2024 presidential election. I think one was that with, with our, our mutual friend and colleague Anthony Fauci, now that he's out of government he's not as visible as he was.(35:58):I think they're, the, the extremists are looking around for another, they need a monster right. To, to galvanize the base. And I think I've become that monster. You know, that's, that's one thing I'm worried about. But also you with, I talk to probably someone you've seen on Twitter. and I've gotten to know her somewhat, I'm very impressed with her. Molly Chong Fast, who's a commentator on c n at M S N B C, and she, you know, put out there, and she told me privately and put it out in public that, you know, one of the reasons why things are so vicious around RFK Jr, as they see him as a third party candidate that could take Biden votes away and help create a path for Trump being elected. So by, you know, by having me debate him, it, it kind of elevated in, in its own way, elevated his stature and made him seem like a more serious person. Right, right. And my refusal, you know, popped their bubble. And that, that's one of the reasons why, why they're so angry. So this is very much tied, I think, to the 2024 presidential look. And that's what you're having seen with the House subcommittee hearings too, portraying scientists as enemies of the state. It's all for, I mean, I don't know if you've seen this, the, that House Subcommittee Twitter site, it actually says something like, we're selling popcorn, you know, we'reEric Topol (37:18):Yeah, I know. I mean,Peter Hotez (37:20):They're, they're not, they're not even pretending it's anything, theEric Topol (37:23):PoliticalPeter Hotez (37:23):Theater for Fox News soundbites. So I think we're gonna see they're the word.Eric Topol (37:27):Alright. Yeah.Peter Hotez (37:28):Yeah. And, and, but, you know, but the attacks on biomedical science, I think are gonna be, you know, have a long-term effect. If for no other reason, I think people are gonna think twice about wanting to do a PhD in biomedical scientist or become an MD PhD scientist when they see that, you know, we'reEric Topol (37:47):. Well, that's what you, you also covered that really well in the Yeah. In the book. But when you think about where we are now with climate crisis, or we're facing future pandemics, not just the one we're still working through here where is the hope that we can counter this? I mean, we need armies of people like you. We need, as you say, the scientific establishment and community all stand up. That, that gets me to one of the things that makes you differentiates you from most physicians and scientists. You write books, you are active on social media. You, you appear on the media. Most scientists grew up to have their head do the work, do good science, get their stuff published, and get grants and, you know, try to advance the field and physicians doing that, are taking care of patients, same kind of thing. What prompted you in your career to say, Hey, you know, that's not enough. I got another dimension. And why, how can we get millions of clinicians and scientists to rally to do what you'rePeter Hotez (39:01):Doing? Well, in my, in my case, I, it's not that I was deliberately seeking to be a public figure or what some call a public intellectual. It was more the case, the issues that I was most interested in, nobody was talking about. Mm. And nobody was going to talk about it. So if I didn't talk about it, it wasn't gonna be talked about. So neglected tropical diseases, you know? Yeah. For guard people was, and, and I had two colleagues in the uk, Alan Fannick and David Mullen, who felt the same way. And so we began be, we became the three Musketeers of the neglected tropical disease space. And I found that extremely meaningful and interesting. And it was the same with vaccines. So although I, I'm often in the, you know, doing a lot of public engagement, if you notice, I don't try to be like some people who do it very well, like as Sanjay Gupta or, or some others that will, or Megan Rainey that will talk about, you know, just about any health issue.(39:56):I, I don't try to do that. I sort of stay, it's a wide lane, but I try to stay in my lane around infectious, neglected diseases and, and, and vaccines. And I think that's very important. Now, in terms of, you know, the statement, most scientists or physician scientists wanna keep their head done, write their grants and paper. I think that's perfectly fine. I don't think you people should be forced to do it, but I think there's enough of us out there that wanna do it, but don't know how to get started and don't feel safe doing it. I, and so I think we need to change that culture. Mm-hmm. I think we need to offer science communication to our graduate students in their PhD programs or in MD PhD programs for those who wanna do it, or in residency training or fellowship training. And so that, because there, there are things you can learn.(40:46):I mean, we had to do it by trial and error, and in my case, more error than trial. But, but, but there is a, there is, there are things you can learn from people who do this professionally. So I think that's important. I think the other is we need to change the culture of the institutions. You know, I, I get evaluated just like you do like everybody, like any, you know, senior scientist or professor at university, and, you know, what do they ask me about? They ask me about my grants and, and my papers preferably in high impact journals, and they ask me, and I don't see patients anymore, so they don't ask me about my clinical revenue, but they ask me about my grants and papers and my grants and papers, and my grants and papers. There's not even any place on my form, my annual evaluation from, to put in the single author books. I've written much less, you know? Yeah. The, the opinion pieces I've written, or certainly not social media or even, or even the cable news channel. So, so it basically, the academic health center is sending the message. And I don't think that's unique. I think that's probably the rule in most places. I think the, the culture of academic health centers is they're basically, they're sending a message just saying, well, we don't consider that stuff important, and somehow we have to make it important. I think for those who wanna do itEric Topol (42:08):AbsolutelyPeter Hotez (42:09):To send that message,Eric Topol (42:10):You're, you're, you're pointing out a critical step that has to be undertaken in the future. it'll take time to get that to gel, hopefully, but if it's promoted actively, I certainly promote that. I know you do. Yeah. I think,Peter Hotez (42:23):I think most, most offices of communications at academic health centers, as I said, Baylor and Texas Children's is pretty good, better than most, but most, you know, don't even like their docs and scientists speaking out. Yeah. Right. They wanna control the message. It's all about, you know, they're very risk averse. They're protecting the reputation of the institution. They only see the risk side. They don't, you know, you know, you wanna speak about social justice or, or combating anti-science. Well, you know, we guess we can't stop you, but they sort of cringe at, at the idea. And then, you know, they say, well, you know, ultimately you're a professor or a scientist here, you have academic freedom.com, but don't screw this up. Right. And don institution at risk. Right.Eric Topol (43:07):Ab you're describing exactly how university communications worked.Peter Hotez (43:12):Yeah. ButEric Topol (43:13):ThePeter Hotez (43:13):Point is, and so you do it with the sort of Damocles over your head, and, and you know, as you know, and as anyone knows, if you do enough, you will screw it up eventually, right? Everybody does. And, and you know, you're gonna make mistakes. That's how you learn. You make mistakes and you, you auto correct. But, but you have to have that freedom to be able to make mistakes and Yeah. And right now that's not there either.Eric Topol (43:35):What, what you're driving at though altogether is that we're defenseless. That is, if you have an organized finance coordinated attack on science, and also of course on vaccines, and you have no defense, you have, I mean, it's hard for the government to stand up because they're part of what's the conspiracy theory is, is, is against, and you, and, and the scientific community, the clinician community is, you know, kind of handcuffed as you are getting at. And also, you know, that's not the culture that's unwilling, but something's gotta give. And this is one thing I think you're really reinforcing that, that should a pathway to countering. I mean, we can't clone you. You know, we can't, we need lots of warriors. We need, you know, thousands and hundreds of thousands of points of light who support data and evidence, you know, as best that they can. And we don't have that today.Peter Hotez (44:36):Yeah. And we, we need to cultivate that. So I'm in discussions not only with people like yourself, but other colleagues about should we try to create, whether it's a nonprofit of 5 0 1 C three or C four the climate scientists are ahead of the game on this. Yeah. Yeah. I, I talk to Michael Mann every now and then, and, you know, they've got a climate science defense fund. They, they seem to be, 'cause it, they've, they've experienced this for longer than we have. You know, the, this all started a decade before with tax against climate scientists, you know, should, in the book I talk about, should we create something like a Southern Poverty Law Center equivalent to, to protect science and scientists? And, and I think we need that because the existing institutions don't seem willing to, to create something like that. It's somehow seen as too edgy or too out there and Right.(45:30):And it shouldn't be. But, but again, this is a I think a, a great opportunity for college presidents to, to step up and, and they're not doing that. They're, they're also pretty risk averse. So I think, you know, getting, getting the heads of the academic health centers, getting the college president, university presidents to say, Hey, this is important because otherwise science is at risk. And, and you're already starting to see some crazy stuff come out of the N I h now about doing international research. They're trying to put in rules to say they want, you know, if you have international collaborators, you're supposed to collect their notebooks and translate the how are you gonna do that? That's, that's completely, IM it's important. I mean, it's, and who's gonna review it and who's gonna sign off in general legal counsel at the university on, that's basically gonna halt international research. And we have to recognize that we need this because the threats are coming. Right? I mean,Eric Topol (46:33):CliPeter Hotez (46:34):Climate change is real, and pandemic threats are real. We're gonna see another major coronavirus pandemic possibly before 2030 or a flu or an arbovirus. And, and we're, we're, we need, this is a time we need to be reinforcing our, our virology research and our infectious disease research, not a time to, you know, start dismantling it, which is what totally the house hearings are, are meant to do, and what some of these new n i h rulings are meant to do. So it's gonna take a lot of strong players and, and, and government and at universities to stand up to this.Eric Topol (47:14):Well, if we ever need to be vaccinated or immunized, it's against this. And I hope that something will give to start to provide an antidote to what is a relentless progression of united science that you so elegantly eloquently in, in your book, Peter. So thanks for writing that. thanks for joining today. I know we'll have, as we do every week conversations yeah. You,Peter Hotez (47:41):You've been a, you've been an amazing friend and colleague, Eric, and I've learned so much from you. And, andEric Topol (47:46):No, no. I, I feel I can't tell you thank you. I, I, I think it's completely reciprocal from what you bring to this table of trying to make this a better place for advancing science search for, for the truth of what's really going on out there, rather than having to deal with wacky, you know, extremists that are advancing things for various purposes that are, that are nefarious in many cases. So, appreciate it. we'll be talking some more and this has been a really for me, an enriching conversation.Peter Hotez (48:21):Same, same Eric. And thank you so much for giving this attention and the dialect to be continued.Thanks for listening, reading and subscribing to Ground Truths!Please share if you found this podcast worthwhileFull video link Get full access to Ground Truths at erictopol.substack.com/subscribe

In this episode of the Epigenetics Podcast, we talked with Capucine van Rechem from Stanford University about her work on the impact of chromatin modifiers on disease development and progression. During her postdoctoral work, Capucine van Rechem studied the effects of Single nucleotide polymorphisms (SNPs) in KDM4A on lung cancer cell lines and discovered a link between KDM4A and mTOR. She found that cells with the SNP had decreased KDM4A levels and increased sensitivity to inhibitors of the translation pathway. In addition, she found that a combination of histone marks was more predictive of replication timing than RNA expression alone, and identified the specific stages of the cell cycle where KDM4 primarily acts. Now in her own lab, the focus of her work shifted to SWI-SNF. The team has discovered the role of SWI-SNF in translation through polysome profiling and confirmed the interaction between SWI-SNF and translation. They are currently working to understand the functions of different complexes in translation and their connection to transcription.   References Black, J. C., Manning, A. L., Van Rechem, C., Kim, J., Ladd, B., Cho, J., Pineda, C. M., Murphy, N., Daniels, D. L., Montagna, C., Lewis, P. W., Glass, K., Allis, C. D., Dyson, N. J., Getz, G., & Whetstine, J. R. (2013). KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors. Cell, 154(3), 541–555. https://doi.org/10.1016/j.cell.2013.06.051 Van Rechem, C., Ji, F., Mishra, S., Chakraborty, D., Murphy, S. E., Dillingham, M. E., Sadreyev, R. I., & Whetstine, J. R. (2020). The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. Biochimica et biophysica acta. Gene regulatory mechanisms, 1863(10), 194624. https://doi.org/10.1016/j.bbagrm.2020.194624 Van Rechem, C., Ji, F., Chakraborty, D., Black, J. C., Sadreyev, R. I., & Whetstine, J. R. (2021). Collective regulation of chromatin modifications predicts replication timing during cell cycle. Cell reports, 37(1), 109799. https://doi.org/10.1016/j.celrep.2021.109799 Ulicna, L., Kimmey, S. C., Weber, C. M., Allard, G. M., Wang, A., Bui, N. Q., Bendall, S. C., Crabtree, G. R., Bean, G. R., & Van Rechem, C. (2022). The Interaction of SWI/SNF with the Ribosome Regulates Translation and Confers Sensitivity to Translation Pathway Inhibitors in Cancers with Complex Perturbations. Cancer research, 82(16), 2829–2837. https://doi.org/10.1158/0008-5472.CAN-21-1360   Related Episodes Oncohistones as Drivers of Pediatric Brain Tumors (Nada Jabado) H3K4me3, SET Proteins, Isw1, and their Role in Transcription (Jane Mellor)   Contact Epigenetics Podcast on Twitter Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Active Motif on Twitter Active Motif on LinkedIn Email: podcast@activemotif.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.31.551302v1?rss=1 Authors: Ling, Y. H., Ye, J., Yu, C., Liang, C., Park, G., Corden, J., Wu, C. Abstract: Efficient gene expression demands RNA Polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in a 3D nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. Here, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is responsible for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation, and reduces transcription bursting. This study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.31.551204v1?rss=1 Authors: Chen, J. K., Liu, T., Cai, S., Ruan, W., Ng, C. T., Shi, J., Surana, U., Gan, L. Abstract: The structure of chromatin at the nucleosome level inside cells is mysterious. Here we present in situ cryo-ET analyses of chromatin in both G1 and metaphase RPE-1 cells. G1 nucleosomes are concentrated in globular chromatin domains and metaphase nucleosomes are concentrated in the chromatids. Classification analysis reveals that canonical mononucleosomes, ordered stacked dinucleosomes, and mononucleosomes with a disordered gyre-proximal density are abundant in both cell-cycle states. Class averages that have more than two stacked nucleosomes or that have side-by-side dinucleosomes are not detected, suggesting that groups of more than two nucleosomes are heterogeneous. Large multi-megadalton structures are abundant in G1 nucleoplasm, but not found in G1 chromatin domains and metaphase chromatin. The macromolecular phenotypes studied here represent a starting point for the comparative analysis of condensation in normal and unhealthy human cells, in other cell-cycle states, other organisms, and in vitro chromatin assemblies. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.28.550934v1?rss=1 Authors: Galan, L., Alvarez-Villanueva, D., Maqueda, M., Barrero, M., IGLESIAS, A., Bertran, j., ALVAREZ, D., GARCIA-PRIETO, C., BALLARE, C., RODRIGUEZ-CORTEZ, V., BUENO, C., VIDAL, A., Villanueva, A., Menendez, P., Di Croce, L., Payer, B., Esteller, M., Espinosa, L., Bigas, A. Abstract: Inflammatory signals are key in development and cell differentiation but their orchestration with pluripotency and stemness signals is poorly understood. Our previous work identified a chromatin function of I{kappa}B, the NF-{kappa}B inhibitor, that is crucial for differentiation in different types of somatic stem cells. Here we demonstrate that deficiency of I{kappa}B imposes a profound chromatin rewiring defect that impacts on DNA methylation, histone post-translational modifications and transcriptional regulation, stabilizing mouse embryonic stem cells (ESCs) in a ground state of pluripotency while preventing them from pluripotency exit and differentiation. By engineering separation-of-function mutants of I{kappa}B with specific binding to either NF-{kappa}B or histones, we demonstrate that regulation of pluripotency state by I{kappa}B is independent of NF-{kappa}B but requires the chromatin-related I{kappa}B function. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Reference Front Immunol.2022; 13: 890056. previous IE lectures 1-3. --- Send in a voice message: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/message

References J Immunol. 2014 Aug 15; 193(4): 1531–1537 Immunology lecture notes-Guerra --- Send in a voice message: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/message

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.22.550032v1?rss=1 Authors: Al-Refaie, N., Padovani, F., Binando, F., Hornung, J., Zhao, Q., Towbin, B. D., Sarinay Cenik, E., Stroustrup, N., Schmoller, K. M., Cabianca, D. S. Abstract: Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom. Yet, how it impacts on 3D genome organization is unknown. Here, we show that fasting induces a tissue-specific, reversible and large-scale spatial reorganization of chromatin in C. elegans. This fasting-induced 3D genome reorganization requires inhibition of the nutrient-sensing mTOR pathway, a major regulator of ribosome biogenesis. Remarkably, loss of transcription by RNA Pol I, but not RNA Pol II nor Pol III, induces a similar 3D genome reorganization in fed animals, and prevents the restoration of the fed-state architecture upon restoring nutrients to fasted animals. Our work documents the first large-scale chromatin reorganization triggered by fasting and reveals that mTOR and RNA Pol I shape genome architecture in response to nutrients. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

In this episode of the Epigenetics Podcast, we talked with Alistair Boettiger from Stanford University about his work on the analysis of 3D chromatin structure of single cells using super-resolution imaging. Alistair Boettiger and his team focus on developing advanced microscopy techniques to understand gene regulation at the level of 3D genome organization. They have developed Optical Reconstruction of Chromatin Architecture (ORCA), a microscopy approach to trace the 3-dimensional DNA path in the nucleus with genomic resolution down to 2 kb and a throughput of ~10,000 cells per experiment. These methods enable the identification of structural features with comparable resolution to Hi-C, while the advantages of microscopy such as single cell resolution and multimodal measurements remain.   References Boettiger, A., Bintu, B., Moffitt, J. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016). https://doi.org/10.1038/nature16496 Bogdan Bintu et al., Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783 (2018). DOI:10.1126/science.aau1783 Mateo, L.J., Sinnott-Armstrong, N. & Boettiger, A.N. Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 16, 1647–1713 (2021). https://doi.org/10.1038/s41596-020-00478-x Rajpurkar, A.R., Mateo, L.J., Murphy, S.E. et al. Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact. Nat Commun 12, 3423 (2021). https://doi.org/10.1038/s41467-021-23831-4 Tzu-Chiao Hung, David M. Kingsley, & Alistair Boettiger. (2023). Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. BioRxiv, 2023.02.06.527380. https://doi.org/10.1101/2023.02.06.527380 Hafner, A., Park, M., Berger, S. E., Murphy, S. E., Nora, E. P., & Boettiger, A. N. (2023). Loop stacking organizes genome folding from TADs to chromosomes. Molecular cell, 83(9), 1377–1392.e6. https://doi.org/10.1016/j.molcel.2023.04.008   Related Episodes Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden) Unraveling Mechanisms of Chromosome Formation (Job Dekker) Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)   Contact Epigenetics Podcast on Twitter Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Active Motif on Twitter Active Motif on LinkedIn Email: podcast@activemotif.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.13.548906v1?rss=1 Authors: Hu, M., Bonas-Guarch, S., Kim, I., Moran, I., Bonnefond, A., Froguel, P., Rutter, G. A. Abstract: Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ZnT8. Although this protein-coding variant was previously thought to be the sole driver of altered disease risk, recent studies have provided evidence for lowered expression of SLC30A8 mRNA in protective allele carriers. In the present study, combined allele-specific expression (cASE) analysis in human islets revealed that multiple variants affect the expression SLC30A8. Chromatin accessibility and epigenomic analyses imply the existence at the SLC30A8 locus of an islet-selective super-enhancer cluster hosting multiple diabetes-associated variants. The variant region is spatially associated with both the SLC30A8 promoter and with the regulatory regions of the neighbouring RAD21, RAD21-AS1, UTP23 and other genes. Deletion of variant-bearing regions from human-derived EndoC-BH3 cells using CRISPR-Cas9 lowered the expression of SLC30A8 and several neighbouring genes, suggesting their co-regulation by this enhancer cluster. Whilst deletion of SLC30A8 had no effect on beta cell survival under the conditions examined, loss of RAD21 or UTP23 markedly reduced cell viability. Thus, the protective effects of variants that lower SLC30A8 activity may be modulated by the altered expression of nearby genes. Direct evidence for this possibility was not, however, obtained by cASE or eQTL analysis of human islet samples. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

References Cancer Discov. 2022 Mar 1; 12(3): 856–871. Sci Signal. 2015 Mar 31;8(370):re4 --- Send in a voice message: https://podcasters.spotify.com/pod/show/dr-daniel-j-guerra/message

References Antioxidants (Basel). 2023 Feb; 12(2): 274 J Lipid Res. 2016 May; 57(5): 868–881. J Biol Chem. 2007 Jan 12;282(2):1384-96. J. Am. Chem. Soc. 2014, 136, 36, 12624–12630 --- Send in a voice message: https://anchor.fm/dr-daniel-j-guerra/message Support this podcast: https://anchor.fm/dr-daniel-j-guerra/support

References Genes (Basel). 2021 Aug; 12(8): 1118. Nature Reviews Immunology 2018. volume 18, pages 617–634. --- Send in a voice message: https://anchor.fm/dr-daniel-j-guerra/message Support this podcast: https://anchor.fm/dr-daniel-j-guerra/support

In this episode, we review the high-yield topic of Chromatin Structure from the Biochemistry section. Follow Medbullets on social media: Facebook: www.facebook.com/medbullets Instagram: www.instagram.com/medbulletsofficial Twitter: www.twitter.com/medbullets --- Send in a voice message: https://anchor.fm/medbulletsstep1/message

Five autism-linked genes widely known as chromatin regulators appear to also shape the cell's internal skeleton.

Five autism-linked genes widely known as chromatin regulators appear to also shape the cell's internal skeleton.

Exposing neurons to valproic acid, a well-known environmental risk factor for autism, disrupts their ability to generate different proteins from the same gene.

Exposing neurons to valproic acid, a well-known environmental risk factor for autism, disrupts their ability to generate different proteins from the same gene.

References Sci Transl Med . 2015 Apr 8;7(282):282ra47 Cell Physiol Biochem . 2018;47(3):1060-1073 Hum Genomics. 2021; 15: 24 --- Send in a voice message: https://anchor.fm/dr-daniel-j-guerra/message

In this episode of the Epigenetics Podcast, we caught up with Sarah Kinkley from the Max Planck Institute of Molecular Genetics to talk about her work on PHF13 and its role in chromatin and transcription. The Kinkley laboratory focuses mainly on unraveling the mechanism of action of the transcription factor PHF13 (PHC Finger Protein 13). PHF13 is a reader of the epigenetic mark H3K4 trimethylation which influences higher chromatin order, transcriptional regulation, and differentiation. The lab has shown that PHF13 plays a crucial role in phase separation and mitotic chromatin compaction.   References Kinkley, S., Staege, H., Mohrmann, G., Rohaly, G., Schaub, T., Kremmer, E., Winterpacht, A., & Will, H. (2009). SPOC1: a novel PHD-containing protein modulating chromatin structure and mitotic chromosome condensation. Journal of cell science, 122(Pt 16), 2946–2956. https://doi.org/10.1242/jcs.047365 Chung, H. R., Xu, C., Fuchs, A., Mund, A., Lange, M., Staege, H., Schubert, T., Bian, C., Dunkel, I., Eberharter, A., Regnard, C., Klinker, H., Meierhofer, D., Cozzuto, L., Winterpacht, A., Di Croce, L., Min, J., Will, H., & Kinkley, S. (2016). PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. eLife, 5, e10607. https://doi.org/10.7554/eLife.10607 Connecting the Dots: PHF13 and cohesin promote polymer-polymer phase separation of chromatin into chromosomes. Francesca Rossi, Rene Buschow, Laura V. Glaser, Tobias Schubert, Hannah Staege, Astrid Grimme, Hans Will, Thorsten Milke, Martin Vingron, Andrea M. Chiariello, Sarah Kinkley. bioRxiv 2022.03.04.482956; doi: https://doi.org/10.1101/2022.03.04.482956   Related Episodes The Role of Blimp-1 in Immune-Cell Differentiation (Erna Magnúsdóttir) H3K4me3, SET Proteins, Isw1, and their Role in Transcription (Jane Mellor) The Role of SMCHD1 in Development and Disease (Marnie Blewitt)   Contact Epigenetics Podcast on Twitter Epigenetics Podcast on Instagram Epigenetics Podcast on Mastodon Active Motif on Twitter Active Motif on LinkedIn Email: podcast@activemotif.com

References PLoS One. 2011;6(5):e17711 J Neuroinflammation. 2020; 17: 207 Front Neurosci. 2019 Nov 26;13:1280 --- Send in a voice message: https://anchor.fm/dr-daniel-j-guerra/message

References Clinical and Molecular Teratology Volume 106, Issue 9 September 2016 Pages 749–760 Alcohol, 2017-12-01, Volume 65, Pages 51-62 --- Send in a voice message: https://anchor.fm/dr-daniel-j-guerra/message

Today we're joined by another awesome scientist, Dr. Christine Cucinotta. Christine studies gene regulation in yeast in her postdoctoral studies in the Tsukiyama Lab at the Fred Hutch. She also organizes Fragile Nucleosome, a Discord community of scientists and researchers that puts on a seminar series (available to watch on YouTube). We chat about the importance of community in science and what she considers to be groundbreaking work in the field of gene regulation in the last decade. We also get into how she felt about the recent eLife decision to publish preprints (hint - she's a fan of change!) and the importance of open science! Christine's Twitter: https://twitter.com/chrstn_eFragile Nucleosome: https://twitter.com/FNucleosome Subscribe to LSP wherever you listen to podcasts. Thanks for listening!

A new research paper was published in Aging (listed as “Aging (Albany NY)” by MEDLINE/PubMed and “Aging-US” by Web of Science) Volume 14, Issue 20, entitled, “Age-associated changes in microglia activation and Sirtuin-1- chromatin binding patterns.” The aging process is associated with changes in mechanisms maintaining physiology, influenced by genetics and lifestyle, and impacting late life quality and longevity. Brain health is critical in healthy aging. Sirtuin 1 (Sirt1), a histone deacetylase with silencing properties, is one of the molecular determinants experimentally linked to health and longevity. In this new study, researchers Liana V. Basova, Nikki Bortell, Bruno Conti, Howard S. Fox, Richard Milner, and Maria Cecilia Garibaldi Marcondes from San Diego Biomedical Research Institute, University of Nebraska Medical Center and Oncovalent Therapeutics compared brain pathogenesis and Sirt1-chromatin binding dynamics in brain pre-frontal cortex from 2 groups of elder rhesus macaques (rhesus monkeys), divided by age of necropsy: shorter-lived animals (18-20 years old (yo)), equivalent to 60-70 human yo; and longer-lived animals (23-29 yo), corresponding to 80-100 human yo and modeling successful aging. These were compared with young adult brains (4-7 yo). “Our findings indicated drastic differences in the microglia marker Iba1, along with factors influencing Sirt1 levels and activity, such as CD38 (an enzyme limiting NAD that controls Sirt1 activity) and mir142 (a microRNA targeting Sirt1 transcription) between the elder groups.” Iba1 was lower in shorter-lived animals than in the other groups, while CD38 was higher in both aging groups compared to young. mir142 and Sirt1 levels were inversely correlated in longer-lived brains (>23yo), but not in shorter-lived brains (18-20 yo). They also found that Sirt1 binding showed signs of better efficiency in longer-lived animals compared to shorter-lived ones, in genes associated with nuclear activity and senescence. “Overall, differences in neuroinflammation and Sirt1 interactions with chromatin distinguished shorter- and longer-lived animals, suggesting the importance of preserving microglia and Sirt1 functional efficiency for longevity.” DOI: https://doi.org/10.18632/aging.204329 Corresponding Author: Maria Cecilia Garibaldi Marcondes - cmarcondes@SDBRI.org Keywords: aging, brain, rhesus macaques, microglia, Sirtuin-1 Sign up for free Altmetric alerts about this article: https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.204329 Video: https://www.youtube.com/watch?v=Cz33TWM4so4 About Aging-US: Launched in 2009, Aging (Aging-US) publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways. Please visit our website at www.Aging-US.com​​ and connect with us: SoundCloud – https://soundcloud.com/Aging-Us Facebook – https://www.facebook.com/AgingUS/ Twitter – https://twitter.com/AgingJrnl Instagram – https://www.instagram.com/agingjrnl/ YouTube – https://www.youtube.com/agingus​ LinkedIn – https://www.linkedin.com/company/aging/ Reddit – https://www.reddit.com/user/AgingUS Pinterest – https://www.pinterest.com/AgingUS/ For media inquiries, please contact media@impactjournals.com

Listen to a blog summary of a recently published research paper in Volume 13 of Oncotarget, entitled, "HDAC inhibitors suppress protein poly(ADP-ribosyl)ation and DNA repair protein levels and phosphorylation status in hematologic cancer cells: implications for their use in combination with PARP inhibitors and chemotherapeutic drugs." _______________________________________ Chromatin constitutes chromosomes in eukaryotic cells and comprises DNA and proteins. Chromosomes produce proteins and enzymes that are essential for cellular function and maintenance, including DNA repair. A critical process for DNA repair is poly(ADP-ribosyl)ation, or PARylation. PARylation is triggered by poly(ADP ribose) polymerase (PARP) enzymes. When DNA becomes damaged, PARP enzymes bind to the damaged location in the cell. In cancer cells, however, this natural process can be counterproductive in respect to cancer treatment. PARylation can produce DNA repair mechanisms in cancer cells that can lead to the evasion of cell death, and even drug resistance. Inhibiting PARylation may be a viable therapeutic strategy for cancer treatment. Histones, the main proteins that constitute chromatin, undergo post-translational modifications that regulate gene expression. Histone acetylation is an important epigenetic process that affects gene expression by relaxing the chromatin structure, making chromatin remodeling more feasible. Histone deacetylases (HDACs) are enzymes that can have the opposite effect. Histone deacetylation makes the chromatin more compact and difficult to remodel. The overexpression of HDAC has also been associated with tumorigenesis. Histone deacetylase inhibitors (HDACi) are a class of therapeutics that have shown promise in the treatment of hematologic malignancies (blood cancer) and solid tumors. In a new study, researchers Benigno C. Valdez, Yago Nieto, Bin Yuan, David Murray, and Borje S. Andersson from the Department of Stem Cell Transplantation and Cellular Therapy at the University of Texas MD Anderson Cancer Center and the Cross Cancer Institute's Department of Experimental Oncology at the University of Alberta investigate the efficacy of HDACi in combination with PARP inhibitors (PARPi) and chemotherapeutic drugs to treat hematologic cancer. On October 14, 2022, their research paper was published in Volume 13 of Oncotarget, entitled, “HDAC inhibitors suppress protein poly(ADP-ribosyl)ation and DNA repair protein levels and phosphorylation status in hematologic cancer cells: implications for their use in combination with PARP inhibitors and chemotherapeutic drugs.” Full blog - https://www.oncotarget.org/2022/10/19/synergy-of-hdaci-parpi-and-chemotherapeutics-against-blood-cancer/ DOI - https://doi.org/10.18632/oncotarget.28278 Correspondence to - Benigno C. Valdez - bvaldez@mdanderson.org Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28278 Keywords - poly(ADP-ribosyl)ation, HDAC inhibitors, PARP inhibitors, chemotherapy, hematologic malignancy About Oncotarget Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. On September 15, 2022, Oncotarget was accepted again for indexing by MEDLINE. Oncotarget is now indexed by Medline/PubMed and PMC/PubMed. To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/OncotargetYouTube LinkedIn - https://www.linkedin.com/company/oncotarget Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget/ Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

The mutations occur spontaneously in noncoding stretches of DNA that control gene expression. The post Mutations disrupting chromatin interactions contribute to autism appeared first on Spectrum | Autism Research News.

The mutations occur spontaneously in noncoding stretches of DNA that control gene expression.

The mutations occur spontaneously in noncoding stretches of DNA that control gene expression.

In this episode of the Epigenetics Podcast, we caught up with John Rinn from the University of Colorado in Boulder to talk about his work on the role of lncRNAs in gene expression and nuclear organization. The Rinn Lab pioneered the approach of screening the human genome for long noncoding RNAs (lncRNAs). More recently, the lab has shifted focus from measuring the number of lncRNAs to finding lncRNAs that have a distinct biological function in human health and disease. One example of such a lncRNA is FIRRE, which is present in all animals, however the sequence is not conserved, except for in primates. FIRRE contains many interesting features, such as repeat sequences and CTCF binding sites. In absence of FIRRE, defects in the immune system can be observed and also some brain defects may also be observed.   References Carter, T., Singh, M., Dumbovic, G., Chobirko, J. D., Rinn, J. L., & Feschotte, C. (2022). Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. eLife, 11, e76257. Advance online publication. https://doi.org/10.7554/eLife.76257 Long, Y., Hwang, T., Gooding, A. R., Goodrich, K. J., Rinn, J. L., & Cech, T. R. (2020). RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. Nature Genetics, 52(9), 931–938. https://doi.org/10.1038/s41588-020-0662-x Kelley, D., & Rinn, J. (2012). Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome biology, 13(11), R107. https://doi.org/10.1186/gb-2012-13-11-r107 Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., Regev, A., Lander, E. S., & Rinn, J. L. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences, 106(28), 11667–11672. https://doi.org/10.1073/pnas.0904715106 Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., Cabili, M. N., Jaenisch, R., Mikkelsen, T. S., Jacks, T., Hacohen, N., Bernstein, B. E., Kellis, M., Regev, A., Rinn, J. L., & Lander, E. S. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223–227. https://doi.org/10.1038/nature07672   Related Episodes The Role of lncRNAs in Tumor Growth and Treatment (Sarah Diermeier) The Role of Small RNAs in Transgenerational Inheritance in C. elegans (Oded Rechavi) Chromatin Structure and Dynamics at Ribosomal RNA Genes (Tom Moss)   Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

Greg Wang, winner of the 2022 ASBMB Young Investigator Award, presented his lecture, "Chromatin-based modulations underlying gene regulation and pathogenesis," at the 2022 ASBMB Annual Meeting in Philadelphia. Learn more about his work: https://www.asbmb.org/asbmb-today/people/121621/wang-s-studies-are-fueled-by-interest-in-cells. On August 9, 2022 he will also be presenting this talk as a webinar. Register here to join and participate in a Q&A session: https://www.asbmb.org/meetings-events/chromatin-based-modulations.

References Dr Guerra's synthesis of the relevant literature BioEssays, Volume: 39, Issue: 5, First published: 20 February 2017. Front Cardiovasc Med. 2020; 7: 2. --- Send in a voice message: https://anchor.fm/dr-daniel-j-guerra/message

In this episode of the Epigenetics Podcast, we caught up with Sara Wickström, Director at the Max Planck Institute for Molecular Biomedicine in Münster, to talk about her work on the effect of mechanotransduction on chromatin structure and transcription in stem cells. Sara Wickström and her team focus on the stem cell niche and how that niche affects stem cell function. In order to study the native niche and to even be able to manipulate it, the Wickström Lab was able to develop a ex vivo culture system, allowing systematic identification of factors driving stem cell dynamics and plasticity. Stem cells in the stem cell niche are exposed to external stimuli such as physical forces which control their growth, fate and self renewal. Recent work in the Wickström lab showed how mechanical signals influence transcriptional regulation, chromatin organization, and nuclear architecture and how this affects aging or lineage commitment. In this Episode we also discuss how chromatin can act as a sensor of mechanical signals taking advantage of the different physical properties of eu- and heterochromatin.   References Le, H. Q., Ghatak, S., Yeung, C. Y., Tellkamp, F., Günschmann, C., Dieterich, C., Yeroslaviz, A., Habermann, B., Pombo, A., Niessen, C. M., & Wickström, S. A. (2016). Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment. Nature cell biology, 18(8), 864–875. https://doi.org/10.1038/ncb3387 Nava, M. M., Miroshnikova, Y. A., Biggs, L. C., Whitefield, D. B., Metge, F., Boucas, J., Vihinen, H., Jokitalo, E., Li, X., García Arcos, J. M., Hoffmann, B., Merkel, R., Niessen, C. M., Dahl, K. N., & Wickström, S. A. (2020). Heterochromatin-Driven Nuclear Softening Protects the Genome against Mechanical Stress-Induced Damage. Cell, 181(4), 800–817.e22. https://doi.org/10.1016/j.cell.2020.03.052 Koester, J., Miroshnikova, Y. A., Ghatak, S., Chacón-Martínez, C. A., Morgner, J., Li, X., Atanassov, I., Altmüller, J., Birk, D. E., Koch, M., Bloch, W., Bartusel, M., Niessen, C. M., Rada-Iglesias, A., & Wickström, S. A. (2021). Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility. Nature cell biology, 23(7), 771–781. https://doi.org/10.1038/s41556-021-00705-x Maki, K., Nava, M. M., Villeneuve, C., Chang, M., Furukawa, K. S., Ushida, T., & Wickström, S. A. (2021). Hydrostatic pressure prevents chondrocyte differentiation through heterochromatin remodeling. Journal of cell science, 134(2), jcs247643. https://doi.org/10.1242/jcs.247643   Related Episodes Nutriepigenetics: The Effects of Diet on Behavior (Monica Dus) Epigenetic Regulation of Stem Cell Self-Renewal and Differentiation (Peggy Goodell) The Effect of Vitamin D on the Epigenome (Folami Ideraabdullah)   Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

No one is exempt from ageing, and with aging comes diseases and sickness. Decreased performance and cell production also occur because of this phenomenon. Lifestyle changes may be inadequate to help your body function properly. Over the past years, longevity science has been evolving, with the emergence of several anti-ageing supplements in the market. However, the body may not absorb these supplements effectively enough to slow down the effects of ageing. In this episode, Dr Elena Seranova explains how the ageing process works. She details how to use supplements, complemented by lifestyle changes, to reverse ageing. She also shares how NMN can be coupled with TMG to create the ultimate longevity supplement. There's no one supplement to optimise your health, but good habits and lifestyle changes are integral to having a longer and healthier life! If you want to learn how to reverse ageing through supplements and lifestyle changes, then this episode is for you! Here are three reasons why you should listen to the full episode: Understand the aging process, its vicious cycle, and how it affects and changes our bodies.  Learn how you can slow down and reverse the effects of aging. Discover how you can combine TMG with NMN for better results. Get Customised Guidance for Your Genetic Make-Up For our epigenetics health programme, all about optimising your fitness, lifestyle, nutrition and mind performance to your particular genes, go to  https://www.lisatamati.com/page/epigenetics-and-health-coaching/. Customised Online Coaching for Runners CUSTOMISED RUN COACHING PLANS — How to Run Faster, Be Stronger, Run Longer  Without Burnout & Injuries Have you struggled to fit in training in your busy life? Maybe you don't know where to start, or perhaps you have done a few races but keep having motivation or injury troubles? Do you want to beat last year's time or finish at the front of the pack? Want to run your first 5-km or run a 100-miler? ​​Do you want a holistic programme that is personalised & customised to your ability, goals, and lifestyle?  Go to www.runninghotcoaching.com for our online run training coaching. Health Optimisation and Life Coaching Are you struggling with a health issue and need people who look outside the square and are connected to some of the greatest science and health minds in the world? Then reach out to us at support@lisatamati.com, we can jump on a call to see if we are a good fit for you. If you have a big challenge ahead, are dealing with adversity or want to take your performance to the next level and want to learn how to increase your mental toughness, emotional resilience, foundational health, and more, contact us at support@lisatamati.com. Order My Books My latest book Relentless chronicles the inspiring journey about how my mother and I defied the odds after an aneurysm left my mum Isobel with massive brain damage at age 74. The medical professionals told me there was absolutely no hope of any quality of life again. Still, I used every mindset tool, years of research and incredible tenacity to prove them wrong and bring my mother back to full health within three years. Get your copy here: https://shop.lisatamati.com/collections/books/products/relentless. For my other two best-selling books Running Hot and Running to Extremes, chronicling my ultrarunning adventures and expeditions all around the world, go to https://shop.lisatamati.com/collections/books. Lisa's Anti-Ageing and Longevity Supplements  NMN: Nicotinamide Mononucleotide, an NAD+ precursor Feel Healthier and Younger* Researchers have found that Nicotinamide Adenine Dinucleotide or NAD+, a master regulator of metabolism and a molecule essential for the functionality of all human cells, is being dramatically decreased over time. What is NMN? NMN Bio offers a cutting edge Vitamin B3 derivative named NMN (beta Nicotinamide Mononucleotide) that can boost the levels of NAD+ in muscle tissue and liver. Take charge of your energy levels, focus, metabolism and overall health so you can live a happy, fulfilling life. Founded by scientists, NMN Bio offers supplements of the highest purity and rigorously tested by an independent, third-party lab. Start your cellular rejuvenation journey today. Support Your Healthy Ageing We offer powerful third-party tested NAD+ boosting supplements so you can start your healthy ageing journey today. Shop now: https://nmnbio.nz/collections/all NMN (beta Nicotinamide Mononucleotide) 250mg | 30 capsules NMN (beta Nicotinamide Mononucleotide) 500mg | 30 capsules 6 Bottles | NMN (beta Nicotinamide Mononucleotide) 250mg | 30 Capsules 6 Bottles | NMN (beta Nicotinamide Mononucleotide) 500mg | 30 Capsules Quality You Can Trust — NMN Our premium range of anti-ageing nutraceuticals (supplements that combine Mother Nature with cutting edge science) combats the effects of aging while designed to boost NAD+ levels. Manufactured in an ISO9001 certified facility Boost Your NAD+ Levels — Healthy Ageing: Redefined Cellular Health Energy & Focus Bone Density Skin Elasticity DNA Repair Cardiovascular Health Brain Health  Metabolic Health My  ‘Fierce' Sports Jewellery Collection For my gorgeous and inspiring sports jewellery collection, 'Fierce', go to https://shop.lisatamati.com/collections/lisa-tamati-bespoke-jewellery-collection. Episode Highlights [01:53] How Longevity Science Is Growing There are a growing number of anti-ageing products as we understand the ageing process better. Multiple cellular processes decline or become imbalanced as people age. There are 9 hallmarks of ageing, and the study recently added another hallmark to include inflammation.  The top four killer diseases are cancer, cardiovascular disease, neurodegeneration, and diabetes. The older you are, the higher your chance of developing one of these diseases.  Our body peaks at 25 and starts the aging process from there. [06:06] Why Is NMN Important?  NMN stands for nicotinamide mononucleotide and is a Vitamin B3 derivative.  It's a natural molecule that you can get from food, but getting an efficient dosage requires supplementation. NMN is a precursor to help our metabolism, and it boosts NAD levels. NAD serves as fuel for SIRTUIN proteins that are involved in rejuvenation processes.  NAD is vital to keep our cells healthy and ensure they don't lose their identity. [09:23] What Happens in the Body as We Age Cell identity is vital. What differentiates cells is how certain parts of the genomes are read. As we age, this process can become chaotic.  Chromatin is a substance in a chromosome. Lightly packed chromatin under active transcription is called euchromatin. Heterochromatin, on the other hand, is more condensed and transcriptionally silent. Epigenetic changes can dictate which areas will be active or inactive. This defines how a cell can be expressed. Sirtuins are crucial in making sure the right genes are active and mediating DNA repair. However, they become less efficient as we age.  This is how our epigenetic regulation becomes loose, leading to genomic instability and loss of cellular identity.  [15:33] How Aging Can Create a Vicious Cycle NAD is the fuel source of sirtuin genes. When these genes are depleted, our DNA can't be repaired. As we age, NAD production depletes. DNA breaks and genome instability also increase.  This becomes a vicious cycle of needing more energy but with less production.  Furthermore, genome instability can increase senescence or zombie cells. These can further increase genome instability.  Senescent cells are cells that forget how to do their function well and stop replicating. These cells can further drain NAD levels. [18:19] The Link Between Fasting and Cell Autophagy Autophagy is the process where cells can get rid of toxins and other things that are not needed anymore. Autophagy ensures housekeeping and can be triggered by fasting.  12 hours of fasting can start autophagy in the liver, while 20 hours of fasting can start the process in other tissues.    Eating can activate mTOR, which is another vital cell regulator. This process is deactivated through supplements like Berberine. Learn to balance both eating and fasting. Hear about Dr Elena's fasting schedule and supplements in the full episode! [27:48] Why Dr Elena Launched TMG Methylation is vital for the body's most critical functions. These include creating neurotransmitters, cell division, energy production, metabolism, and epigenetics.  Dr Elena launched TMG to boost NMN's effectiveness and metabolism.  Methylation and TMG can control homocysteine levels, which correlate with cardiovascular diseases. TMG may also enhance athletic performance. It also has a good safety profile with no side effects despite higher dosage. Dr Elena recommends a 1:2 or 1:3 ratio of NMN to TMG. For every 500 milligrams of NMN, take 1 to 2 grams of TMG. [33:31] Do We Need to Worry about Hyper-methylation?  It's difficult to hyper-methylate. However, individual genetic factors can affect homocysteine levels.  To check your homocysteine levels, you can undergo a blood test or check your gene variants with a genetic test TMG is an osmoregulator that helps regulate cell balance and can optimize methylation. After taking over 20 grams, a laxative effect may appear. [39:41] Where to Start Dr Elena recommends taking NMN, TMG, and extra virgin olive oil for anti-ageing. NMN can also help increase insulin sensitivity and boost collagen production, as seen in human clinical trial in prediabetic women. The market has a lot of collagen supplements, but not all of them are absorbed by the body effectively. Insulin sensitivity decreases as we age. This is the body's ability to let glucose flow freely into cells. You can reverse ageing problems with a better lifestyle and supplements. Dr Elena recommends avoiding carbohydrates in your diet. [42:55] How to Have a Healthier Diet Around 80% of adults in the West may be pre-diabetic. So many foods nowadays are made to be addictive.  While a vegan diet can help you detox at first, you will eventually experience amino acid depletion. Dr Elena prefers a carnivore diet. She also does fasting with a three-hour eating window. You can start with a longer eating window and slowly reduce it.  You don't want a glucose spike in the morning. [48:06] You Don't Need to Be Perfect  You don't have to be perfect every day, but make sure you stay consistent with your overall longevity routine.  Exercise and saunas activate Sirtuins. Try to have a routine for one or both. Optimize your routine and find out what works for you.  [50:52] NMN Bio's Growth Dr Elena shares that her company has been growing rapidly. They now have a UK warehouse, UK Amazon FBA, and another warehouse in Europe.  They are also expanding to the United States.  Remember that no one supplement will do everything for you. You also need to change your lifestyle, which includes diet, exercise, and even biorhythms.   There's a lot of information about longevity online, and it can become overwhelming. This is why Dr Elena created an online course about longevity.  Dr Elena recommends making sure your circadian rhythm is not disrupted.  Resources Gain exclusive access and bonuses to Pushing the Limits Podcast by becoming a patron! Tune in to more Pushing the Limits episodes on health and ageing! Episode 231: The Immune System and How It Fights Cancer Cells and Viruses with Dr Elizabeth Yurth  Episode 196: Rethinking the Function of Mitochondria for Our Health with Dr Elizabeth Yurth  Episode 189: Understanding Autophagy and Increasing Your Longevity with Dr Elena Seranova  Episode 187: Back to Basics: Slow Down Ageing and Promote Longevity with Dr Elizabeth Yurth Episode 183: Sirtuins and NAD Supplements for Longevity with Dr Elena Seranova  Want to dive deeper into longevity and work out a protocol for yourself? Take the Foundations of Longevity and Life Extension Online Course by Dr Elena Seranova and Jesse Coomer  The Ultimate Anti-Aging Combination: TMG & NMN to Live Significantly Longer? By NMN Bio  The Hallmarks of Aging  Nicotinamide Mononucleotide Increases Muscle Insulin Sensitivity in Prediabetic Women Visit NMN Bio to know more about NMN supplements!      Lifespan by Dr David Sinclair    7 Powerful Quotes [04:28] ‘The older you are, the highest your risk of getting one of these diseases; so if it's not gonna be one of them, it's gonna be the other one… Now we start realising when does aging start, which is actually at quite a young age, basically at the age of 25. Because this is where our hormones peak…' [12:25] ‘There are multiple functions that Sirtuins need to attend to within the cell. With age, this function becomes less and less efficient, basically, because sirtuins become more forgetful.' [16:02] ‘So as we age, the production of NAD is declining. So this means that there is less NAD available for sirtuins to use as their fuel to do their job.' [39:52] ‘There are so many collagen supplements on the market, but not all of them are efficient. And actually not all of them are being absorbed properly because when you do take collagen orally, basically, it's broken down into amino acids in your digestive system. And then those amino acids may or may not be used to produce more collagen.' [47:56] ‘We're all on this road of re-educating ourselves and don't go for perfection. Just go for better, I think is a message as well, you don't have to be perfect.' [52:22] ‘With regards to the longevity field, I think that it's very important for people to understand that there is no such thing as the fountain of youth. There is no one supplement that you're going to take that is going to do everything for you.' [56:40] ‘If your melatonin is disrupted, then you will have less defense against reactive oxygen species and that there is another plethora of processes that melatonin is also implicated in and then you don't have all these benefits. And then you're basically aging faster… Takeaway message from today's podcasts. Make sure that you go to sleep early, everyone.' About Dr Elena  Dr Elena Seranova is a scientist, serial entrepreneur and business mentor. She has now founded multiple innovative biotechnological businesses. She first studied at the University of Ioannina with a major in Psychology. Dr Elena then started a private practice before developing an interest in neuroscience. She continued her studies and earned her Master's Degree in Translational Neuroscience at the University of Sheffield. She now also holds a Doctorate Degree in Stem Cell Biology and Autophagy from the University of Birmingham. Dr Elena's expertise in these fields has led her to become the co-founder of a biotech start-up, SkyLab Bio. She has written several peer-reviewed articles on autophagy throughout her career. In addition to these accomplishments, she started her latest business, NMN Bio. Her own experiences with the use of supplements have inspired her to expand the market to supply the public with cutting-edge anti-ageing supplements. NMN Bio reaches New Zealand, the UK, and Europe. Dr Elena found her passion for drug discovery and autophagy. She has endeavoured to share this with the public through her research and work as an entrepreneur.  To learn more about Dr Elena and her work, visit NMN Bio. Enjoy The Podcast? If you did, be sure to subscribe and share it with your friends! Post a review and share it! If you enjoyed tuning in, then leave us a review. You can also share this with your family and friends so they can know how to optimise sleep.  Have any questions? You can contact me through email (support@lisatamati.com) or find me on Facebook, Twitter, Instagram and YouTube. For more episode updates, visit my website. You may also tune in on Apple Podcasts. To pushing the limits, Lisa  

In 2021, researchers from Harvard University and the Broad Institute wrote a theory article that was published in Aging's Volume 13, Issue 12, and entitled, “Shifting epigenetic contexts influence regulatory variation and disease risk.” The authors described common epigenetic trends throughout human growth, development, and aging. They also aimed to show how changing epigenetic contexts may influence the behavior of evolutionary forces and risk of genetic disease. FETAL TO ADULT EPIGENETIC SHIFTS The researchers point out that in order to better understand the contribution of epigenetic changes to disease and aging, it is important to understand the developmental changes that occur between fetal and adult tissues, and their interaction with epigenetic aging. “Furthermore, these fetal to adult epigenetic shifts can be compounded by additional modifications through aging-associated epigenetic changes.” Characterizing these epigenetic trends and examining their potential interaction with later-in-life epigenetic aging were main goals of this study. In order to do this, the researchers defined genomic regions where, over the course of development and aging, chromatin accessibility consistently shifts. Chromatin can be broadly classified in either of two epigenetic states: activating or repressing modifications. These states refer to chromatin accessibility and the increased or decreased ability of DNA to access gene-regulatory machinery, such as transcription factors. The authors note that they used an accessibility-based definition of epigenetic context, and that there are other marks of epigenetic changes (e.g. methylation, and etc.) that are not captured by this definition. “Epigenetic marks established during development can persist into adulthood, but they do so in the context of shifts in epigenetic states as tissues transition into their adult forms and functions.” Read the full blog post: https://www.impactjournals.com/journals/blog/aging/trending-with-impact-epigenetic-shifts-aging-and-disease/ Sign up for free Altmetric alerts about this theory article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.203194 DOI - https://doi.org/10.18632/aging.203194 Full text - https://www.aging-us.com/article/203194/text Correspondence to: Terence D. Capellini email: tcapellini@fas.harvard.edu Keywords: development, evolution, GWAS, disease, aging About Aging Launched in 2009, Aging publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways. Please visit our website at http://www.Aging-US.com​​ or connect with us on: Twitter - https://twitter.com/AgingJrnl​ Facebook - https://www.facebook.com/AgingUS/​ SoundCloud - https://soundcloud.com/aging-us​ YouTube - https://www.youtube.com/agingus​ LinkedIn - https://www.linkedin.com/company/aging​ Aging is published by Impact Journals, LLC please visit http://www.ImpactJournals.com​​ or connect with @ImpactJrnls Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

Many of the genes strongly linked to autism are involved in the remodeling of chromatin, the complex of DNA and proteins that makes up chromosomes. Scientists are just beginning to understand why.

Discusses HAT and HDAC enzymes to uncoil/coil DNA (uncoil = activate for transcription) then transitioned into DNA methylation as it relates to CpG Islands and MBB's.