Podcasts about micrornas mirnas

In a groundbreaking study conducted by researchers in Austria, the focus was on understanding the role of extracellular microRNAs (miRNAs) in lipedema. The research paper titled “SVF-Derived Extracellular Vesicles Carry Characteristic miRNAs in Lipedema” was published in the peer-reviewed journal Scientific Reports in April 2020.

Welcome to another episode of The Synthesis of Wellness Podcast! This in a super in-depth episode dedicated to understanding how genetics work, how epigenetics work, and how you can essentially "hack" the way your genes are expressed in order to optimize you biological state. Topics: 1. Introduction - Defining epigenetics and its role in gene expression - Overcoming limiting beliefs about genetic predispositions 2. DNA Structure and Organization - Nucleotides: The building blocks of DNA - Double helix structure and base pairing - Chromosomes and genes: Organizing genetic information 3. Epigenetic Regulation: DNA Methylation - DNA methylation and its impact on gene expression - Enzymes involved in DNA methylation (DNMTs) - Factors affecting DNA methylation, including toxins 4. Epigenetic Regulation: Histone Modifications - Histone acetylation and deacetylation - Other histone modifications and their role in gene expression 5. Epigenetic Regulation: Non-coding RNAs - Non-coding RNAs (ncRNAs) and their regulatory functions - MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) - Influence of ncRNAs on gene transcription and expression 6. Strategies for Optimizing Epigenetic Expression - Dietary considerations for DNA methylation support - Impact of polyphenols and SCFAs on histone acetylation - Sleep optimization and its effect on gene expression 7. Environmental Factors and Epigenetics - Avoiding toxins and their influence on epigenetic regulation - Role of infections in epigenetic modifications - Air pollution, PCBs, phthalates, and their impact on gene expression 8. Mindfulness and Stress Reduction - Mindfulness practices to mitigate epigenetic dysregulation - Reducing stress and its effects on gene expression Thanks for tuning in! If you liked this episode, please leave a rating and review or share it to your stories over on Instagram. If you tag @synthesisofwellness, Chloe would love to personally thank you for listening! Follow Chloe on Instagram @synthesisofwellness, or use the link: ⁠https://www.instagram.com/synthesisofwellness/⁠ Follow Chloe on TikTok @chloe_c_porter Visit ⁠synthesisofwellness.com⁠ to purchase products, subscribe to our mailing list, and more! Or visit ⁠linktr.ee/synthesisofwellness⁠ to see all of Chloe's links, schedule a BioPhotonic Scanner consult with Chloe, or support the show! Thanks again for tuning in! --- Support this podcast: https://podcasters.spotify.com/pod/show/chloe-porter6/support

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.07.10.548401v1?rss=1 Authors: Chen, X., Sokirniy, I., Wang, X., Jiang, M., Mseis-Jackson, N., Williams, C., Mayes, K., Jiang, N., Puls, B., Du, Q., Shi, Y., Li, H. Abstract: While astrocyte-to-neuron (AtN) reprogramming holds great promise in regenerative medicine, the molecular mechanisms that govern this unique biological process remain elusive. MicroRNAs (miRNAs), as post-transcriptional regulators of gene expression, play crucial roles during development and under various pathological conditions. To understand the function of miRNAs during AtN reprogramming process, we performed RNA-seq of both mRNAs and miRNAs on human astrocyte (HA) cultures upon NeuroD1 overexpression. Bioinformatics analyses showed that NeuroD1 not only activates essential neuronal genes to initiate reprogramming process but also induces miRNA changes in HA. Among the upregulated miRNAs, we identified miR-375 and its targets, neuronal ELAVL genes (nELAVLs), which encode a family of RNA-binding proteins and are also upregulated by NeuroD1. We further showed that manipulating miR-375 level regulates nELAVLs expression during NeuroD1-mediated reprogramming. Interestingly, miR-375/nELAVLs are also induced by reprogramming factors Neurog2 and ASCL1 in HA suggesting a conserved function to neuronal reprogramming, and by NeuroD1 in the mouse astrocyte culture and spinal cord. Functionally, we showed that miR-375 overexpression improves NeuroD1-mediated reprogramming efficiency by promoting cell survival at early stages in HA even in cultures treated with the chemotherapy drug Cisplatin. Moreover, miR-375 overexpression does not appear to compromise maturation of the reprogrammed neurons in long term HA cultures. Lastly, overexpression of miR-375-refractory ELAVL4 induces apoptosis and reverses the cell survival-promoting effect of miR-375 during AtN reprogramming. Together, we demonstrate a neuro-protective role of miR-375 during NeuroD1-mediated AtN reprogramming and suggest a strategy of combinatory overexpression of NeuroD1 and miR-375 for improving neuronal reprogramming efficiency. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

A new research paper was published on the cover of Aging (Aging-US) Volume 15, Issue 12, entitled, “Age prediction from human blood plasma using proteomic and small RNA data: a comparative analysis.” Aging clocks, built from comprehensive molecular data, have emerged as promising tools in medicine, forensics, and ecological research. However, few studies have compared the suitability of different molecular data types to predict age in the same cohort and whether combining them would improve predictions. In this new study, researchers Jérôme Salignon, Omid R. Faridani, Tasso Miliotis, Georges E. Janssens, Ping Chen, Bader Zarrouki, Rickard Sandberg, Pia Davidsson, and Christian G. Riedel from Karolinska Institutet, University of New South Wales, Garvan Institute of Medical Research, and AstraZeneca explored this at the level of proteins and small RNAs in 103 human blood plasma samples. “Here we expand the limited portfolio of comparisons between aging clocks built from different types of molecular data from the same cohort.” First, the researchers used a two-step mass spectrometry approach measuring 612 proteins to select and quantify 21 proteins that changed in abundance with age. Notably, proteins increasing with age were enriched for components of the complement system. Next, they used small RNA sequencing to select and quantify a set of 315 small RNAs that changed in abundance with age. Most of these were microRNAs (miRNAs), downregulated with age, and predicted to target genes related to growth, cancer, and senescence. Finally, the team used the collected data to build age-predictive models. Among the different types of molecules, proteins yielded the most accurate model (R² = 0.59 ± 0.02), followed by miRNAs as the best-performing class of small RNAs (R² = 0.54 ± 0.02). Interestingly, the use of protein and miRNA data together improved predictions (R2 = 0.70 ± 0.01). Future work using larger sample sizes and a validation dataset will be necessary to confirm these results. “Nevertheless, our study suggests that combining proteomic and miRNA data yields superior age predictions, possibly by capturing a broader range of age-related physiological changes. It will be interesting to determine if combining different molecular data types works as a general strategy to improve future aging clocks.” DOI - https://doi.org/10.18632/aging.204787 Corresponding author - Christian G. Riedel - christian.riedel@ki.se Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.204787 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, human blood plasma, small RNAs, proteomics, age prediction About Aging-US Launched in 2009, 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-US 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 https://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/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2023.04.01.535193v1?rss=1 Authors: Huang, Y., Abdelgawad, A. G. A., Turchinovich, A., Queen, S., Abreu, C. M., Zhu, X., Batish, M., Zheng, L., Witwer, K. W. Abstract: Introduction: Antiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Extracellular vesicle (EV) RNAs have emerged as important participants in HIV disease pathogenesis. Brain tissue-derived EVs (bdEVs) act locally in the source tissue and may indicate molecular mechanisms in HIV CNS pathology. Using brain tissue and bdEVs from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation. Methods: Postmortem occipital cortex tissues were obtained from pigtailed macaques either not infected or dual-inoculated with SIV swarm B670 and clone SIV/17E-Fr. SIV-inoculated groups included samples collected at different time points during acute infection or chronic infection without or with CNS pathology (CP- or CP+). bdEVs were separated and characterized in accordance with international consensus standards. RNAs from bdEVs and source tissue were used for sequencing and qPCR to detect mRNA, miRNA, and circRNA levels. Results: Multiple dysregulated bdEV RNAs, including mRNAs, miRNAs, and circRNAs, were identified in acute and CP+. Most dysregulated mRNAs in bdEVs reflected dysregulation in their source tissues. These mRNAs are disproportionately involved in inflammation and immune responses, especially interferon pathways. For miRNAs, qPCR assays confirmed the differential abundance of miR-19a-3p, let-7a-5p, and miR-29a-3p (acute phase), and miR-146a-5p and miR-449a-5p (CP+) in bdEVs. In addition, target prediction suggested that several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in small RNA levels in bdEVs during SIV infection. Conclusions: RNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

A new research paper was published in Aging (Aging-US) Volume 15, Issue 5, entitled, “Senescence-associated exosomes transfer miRNA-induced fibrosis to neighboring cells.” Radiation-induced fibrosis is a common side effect of radiotherapy, which is the most common treatment for cancer. However, radiation also causes p53-mediated cell cycle arrest, prolonged expression of p21, and the development of senescence in normal cells that reside in irradiated tissues. Bone marrow-derived mesenchymal stem cells (MSCs) accumulate in primary tumor sites because of their natural tropism for inflammatory and fibrotic tissues. MSCs are extremely sensitive to low doses of ionizing radiation and acquire senescence as a result of bystander radiation effects. Senescent cells remain metabolically active but develop a potent senescence-associated secretory phenotype (SASP) that correlates to hyperactive secretion of cytokines, pro-fibrotic growth factors, and exosomes (EXOs). Integrative pathway analysis has highlighted that radiation-induced senescence significantly enriched cell-cycle, extracellular matrix, transforming growth factor-β (TGF-β) signaling, and vesicle-mediated transport genes in MSCs. EXOs are cell-secreted nanovesicles (a subclass of small extracellular vesicles) that contain biomaterials—proteins, RNAs, microRNAs (miRNAs)—that are critical in cell-cell communication. miRNA content analysis of secreted EXOs further revealed that radiation-induced senescence uniquely altered miRNA profiles. “In fact, several of the standout miRNAs directly targeted TGF-β or downstream genes.” In this new study, researchers Amy H. Lee, Deepraj Ghosh, Ivy L. Koh, and Michelle R. Dawson from Brown University further treated normal MSCs with senescence-associated EXOs (SA-EXOs) to examine bystander effects of radiation-induced senescence. The researchers found that these modulated genes were related to TGF-β pathway and elevated both alpha smooth muscle actin (protein increased in senescent, activated cells) and Ki-67 (proliferative marker) expression in SA-EXO treated MSCs compared to untreated MSCs. They revealed that SA-EXOs possess unique miRNA content that influence myofibroblast phenotypes via TGF-β pathway activation. This highlights that SA-EXOs are potent SASP factors that play a large role in cancer-related fibrosis. “Our integrated omics and EXO microarray analyses show that senescent MSCs possess differential transcriptional genes and secrete vesicles that contain unique post-transcriptional cargo. We subsequently demonstrated that these EXO miRNAs can play important roles in cell-cell communication during disease progression.” Paper: DOI: https://doi.org/10.18632/aging.204539 Corresponding Author: Michelle R. Dawson - michelle_dawson@brown.edu Keywords: radiation-induced senescence, exosomes (EXOs), microRNA (miRNA), transforming growth factor-β (TGF-β), mesenchymal stem cells (MSCs) About Aging-US Launched in 2009, 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-US 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 https://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/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.11.29.518326v1?rss=1 Authors: Goody, P. R., Christmann, D., Goody, D., Nehl, D., Backer, K., Wilhelm-Juengling, K., Uchida, S., Moore, J. B., Zimmer, S., Bakhtiary, F., Pfeifer, A., Latz, E., Nickenig, G., Jansen, F., Hosen, M. R. Abstract: Rationale: Aortic valve stenosis (AVS) is a major contributor to cardiovascular death in the elderly population worldwide. MicroRNAs (miRNAs) are highly dysregulated in patients with AVS undergoing surgical aortic valve replacement (SAVR). However, miRNA-dependent mechanisms regulating inflammation and calcification or miRNA-mediated cell-cell crossstalk during the pathogenesis of AVS are still poorly understood. Here, we explored the role of extracellular vesicles (EV)-associated miR-145-5p, which we showed to be highly upregulated upon valvular calcification in AVS in mice and humans. Methods: Human TaqMan miRNA arrays identified dysregulated miRNAs in aortic valve tissue explants from AVS patients compared to non-calcified valvular tissue explants of patients undergoing SAVR. Echocardiographic parameters were measured in association with the quantification of dysregulated miRNAs in a murine AVS model. In vitro calcification experiments were performed to explore the effects of EV-miR-145-5p on calcification and crosstalk in valvular cells. To dissect molecular miRNA signatures and their effect on signaling pathways, integrated OMICS analyses were performed. RNA sequencing (RNA-seq), high-throughput transcription factor (TF) and proteome arrays showed that a number of genes, miRNAs, TFs, and proteins are crucial for calcification and apoptosis, which are involved in the pathogenesis of AVS. Results: Among several miRNAs dysregulated in valve explants of AVS patients, miR-145-5p was the most highly gender-independently dysregulated miRNA (AUC, 0.780, p-value, 0.01). MiRNA arrays utilizing patient-derived- and murine aortic-stenosis samples demonstrated that the expression of miR-145-5p is significantly upregulated and correlates positively with cardiac function based on echocardiography. In vitro experiments confirmed that miR-145-5p is encapsulated into EVs and shuttled into valvular interstitial cells. Based on the integrated OMICs results, miR-145-5p interrelates with markers of inflammation, calcification, and apoptosis. In vitro calcification experiments demonstrated that miR-145-5p regulates the ALPL gene, a hallmark of calcification in vascular and valvular cells. EV-mediated shuttling of miR-145-5p suppressed the expression of ZEB2, a negative regulator of the ALPL gene, by binding to its 3' untranslated region to inhibit its translation, thereby diminishing the calcification of target valvular interstitial cells. Conclusion: Elevated levels of pro-calcific and pro-apoptotic EV-associated miR-145-5p contribute to the progression of AVS via the ZEB2-ALPL axis, which could potentially be therapeutically targeted to minimize the burden of AVS. Keywords: aortic valve stenosis, microRNA, extracellular vesicles, cellular crosstalk, valvular calcification Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

Listen to a blog summary about a trending research paper published by Aging (Aging-US as the cover of Volume 14, Issue 17, entitled, "Extracellular microRNA and cognitive function in a prospective cohort of older men: The Veterans Affairs Normative Aging Study.” __________________________________________ Can factors in our bloodstream tell us about our cognitive abilities or predict cognitive decline later in life? Among individuals with dementias, including Alzheimer's disease (AD), studies have identified extracellular microRNAs (miRNAs) as potential biomarkers of cognitive impairment. In cognitively normal individuals, however, this association has not yet been fully investigated. “Understanding the functions of miRNAs in the earliest stages of cognitive decline will expand our knowledge on the biology of prodromal AD and the roles of circulating miRNAs in neurodegenerative diseases and could result in identification of therapeutic targets to guide drug development [17].” In a new research paper, published on the cover of Volume 14, Issue 17, of Aging (listed as “Aging (Albany NY)” by Medline/PubMed and “Aging-US” by Web of Science), researchers Nicole Comfort, Haotian Wu, Peter De Hoff, Aishwarya Vuppala, Pantel S. Vokonas, Avron Spiro, Marc Weisskopf, Brent A. Coull, Louise C. Laurent, Andrea A. Baccarelli, and Joel Schwartz from Columbia University Mailman School of Public Health, University of California San Diego, VA Boston Healthcare System, Boston University School of Medicine, and Harvard TH Chan School of Public Health investigated expression levels of extracellular miRNAs circulating in blood plasma taken from cognitively normal men and the association between these miRNAs and cognitive function. Their secondary goal was to investigate the genes and biological pathways associated with miRNAs linked to cognitive function or decline. The research paper was published on September 6, 2022, and entitled, “Extracellular microRNA and cognitive function in a prospective cohort of older men: The Veterans Affairs Normative Aging Study.” Full blog - https://aging-us.org/2022/09/can-micrornas-in-the-bloodstream-signal-cognitive-decline/ DOI - https://doi.org/10.18632/aging.204268 Corresponding author - Nicole Comfort - nicole.comfort@columbia.edu Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.204268 Press release - https://aging-us.com/news_room/Extracellular-microRNA-and-cognitive-function-in-a-prospective-cohort-of-older-men Keywords - aging, plasma, extracellular RNA, RNA-seq, microRNA, cognitive decline, cognitive impairment About Aging-US Launched in 2009, 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-US 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 https://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/ Pinterest - https://www.pinterest.com/AgingUS/ Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

A new research paper was published on the cover of Aging (Aging-US) Volume 14, Issue 17, entitled, “Extracellular microRNA and cognitive function in a prospective cohort of older men: The Veterans Affairs Normative Aging Study.” Aging-related cognitive decline is an early symptom of Alzheimer's disease and other dementias, and on its own can have substantial consequences on an individual's ability to perform important everyday functions. Despite increasing interest in the potential roles of extracellular microRNAs (miRNAs) in central nervous system (CNS) pathologies, there has been little research on extracellular miRNAs in early stages of cognitive decline. In a new study, researchers Nicole Comfort, Haotian Wu, Peter De Hoff, Aishwarya Vuppala, Pantel S. Vokonas, Avron Spiro, Marc Weisskopf, Brent A. Coull, Louise C. Laurent, Andrea A. Baccarelli, and Joel Schwartz from Columbia University Mailman School of Public Health, University of California San Diego, VA Boston Healthcare System, Boston University School of Medicine, and Harvard TH Chan School of Public Health leveraged the longitudinal Normative Aging Study (NAS) cohort to investigate associations between plasma miRNAs and cognitive function among cognitively normal men. “In a cohort of older men from Massachusetts, we investigated associations between plasma miRNAs and global cognition and rate of global cognitive decline measured by the MMSE.” Full press release - https://aging-us.net/2022/09/15/aging-extracellular-microrna-and-cognitive-function-in-a-prospective-cohort-of-older-men-the-veterans-affairs-normative-aging-study/ DOI: https://doi.org/10.18632/aging.204268 Corresponding Author: Nicole Comfort – nicole.comfort@columbia.edu Keywords: plasma, extracellular RNA, RNA-seq, microRNA, cognitive decline, cognitive impairment Sign up for free Altmetric alerts about this article: https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.204268 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, contact media@impactjournals.com.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.08.24.505085v1?rss=1 Authors: Taylor, S., Kobayashi, M., Vilella, A., Tiwari, D., Zolboot, N., Hartzell, A., Girgiss, C., Abaci, Y., De Sanctis, C., Bellenchi, G. C., Darnell, R. B., Gross, C., Zoli, M., Berg, D. K., Lippi, G. Abstract: The assembly of the mammalian brain is orchestrated by temporally coordinated waves of gene expression. A key aspect of this developmental program is mediated at the post-transcriptional level by microRNAs (miRNAs). Deletion of neuronal enriched miRNAs induces strong developmental phenotypes, and multiple reports have found altered levels of miRNAs in patients with neurodevelopmental disorders. However, cellular and molecular mechanisms used by miRNAs to instruct proper brain development remain largely unexplored. Here, through multiple screens, we identified miR-218 as a critical regulator of hippocampal assembly in mice. MiR-218 is highly expressed in the hippocampus and enriched in both excitatory principal neurons and GABAergic inhibitory interneurons. Transient inhibition of miR-218 in early life results in an adult brain with heightened network activity and a predisposition to seizures. We used RNA-seq and FACS-seq (fluorescence-activated cell sorting followed by RNA-seq) to identify global and cell type-specific changes in gene expression in the absence of miR-218 and narrow down which altered developmental processes would lead to long-term network instability. We find that miR-218 inhibition results in the disruption of early depolarizing GABAergic signaling, structural defects in dendritic spines, and altered intrinsic membrane excitability. Finally, conditional knockout of miR-218 in interneurons, but not pyramidal neurons is sufficient to recapitulate the effects on long-term stability. Taken together, the data suggest that miR-218 orchestrates hippocampal network assembly to produce a stable network in the adult, primarily by regulating interneuron function in early postnatal life. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

This episode explores the very personal journey of Step work, specific to Step 3, and trauma healing. Both processes are incredibly personal. Resources mentioned, as always, provided below.  1:05 - Step 3 from the original 'Big Book', Alcoholics Anonymous1:30 - Perfect is the enemy of good originally came from Voltaire quoting an Italian proverb the Dictionnaire philosophique in 1770, "Le meglio è l'inimico del bene". 5:40 - Families Anonymous Step 35:50 - CoDependents Anonymous Step 36:55 - Higher Power7:00 - Sponsorship article from Recovery.org, Sponsor, Recovery Coach or Professional Counselor: Which is Right for You?9:00 - Trauma overview is addressed in Episode 29:20 - Psychology Today definition of Trauma10:05 - PTSD, a Georgia Tech study on possible avenues of treatment10:05 - PTSD, a Johns Hopkins University study on possible avenues of treatment10:15 - RNA definition from National Human Genome Research Institute10:35 - Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice11:45 - Summary of above article, "Gene-environment interactions are determining factors for the etiology of psychiatric disorders, diabetes and cancer, and are thought to contribute to disease inheritance across generations. Small non-coding RNAs (sncRNAs) are potential vectors at the interface between genes and environment. Here, we report that environmental conditions involving traumatic stress in early life in mice altered microRNAs (miRNAs) expression, and behavioral and metabolic responses in the progeny. Several miRNAs were affected in the serum and brain of both, the traumatized animals and their progeny when adult, but also in the sperm of traumatized males. Injection of sperm RNAs from these males into fertilized wild-type oocytes reproduced the behavioral and metabolic alterations in the resulting offspring. These results strongly suggest that sncRNAs are sensitive to environmental factors in early life, and contribute to the inheritance of trauma-induced phenotypes across generations. They may offer potential diagnostic markers for associated pathologies in humans."12:30 - 2018 Bronx Veterans Affairs Hospital Publication on Intergenerational Trauma, "Intergenerational transmission of trauma effects: putative role of epigenetic mechanisms"14:40 - Family of Origin study from Texas A&M, specific to addiction,Thank you for listening and please visit www.siblinghoodofrecovery.com for free resources, links to organizations, groups and individuals who can offer help in the Journey of Recovery towards healing from substance use disorders. If you like this Podcast, please leave a rating on wherever you're listening. It will help to get the word out. If there is one message I can leave you with, the best you can offer your loved one battling addiction is love and a healthier you. Walk gently, my friend.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.02.365049v1?rss=1 Authors: Verma, S., Dwivedy, A., Kumar, N., Biswal, B. K. Abstract: Background: Over the past two decades, there has been a continued research on the role of small non-coding RNAs including microRNAs (miRNAs) in various diseases. Studies have shown that viruses modulate the host cellular machinery and hijack its metabolic and immune signaling pathways by miRNA mediated gene silencing. Given the immensity of coronavirus disease 19 (COVID-19) pandemic and the strong association of viral encoded miRNAs with their pathogenesis, it is important to study Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) miRNAs. Results: To address this unexplored area, we identified 8 putative novel miRNAs from SARS-CoV-2 genome and explored their possible human gene targets. A significant proportion of these targets populated key immune and metabolic pathways such as MAPK signaling pathway, maturity-onset diabetes of the young, Insulin signaling pathway, endocytosis, RNA transport, TGF-{beta} signaling pathway, to name a few. The data from this work is backed up by recently reported high-throughput transcriptomics datasets obtains from SARS-CoV-2 infected samples. Analysis of these datasets reveal that a significant proportion of the target human genes were down-regulated upon SARS-CoV-2 infection. Conclusions: The current study brings to light probable host metabolic and immune pathways susceptible to viral miRNA mediated silencing in a SARS-CoV-2 infection, and discusses its effects on the host pathophysiology. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.08.286955v1?rss=1 Authors: Diaz, J. L., Siththanandan, V., Lu, V., Gonzalez-Nava, N., Pasquina, L., MacDonald, J., Woodworth, M. B., Ozkan, A., Nair, R., He, Z., Sahni, V., Sarnow, P., Palmer, T. D., Macklis, J., Tharin, S. Abstract: The corticospinal tract is unique to mammals and the corpus callosum is unique to placental mammals (eutherians). The emergence of these structures is thought to underpin the evolutionary acquisition of complex motor and cognitive skills. Corticospinal motor neurons (CSMN) and callosal projection neurons (CPN) are the archetypal projection neurons of the corticospinal tract and corpus callosum, respectively. Although a number of conserved transcriptional regulators of CSMN and CPN development have been identified in vertebrates, none are unique to mammals and most are co-expressed across multiple projection neuron subtypes. Here, we discover seventeen CSMN-enriched microRNAs (miRNAs), fifteen of which map to a single genomic cluster that is exclusive to eutherians. One of these, miR-409-3p, promotes CSMN subtype identity in part via repression of LMO4, a key transcriptional regulator of CPN development. In vivo, miR-409-3p is sufficient to convert deep-layer CPN into CSMN. This is the first demonstration of an evolutionarily acquired miRNA in eutherians that refines cortical projection neuron subtype development. Our findings implicate miRNAs in the eutherians increase in neuronal subtype and projection diversity, the anatomic underpinnings of their complex behavior. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.08.01.232306v1?rss=1 Authors: Sengupta, P., Saha, S., Maji, M., Ghosh, M. Abstract: Background: The architecture of the protein-protein interaction (PPI) network in any organism relies on their gene expression signature. microRNAs (miRNAs) have recently emerged as major post transcriptional regulators that control PPI by targeting mainly untranslated regions of the gene encoding proteins. Here, we aimed to unveil the role of miRNAs in the PPI network for identifying potential molecular targets for lung adenocarcinoma (LUAD). Materials and methods: The expression profiles of miRNAs and mRNAs were collected from the NCBI Gene Expression Omnibus (GEO) database (GSE74190 and GSE116959). Abnormally expressed mRNAs from the data were appointed to construct a PPI network and hence incorporated with the miRNA-mRNA regulatory network. The miRNAs and mRNAs in this network were subjected to functional enrichment. Through the network analysis, hubs were identified and their mutation rate and probability of cooccurrence were calculated. Results: We identified 17 miRNAs and 429 mRNAs signature for differentially altered transcriptome in LUAD. The combined miRNA-mRNA regulatory network exhibited scale-free characteristics. Network analysis showed 5 miRNA (including hsa-miR-486-5p, hsa-miR-200b-5p, and hsa-miR-130b-5p) and 10 mRNA (including ASPM, CCNB1, TTN, TPX2, and BIRC5) which expressively contribute in the LUAD. We further investigated the hub genes and noticed that ASPM and TTN had the maximum rate of mutation and possessed a high tendency of cooccurrence in LUAD. Conclusion: This study provides a unique network approach to the exploration of the underlying molecular mechanism in LUAD. Identified mRNAs and miRNAs may therefore, serve as significant prognostic predictors and therapeutic targets. Copy rights belong to original authors. Visit the link for more info

The intestine is a pivotal organ which is divided into two anatomical parts: the small intestine and the large intestine (colon and rectum). Both parts are made up of single layered epithelium. This epithelium is composed of villi (protrusions) – found only in the small intestine - and crypts (invaginations) leading to an increase of the surface of the intestinal lumen whereby the uptake of nutrients and water is improved. Every five days, the intestinal epithelium is renewed whereby both, crypts and eventually villi, are filled up with new cells. The homeostasis of the crypts/villi relies on adult stem cells (SCs), especially crypt base columnar (CBC) cells, which are located at the base of the crypts. These are regulated by an active Wnt signaling pathway. A deregulation of the Wnt signaling pathway leads to cancer formation found in humans almost exclusively in the colon and rectum. Colorectal cancer (CRC) is worldwide the third most common cause for cancer related deaths. In the majority of CRC, origin and progress are caused by mutations in the adenomatous polyposis coli (APC) gene which encodes an essential component of the β-catenin destruction complex that is the central element of the Wnt signaling pathway. As a consequence of these mutations, the executor of the Wnt signaling pathway, β-catenin, which is in this context a transcription factor, cannot be downregulated any more. As a consequence target genes of β-catenin are expressed in an unregulated manner. These target genes regulate features of stem cell biology which confer cancer stemness, metastasis, EMT (epithelial-mesenchymal transition), chemoresistance and other characteristics to colorectal tumor cells. Interestingly, APC mutations have only an effect when they occur in the adult stem cells. Thus, the descendend tumor cells show characteristics of these cells and have been termed cancer stem cells (CSCs). Like adult stem cells in the normal crypt CSCs are the origin of cancer and are characterized by an activated - here deregulated - Wnt signaling pathway and thus, by the aforementioned features. Clinically, cancer death is caused in most cases by metastasis which is treated by chemotherapy from which most if not all CRCs escape by the development of chemoresistance which is an intrinsic feature of the CSCs. Therefore, CSC specific targeted therapies might be a promising therapeutic tool for a successful treatment of CRCs. One possibility is the interference of CSC sustaining molecules as these molecules are involved in the induction and maintenance of CSCs. Here, a promising molecule is olfactomedin-4 (OLFM4) which was discussed to be a CSC marker. But the role of OLFM4 as a CSC marker and important factor for tumorigenesis has been controversially described. Therefore, I investigated in the first part of my thesis the role of OLFM4 in CRC cells. I demonstrate that OLFM4 was expressed only in two out of 14 CRC cell lines. The assumption that OLFM4 was only expressed in cells with characteristics of CSCs and thus, was not detected in the cell lines as they possess only a small proportion of CSCs, was not confirmed. I found that CSCs showed a reduced OLFM4 expression and thus, OLFM4 was not coexpressed with other SC markers. These results indicate that OLFM4 is not a marker of CSCs in CRC. In order to analyze the functional role of OLFM4 in CRC cells, I overexpressed OLFM4 lentivirally. However, the overexpression of OLFM4 and thus, high OLFM4 protein levels did not influence the expression of CSC, EMT or differentiation marker. Likewise, OLFM4 did not play a functional role for proliferation, stemness and metastatic features. Therefore, this study demonstrates that OLFM4 is not a CSC marker and has no functional role for the driving activity in the process of colorectal carcinogenesis. Additionally, I evaluated in the second part of my thesis the role of the microRNAome (miRNAome) in colorectal carcinogenesis, the influence on CSC features and whether the miRNAome might be a tool for specific CSC targeted therapies. microRNAs (miRNAs) are generally downregulated in tumors whereby the miRNA loss promotes tumorigenesis. As the majority of the CRC cases are driven by an APC mutation in the SC compartment, I used for my investigations a mouse model with a conditional Apc knockout in CBC cells which develops efficiently intestinal adenomas. This mouse model was crossed with another mouse model harboring a conditional knockout of the essential miRNA generator Dicer1 to investigate the role of a loss of the miRNAome in murine Wnt driven intestinal tumors. In this part of my study I demonstrated that hetero- and homozygous deletion of Dicer1 in CBC cells, in combination with an Apc knockout, enhances significantly the number of adenomas. Moreover, deletion of Dicer1 resulted in smaller adenomas caused by reduced proliferation. Further analysis of DICER1 deletion in human CRC cell lines revealed that loss of DICER1 and thus, miRNAs led likewise to a decreased proliferation. Additionally, I showed that loss of miRNAs increased the expression/protein levels of CSC markers and CSC features indicating that loss of DICER1 promotes tumorigenesis. Moreover, I translated these mouse model/cell culture results into human colonic normal and tumor tissue as well as CRC. In a collection of different tissues (normal tissue, adenomas and cancers of stages I to IV), increased DICER1 levels were seen from normal tissue to adenomas followed by decreased levels during carcinoma progression. Increased levels of DICER1 were also found in the murine Wnt driven adenomas. In support with this I provided finally evidence that DICER1 expression is regulated by the Wnt signaling pathway thus already early in the beginning of the colorectal tumorigenesis. Thus, this data showed that DICER1 is a tumor suppressor in intestinal cancer and the loss of DICER1 and hence, of the miRNAome, influences CSC marker expression and marker protein levels as well as proliferation and CSC features. Therefore, the miRNAome might possibly become a therapeutic target for CSC targeted therapy.

MicroRNAs (miRNAs) are a class of non-coding RNAs that post-transcriptionally silence target mRNAs. Dysregulation of miRNAs is a frequent event in several diseases, including cancer. One miRNA that has gained special interest in the field of cancer research is miRNA-125b (miR-125b). MiR-125b is a ubiquitously expressed miRNA that is aberrantly expressed in a great variety of tumors. In some tumor types, e. g. colon cancer and hematopoietic tumors, miR-125b is upregulated and displays oncogenic potential, as it induces cell growth and proliferation, while blocking the apoptotic machinery. In contrast, in other tumor entities, e. g. mammary tumors and hepatocellular carcinoma, miR-125b is heavily downregulated. This downregulation is accompanied by de-repression of cellular proliferation and anti-apoptotic programs, contributing to malignant transformation. The reasons for these opposing roles are poorly understood. We summarize the current knowledge of miR-125b and its relevant targets in different tumor types and offer several hypotheses for the opposing roles of miR-125b: miR-125b targets multiple mRNAs, which have diverse functions in individual tissues. These target mRNAs are tissue and tumor specifically expressed, suggesting that misregulation by miR-125b depends on the levels of target gene expression. Moreover, we provide several examples that miR-125b upregulation dictates oncogenic characteristics, while downregulation of miR-125b corresponds to the loss of tumor suppressive functions. Thus, in different tumor entities increased or decreased miR-125b expression may contribute to carcinogenesis.

Background: Dilated cardiomyopathy (DCM) is the most common heart disease in Doberman Pinschers. MicroRNAs (miRNAs) are short non-coding RNAs playing important roles in gene regulation. Different miRNA expression patterns have been described for DCM in humans and might represent potential diagnostic markers. There are no studies investigating miRNA expression profiles in canine DCM. The aims of this study were to Screen the miRNA expression profile of canine serum using miRNA microarray and to compare expression patterns of a group of Doberman Pinschers with DCM and healthy controls. Results: Eight Doberman Pinschers were examined by echocardiography and 24-hour-ECG and classified as healthy (n = 4) or suffering from DCM (n = 4). Total RNA was extracted from serum and hybridized on a custom-designed 8x60k miRNA microarray (Agilent) containing probes for 1368 individual miRNAs. Although total RNA concentrations were very low in serum samples, 404 different miRNAs were detectable with sufficient signal intensity on miRNA microarray. 22 miRNAs were differentially expressed in the two groups (p < 0.05 and fold change (FC) > 1.5), but did not reach statistical significance after multiple testing correction (false discovery rate adjusted p > 0.05). Five miRNAs were selected for further analysis using quantitative Real-Time RT-PCR (qPCR) assays. No significant differences were found using specific miRNA qPCR assays (p > 0.05). Conclusions: Numerous miRNAs can be detected in canine serum. Between healthy and DCM dogs, miRNA expression changes could be detected, but the results did not reach statistical significance most probably due to the small group size. miRNAs are potential new circulating biomarkers in veterinary medicine and should be investigated in larger patient groups and additional canine diseases.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant muscle disorder, which is linked to the contraction of the D4Z4 array at chromosome 4q35. Recent studies suggest that this shortening of the D4Z4 array leads to aberrant expression of double homeobox protein 4 (DUX4) and causes FSHD. In addition, misregulation of microRNAs (miRNAs) has been reported in muscular dystrophies including FSHD. In this study, we identified a miRNA that is differentially expressed in FSHD myoblasts and investigated its function. Methods: To identify misregulated miRNAs and their potential targets in FSHD myoblasts, we performed expression profiling of both miRNA and mRNA using TaqMan Human MicroRNA Arrays and Affymetrix Human Genome U133A plus 2.0 microarrays, respectively. In addition, we over-expressed miR-411 in C2C12 cells to determine the effect of miR-411 on myogenic markers. Results: Using miRNA and mRNA expression profiling, we identified 8 miRNAs and 1,502 transcripts that were differentially expressed in FSHD myoblasts during cell proliferation. One of the 8 differentially expressed miRNAs, miR-411, was validated by quantitative RT-PCR in both primary (2.1 fold, p

Exosomes are cellular secretory vesicles containing microRNAs (miRNAs). Once secreted, exosomes are able to attach to recipient cells and release miRNAs potentially modulating the function of the recipient cell. We hypothesized that exosomal miRNA expression in brains of patients diagnosed with schizophrenia (SZ) and bipolar disorder (BD) might differ from controls, reflecting either disease-specific or common aberrations in SZ and BD patients. The sources of the analyzed samples included McLean 66 Cohort Collection (Harvard Brain Tissue Resource Center), BrainNet Europe II (BNE, a consortium of 18 brain banks across Europe) and Boston Medical Center (BMC). Exosomal miRNAs from frozen postmortem prefrontal cortices with well-preserved RNA were isolated and submitted to profiling by Luminex FLEXMAP 3D microfluidic device. Multiple statistical analyses of microarray data suggested that certain exosomal miRNAs were differentially expressed in SZ and BD subjects in comparison to controls. RT-PCR validation confirmed that two miRNAs, miR-497 in SZ samples and miR-29c in BD samples, have significantly increased expression when compared to control samples. These results warrant future studies to evaluate the potential of exosome-derived miRNAs to serve as biomarkers of SZ and BD.

In biological research, diverse high-throughput techniques enable the investigation of whole systems at the molecular level. The development of new methods and algorithms is necessary to analyze and interpret measurements of gene and protein expression and of interactions between genes and proteins. One of the challenges is the integrated analysis of gene expression and the associated regulation mechanisms. The two most important types of regulators, transcription factors (TFs) and microRNAs (miRNAs), often cooperate in complex networks at the transcriptional and post-transcriptional level and, thus, enable a combinatorial and highly complex regulation of cellular processes. For instance, TFs activate and inhibit the expression of other genes including other TFs whereas miRNAs can post-transcriptionally induce the degradation of transcribed RNA and impair the translation of mRNA into proteins. The identification of gene regulatory networks (GRNs) is mandatory in order to understand the underlying control mechanisms. The expression of regulators is itself regulated, i.e. activating or inhibiting regulators in varying conditions and perturbations. Thus, measurements of gene expression following targeted perturbations (knockouts or overexpressions) of these regulators are of particular importance. The prediction of the activity states of the regulators and the prediction of the target genes are first important steps towards the construction of GRNs. This thesis deals with these first bioinformatics steps to construct GRNs. Targets of TFs and miRNAs are determined as comprehensively and accurately as possible. The activity state of regulators is predicted for specific high-throughput data and specific contexts using appropriate statistical approaches. Moreover, (parts of) GRNs are inferred, which lead to explanations of given measurements. The thesis describes new approaches for these tasks together with accompanying evaluations and validations. This immediately defines the three main goals of the current thesis: 1. The development of a comprehensive database of regulator-target relation. Regulators and targets are retrieved from public repositories, extracted from the literature via text mining and collected into the miRSel database. In addition, relations can be predicted using various published methods. In order to determine the activity states of regulators (see 2.) and to infer GRNs (3.) comprehensive and accurate regulator-target relations are required. It could be shown that text mining enables the reliable extraction of miRNA, gene, and protein names as well as their relations from scientific free texts. Overall, the miRSel contains about three times more relations for the model organisms human, mouse, and rat as compared to state-of-the-art databases (e.g. TarBase, one of the currently most used resources for miRNA-target relations). 2. The prediction of activity states of regulators based on improved target sets. In order to investigate mechanisms of gene regulation, the experimental contexts have to be determined in which the respective regulators become active. A regulator is predicted as active based on appropriate statistical tests applied to the expression values of its set of target genes. For this task various gene set enrichment (GSE) methods have been proposed. Unfortunately, before an actual experiment it is unknown which genes are affected. The missing standard-of-truth so far has prevented the systematic assessment and evaluation of GSE tests. In contrast, the trigger of gene expression changes is of course known for experiments where a particular regulator has been directly perturbed (i.e. by knockout, transfection, or overexpression). Based on such datasets, we have systematically evaluated 12 current GSE tests. In our analysis ANOVA and the Wilcoxon test performed best. 3. The prediction of regulation cascades. Using gene expression measurements and given regulator-target relations (e.g. from the miRSel database) GRNs are derived. GSE tests are applied to determine TFs and miRNAs that change their activity as cellular response to an overexpressed miRNA. Gene regulatory networks can constructed iteratively. Our models show how miRNAs trigger gene expression changes: either directly or indirectly via cascades of miRNA-TF, miRNA-kinase-TF as well as TF-TF relations. In this thesis we focus on measurements which have been obtained after overexpression of miRNAs. Surprisingly, a number of cancer relevant miRNAs influence a common core of TFs which are involved in processes such as proliferation and apoptosis.

Dendritic cells (DCs) play a key role in the initiation of adaptive immune responses and the maintenance of self-tolerance. Due to their therapeutic potential, understanding the mechanisms that guide DC differentiation and effector functions is important. DC differentiation and activation depends on transcription factor control of stage-specific gene expression. The recent identification of posttranscriptional control of gene expression by microRNAs (miRNAs) has added another layer of gene regulation that might be important in DC biology. We analyzed the miRNA expression profiles of different DC subsets and identified several miRNAs differentially expressed between plasmacytoid DCs (pDCs) and conventional DCs (cDCs). In terms of miRNA expression, pDCs were more closely related to CD4+ T cells than to cDCs. We also observed that pDCs and cDCs preferentially expressed miRNAs associated with lymphoid or myeloid lineage differentiation, respectively. By knocking down miR-221 or miR-222 during in vitro DC differentiation, we obtained a higher pDC frequency. While p27kip1 and c-kit are confirmed miR-221/222 targets, we additionally identified the pDC cell fate regulator E2-2 as a potential miR-221/222 target. Thus, our analysis points to a role for miRNAs in directing and stabilizing pDC and cDC cell fate decisions. To assess the general influence of miRNAs on DCs, we generated mice with a DC-specific conditional knockout of the key miRNA-producing enzyme Dicer. Dicer-deficient mice dis- played no alterations in short-lived spleen and lymph node DCs. However, long-lived epidermal DCs, known as Langerhans cells (LCs), showed increased turnover and apoptosis rates, leading to their progressive loss. Upon stimulation, Dicer-deficient LCs were able to properly upregulate the surface molecules MHC class I and CCR7, but not MHC class II, CD40 and CD86. In consequence, they were incapable of stimulating CD4+ T cell proliferation. The work presented in this thesis indicates a role for miRNAs in DC regulation not covered by transcription factors. Having demonstrated a role for miRNAs in DC lineage fate decisions, as well as in LC homeostasis, maturation and function, we conclude that miRNAs regulate various aspects of DC biology and thereby contribute to the control of adaptive immune responses.

MicroRNAs (miRNAs) are a conserved class of small non-coding RNA genes with 19 to 25 nucleotides in length that are found in all higher eukaryotes as well as some DNA viruses. MiRNAs have been elucidated to exert important regulatory functions in many biological and pathological processes, by imperfect base pairing to the 3’ untranslated region (UTR) of target mRNAs, leading to translational repression or mRNA degradation. In the recent years, the rapid development of next generation sequencing (NGS) technologies has tremendously enhanced the identification of novel miRNA genes as well as the profiling of miRNA expression levels. In this study, NGS method has been applied to two different gammaherpesviruses (γ-herpesviruses) associated models: Epstein-Barr virus (EBV)-infected nasopharyngeal carcinoma (NPC) in human and murine gammaherpesvirus 68 (MHV-68)-infected cell lines from mouse. As a result, two novel miRNA precursors from EBV and six novel miRNA precursors from MHV-68 have been successfully identified and characterized. In addition, the completion of MHV-68 miRNA set has revealed a unique viral tRNA (vtRNA)-miRNA-miRNA structure in MHV-68 genome. Furthermore, expression levels of the viral miRNAs suggest a distinct pattern during different stages of the viral life cycle. On the other hand, the profiling of cellular miRNAs also defined a number of miRNAs that have been dysregulated in EBV-positive NPC tissues compared to healthy control tissues, and in MHV-68-infected compared to non-infected NIH 3T3 murine fibroblasts. Among them, miR-15 and miR-16 were upregulated upon EBV or MHV-68 infection. The tumor suppressor gene BRCA1 has been revealed to be the repressed target protein of miR-15/16 in both models, implying an interesting role of miRNAs in the pathogenesis of γ-herpesviruses. Meanwhile, to facilitate the analysis of NGS data, an automated software was designed and developed. Additional information gained during the analysis processes revealed the possible mis-annotations existing in the miRNA registry database, suggesting that the definition and characterization of novel miRNA genes has to be performed with much more caution.

microRNAs (miRNAs) are small non-coding RNAs of 21-24 nt in size, which are endogenously expressed in higher eukaryotes and play important roles in processes such as tissue development and stress response and in several diseases including cancers. In mammals, miRNAs guide proteins of the Argonaute family (Ago proteins) to partially complementary sequences typically located in the 3’-untranslated regions (3’-UTRs) of specific target mRNAs, leading to translational repression or mRNA degradation. To gain further insight into the function of human miRNAs, we analyzed the protein as well as the RNA composition of miRNA-Ago protein complexes in molecular detail. To identify novel Ago-interacting proteins, we isolated Ago complexes and investigated them by mass spectrometry and co-immunoprecipitation experiments. We found that trinucleotide repeat-containing 6B (TNRC6B), Moloney leukemia virus 10 (MOV10), RNA binding motif protein 4 (RBM4) and Importin 8 (Imp8) interact with human Ago proteins. Moreover, using RNA interference and EGFP and dual luciferase reporter assays, we demonstrated that these factors are required for miRNA function, indicating that we have identified new components of the miRNA pathway. Intriguingly, depletion of Imp8 does not affect the levels of mature miRNAs or the interaction of miRNAs with Ago proteins, but is required for efficient association of Ago-miRNA complexes with their target mRNAs. Thus, Imp8 is the first factor acting at the level of target mRNA binding, establishing a novel layer of regulation for the miRNA pathway. Imp8 is an Importin-β-like protein, which has previously been implicated in nuclear import of substrate proteins. In line with these results, we demonstrated that a detectable fraction of Ago2 localizes to the nucleus of human cells. Moreover, knockdown of Imp8 by RNAi reduces the nuclear signal of Ago2, suggesting that Imp8 affects the nuclear localization of Ago2. Therefore, our data suggest that Imp8 has a dual function both in the cytoplasmic miRNA pathway and in nuclear transport of Ago proteins. To identify small RNAs, which associate with human Ago proteins, we isolated, cloned and sequenced small RNAs bound to Ago1 and Ago2 complexes. In addition to known miRNAs, we found several small RNAs, which derive from small nucleolar RNAs (snoRNAs). We therefore investigated the function of one particular small RNA, which is derived from the snoRNA ACA45 and showed that it functions like a miRNA. Interestingly, this small RNA is processed by the miRNA maturation factor Dicer, but does not require the microprocessor complex that is essential for processing of primary miRNA transcripts. Thus, we have identified a novel biogenesis pathway of a new class of small RNAs that can function like miRNAs. To experimentally identify mRNAs that are stably associated with miRNA-Ago protein complexes, we isolated and analyzed Ago1 and Ago2-bound mRNAs by cloning and sequencing and by microarray hybridization techniques. Using dual luciferase reporter assays, we demonstrated that many Ago-associated mRNAs are indeed miRNA targets. Therefore, we have developed a method allowing for the identification of miRNA target mRNAs from cell lines or tissues of interest independently of computational predictions. In a project that was independent of our studies on Ago protein complexes, we investigated structural and functional requirements for the activity of small interfering RNAs (siRNAs). siRNAs are small double-stranded RNAs of appr. 21 nt in size, which trigger the sequence-specific endonucleolytic degradation of perfectly complementary target transcripts upon binding to Ago2. However, both single strands of a siRNA duplex can potentially have unwanted “off-target effects” by repressing partially complementary target mRNAs through binding to their 3’-UTRs. We therefore developed a method to selectively inhibit the activity of the siRNA strand that is dispensable for target silencing (“passenger strand”) through chemical modification of its 5’-end. This method could be a useful tool for the design of highly specific siRNAs. Taken together, we have analyzed the composition of Ago-miRNA protein complexes by a variety of methods and identified novel protein factors of the miRNA pathway, a novel class of small RNAs as well as a panel of previously unknown miRNA target mRNAs. The techniques for the purification and the analysis of Ago complexes that were developed in this study will provide useful tools for future analyses of miRNA pathway factors, small RNAs and miRNA target mRNAs from any tissue or cell line of interest.