Podcasts about dnmt3b

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.01.30.526165v1?rss=1 Authors: Yang, A., Zeng, W., Hao, Y., Zhang, H., Wang, Q., Sun, Y., Quan, S., Ding, N., Yang, X., Sun, J., Zhang, H., Liu, B., Jiao, Y., Wu, K., Jiang, Y. Abstract: Autophagy plays a critical role in the physiology and pathophysiology of hepatocytes. High levels of homocysteine (Hcy) promote autophagy in hepatocytes, but the underlying mechanism is still unknown. Here, we investigated the relation between Hcy increased autophagy levels and the expression of nuclear transcription factor EB (TFEB). We demonstrate that Hcy increased autophagy levels is mediated by upregulation of TFEB. Silencing TFEB decreases the autophagy-related protein LC3BII/I and increases p62 expression levels in hepatocytes after exposure to Hcy. Moreover, the effect of Hcy on the expression of TFEB is regulated by hypomethylation of TFEB promoter catalyzed by DNA methyltransferase 3b (DNMT3b). In summary, this study shows that Hcy can activate autophagy by inhibiting DNMT3b-mediated DNA methylation and upregulating TFEB expression. These findings provide another new mechanism for Hcy-induced autophagy in hepatocytes. 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 caught up with Nada Jabado from McGill University to talk about her work on oncohistones as drivers of Pediatric Brain Tumors. Nada Jabado and her team were amongst the first to identify mutations in Histone 3.3 Tails which lead to differentially remodeled chromatin in pediatric glioblastoma. Mutations that occur include the Lysine at position 27 and the Glycine at position 34. If those residues are mutated it will influence the equilibrium of chromatin associated proteins like the Polycomb Repressive Complex (PRC) and hence domains of heterochromatin will be shifted. This, in turn, will lead to differential gene expression and development of developmental disorders or cancer.   References Schwartzentruber, J., Korshunov, A., Liu, X. Y., Jones, D. T., Pfaff, E., Jacob, K., Sturm, D., Fontebasso, A. M., Quang, D. A., Tönjes, M., Hovestadt, V., Albrecht, S., Kool, M., Nantel, A., Konermann, C., Lindroth, A., Jäger, N., Rausch, T., Ryzhova, M., Korbel, J. O., … Jabado, N. (2012). Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature, 482(7384), 226–231. https://doi.org/10.1038/nature10833 Kleinman, C. L., Gerges, N., Papillon-Cavanagh, S., Sin-Chan, P., Pramatarova, A., Quang, D. A., Adoue, V., Busche, S., Caron, M., Djambazian, H., Bemmo, A., Fontebasso, A. M., Spence, T., Schwartzentruber, J., Albrecht, S., Hauser, P., Garami, M., Klekner, A., Bognar, L., Montes, J. L., … Jabado, N. (2014). Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nature genetics, 46(1), 39–44. https://doi.org/10.1038/ng.2849 Papillon-Cavanagh, S., Lu, C., Gayden, T., Mikael, L. G., Bechet, D., Karamboulas, C., Ailles, L., Karamchandani, J., Marchione, D. M., Garcia, B. A., Weinreb, I., Goldstein, D., Lewis, P. W., Dancu, O. M., Dhaliwal, S., Stecho, W., Howlett, C. J., Mymryk, J. S., Barrett, J. W., Nichols, A. C., … Jabado, N. (2017). Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Nature genetics, 49(2), 180–185. https://doi.org/10.1038/ng.3757 Chen, C., Deshmukh, S., Jessa, S., Hadjadj, D., Lisi, V., Andrade, A. F., Faury, D., Jawhar, W., Dali, R., Suzuki, H., Pathania, M., A, D., Dubois, F., Woodward, E., Hébert, S., Coutelier, M., Karamchandani, J., Albrecht, S., Brandner, S., De Jay, N., … Jabado, N. (2020). Histone H3.3G34-Mutant Interneuron Progenitors Co-opt PDGFRA for Gliomagenesis. Cell, 183(6), 1617–1633.e22. https://doi.org/10.1016/j.cell.2020.11.012 Chaouch, A., Berlandi, J., Chen, C., Frey, F., Badini, S., Harutyunyan, A. S., Chen, X., Krug, B., Hébert, S., Jeibmann, A., Lu, C., Kleinman, C. L., Hasselblatt, M., Lasko, P., Shirinian, M., & Jabado, N. (2021). Histone H3.3 K27M and K36M mutations de-repress transposable elements through perturbation of antagonistic chromatin marks. Molecular cell, 81(23), 4876–4890.e7. https://doi.org/10.1016/j.molcel.2021.10.008   Related Episodes Cancer and Epigenetics (David Jones) Epigenetics & Glioblastoma: New Approaches to Treat Brain Cancer (Lucy Stead) Targeting COMPASS to Cure Childhood Leukemia (Ali Shilatifard)   Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on LinkedIn Active Motif on Facebook Email: podcast@activemotif.com

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.22.308692v1?rss=1 Authors: Zocher, S., Overall, R. W., Berdugo-Vega, G., Rund, N., Karasinsky, A., Adusumilli, V., Steinhauer, C., Scheibenstock, S., Haendler, K., Schultze, J. L., Calegari, F., Kempermann, G. Abstract: Dynamic DNA methylation controls gene-regulatory networks underlying cell fate specification. How DNA methylation patterns change during adult hippocampal neurogenesis and their relevance for adult neural stem cell differentiation and related brain function has, however, remained unknown. Here, we show that neurogenesis-associated de novo DNA methylation is critical for maturation and functional integration of adult-born hippocampal neurons. Cell stage-specific bisulfite sequencing revealed a pronounced gain of DNA methylation at neuronal enhancers, gene bodies and binding sites of pro-neuronal transcription factors during adult neurogenesis, which mostly correlated with transcriptional up-regulation of the associated loci. Inducible deletion of both de novo DNA methyltransferases Dnmt3a and Dnmt3b in adult neural stem cells specifically impaired dendritic outgrowth and synaptogenesis of new-born neurons, resulting in reduced hippocampal excitability and specific deficits in hippocampus-dependent learning and memory. Our results highlight that, during adult neurogenesis, remodeling of neuronal methylomes is fundamental for proper hippocampal function. Copy rights belong to original authors. Visit the link for more info

In this episode of the Epigenetics Podcast, we caught up with Dr. Dirk Schübeler, Director of the Friedrich Miescher Institute (FMI) in Basel, Switzerland, to talk about his work on the effects of DNA methylation on chromatin structure and transcription. Dirk Schübeler was born in Germany and started his scientific career in Braunschweig, Germany. After his postdoc at the Fred Hutchinson Cancer Research Center in Seattle, he joined the FMI in 2003 and never left. He was recently appointed as the Director of the FMI in March 2020. Dirk Schübeler’s research focuses on DNA methylation and its effects on chromatin and transcription. It is widely known that DNA methylation leads to gene silencing, but many of the mechanisms and regulatory factors involved in this process remain understudied. Therefore, Dirk Schübeler and his team set out to characterize the DNA methylation profiles in normal human somatic cells and compare them with the methylation profiles in transformed human cells. More recent work in his lab led by postdoc Tuncay Baubec focused on factors that bind to methylated DNA regions and modify chromatin structure. The factors they studied include the MBD protein family and also proteins like DNMT3B. In this interview, we discuss the impact of DNA methylation on chromatin states, how CpG-binding factors influence those processes, and we also talk about his new role as Director of the Friedrich Miescher Institute. References Tuncay Baubec, Daniele F. Colombo, … Dirk Schübeler (2015) Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation (Nature) DOI: 10.1038/nature14176  Paul Adrian Ginno, Lukas Burger, … Dirk Schübeler (2018) Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape (Nature Communications) DOI: 10.1038/s41467-018-06007-5  Michael B. Stadler, Rabih Murr, … Dirk Schübeler (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions (Nature) DOI: 10.1038/nature10716  Silvia Domcke, Anaïs Flore Bardet, … Dirk Schübeler (2015) Competition between DNA methylation and transcription factors determines binding of NRF1 (Nature) DOI: 10.1038/nature16462  Florian Lienert, Christiane Wirbelauer, … Dirk Schübeler (2011) Identification of genetic elements that autonomously determine DNA methylation states (Nature Genetics) DOI: 10.1038/ng.946 Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com

DNA methylation plays a crucial role in the epigenetic control of gene expression during mammalian development and differentiation. Whereas the de novo DNA methyltransferases (Dnmts), Dnmt3a and Dnmt3b, establish DNA methylation patterns during development; Dnmt1 stably maintains DNA methylation patterns during replication. DNA methylation patterns change dynamically during development and lineage specification, yet very little is known about how DNA methylation affects gene expression profiles upon differentiation. Therefore, we determined genome-wide expression profiles during differentiation of severely hypomethylated embryonic stem cells (ESCs) lacking either the maintenance enzyme Dnmt1 (dnmt1-/- ESCs) or all three major Dnmts (dnmt1-/-; dnmt3a-/-, dnmt3b-/- or TKO ESCs), resulting in complete loss of DNA methylation, and assayed their potential to transit in and out of the ESC state. Our results clearly demonstrate that upon initial differentiation to embryoid bodies (EBs), wild type, dnmt1-/- and TKO cells are able to activate differentiation processes. However, transcription profiles of dnmt1-/- and TKO EBs progressively diverge with prolonged EB culture, with dnmt1-/- EBs being more similar to wild type EBs, indicating a higher differentiation potential of dnmt1-/- EBs compared to TKO EBs. Remarkably though, after dissociation of late EBs and further cultivation under pluripotency promoting conditions, both dnmt1-/- and TKO but not wild type cells rapidly revert to expression profiles typical of undifferentiated ESCs. Thus, while DNA methylation is dispensable for the initial activation of differentiation programs, it seems to be crucial for permanently restricting the developmental fate during differentiation. Based on the essential role of Uhrf1 in maintenance DNA methylation, we investigated the structurally highly similar second member of the Uhrf protein family, Uhrf2, whose function in maintenance methylation or other biological processes is completely unknown. Expression analysis of uhrf1 and uhrf2 in various cell lines and tissues revealed a time- and developmental switch in transcript levels of both genes with uhrf1 being highly expressed in undifferentiated, proliferating cells and uhrf2 being predominately expressed in differentiated, non-dividing cells. These opposite expression patterns together with no detectable effect on DNA methylation levels upon knock down of uhrf2 suggests that Uhrf2 is rather involved in maintaining DNA methylation patterns in differentiated cells and points to non-redundant functions of both proteins. The discovery of the “6th base” of the genome, 5-hydroxymethylcytosine (5hmC), resulting from the oxidation of 5mC by the family of Tet dioxygenases (Tet1-3), once again ignited the debate about how DNA methylation marks can be modified and removed. To gain insights into the biological function of this newly identified modification, we developed a sensitive enzymatic assay for quantification of global 5hmC levels in genomic DNA. Similar to 5mC levels, we found that also 5hmC levels dynamically change during differentiation of ESCs to EBs, which correlates with the differential expression of tet1-3. Furthermore, we characterized a novel endonuclease, PvuRts1I that selectively cleaves 5hmC containing DNA and show first data on its application as a tool to map and analyze 5hmC patterns in mammalian genomes. Finally, we investigated designer transcription activator-like effector (dTALEs) proteins targeting the oct4 locus. Our results show that the epigenetic state of the target locus interferes with the ability of dTALEs to activate transcriptionally silent genes, which however can be overcome using dTALEs in combination with low doses of epigenetic inhibitors. In conclusion, this work gives further insights into the biological roles of methylation mark writers (Dnmts), readers (Uhrfs) and modifiers (Tets) and advances our understanding on the function of DNA methylation in the epigenetic control of gene expression during development and cellular differentiation.

Background: We analyzed prospectively whether MGMT (O(6)-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression. 12 Hide Figures Abstract Introduction Methods Results Discussion Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Background We analyzed prospectively whether MGMT (O6-methylguanine-DNA methyltransferase) mRNA expression gains prognostic/predictive impact independent of MGMT promoter methylation in malignant glioma patients undergoing radiotherapy with concomitant and adjuvant temozolomide or temozolomide alone. As DNA-methyltransferases (DNMTs) are the enzymes responsible for setting up and maintaining DNA methylation patterns in eukaryotic cells, we analyzed further, whether MGMT promoter methylation is associated with upregulation of DNMT expression. Methodology/Principal Findings: Adult patients with a histologically proven malignant astrocytoma (glioblastoma: N = 53, anaplastic astrocytoma: N = 10) were included. MGMT promoter methylation was determined by methylation-specific PCR (MSP) and sequencing analysis. Expression of MGMT and DNMTs mRNA were analysed by real-time qPCR. Prognostic factors were obtained from proportional hazards models. Correlation between MGMT mRNA expression and MGMT methylation status was validated using data from the Cancer Genome Atlas (TCGA) database (N = 229 glioblastomas). Low MGMT mRNA expression was strongly predictive for prolonged time to progression, treatment response, and length of survival in univariate and multivariate models (p

Background: Immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome) is a rare autosomal recessive disease characterised by facial dysmorphism, immunoglobulin deficiency and branching of chromosomes 1, 9 and 16 after PHA stimulation of lymphocytes. Hypomethylation of DNA of a small fraction of the genome is an unusual feature of ICF patients which is explained by mutations in the DNA methyltransferase gene DNMT3B in some, but not all, ICF patients. Objective: To obtain a comprehensive description of the clinical features of this syndrome as well as genotype– phenotype correlations in ICF patients. Methods: Data on ICF patients were obtained by literature search and additional information by means of questionnaires to corresponding authors. Results and conclusions: 45 patients all with proven centromeric instability were included in this study. Facial dysmorphism was found to be a common characteristic (n=41/42), especially epicanthic folds, hypertelorism, flat nasal bridge and low set ears. Hypo- or agammaglobulinaemia was demonstrated in nearly all patients (n=39/44). Opportunistic infections were seen in several patients, pointing to a T cell dysfunction. Haematological malignancy was documented in two patients. Life expectancy of ICF patients is poor, especially those with severe infections in infancy or chronic gastrointestinal problems and failure to thrive. Early diagnosis of ICF is important since early introduction of immunoglobulin supplementation can improve the course of the disease. Allogeneic stem cell transplantation should be considered as a therapeutic option in patients with severe infections or failure to thrive. Only 19 of 34 patients showed mutations in DNMT3B, suggesting genetic heterogeneity. No genotype–phenotype correlation was found between patients with and without DNMT3B mutations.