Epigenetics Podcast

In this episode of the Epigenetics Podcast, we talked with Giacomo Cavalli from the Institute of Human Genetics in Montpellier about his work on critical aspects of epigenetic regulation, particularly the role of Polycomb proteins and chromatin architecture. We start the Interview by talking about Dr. Cavalli's work on Polycomb function in maintaining chromatin states and how it relates to gene regulation. He shares insights from his early lab experiences, where he aimed to understand the inheritance mechanisms of chromatin states through various models, including the FAB7 cellular memory module. The discussion uncovers how Polycomb proteins can silence gene expression and the complex interplay between different epigenetic factors that govern this process. Dr. Cavalli also addresses how he has investigated the recruitment mechanisms of Polycomb complexes, highlighting the roles of several DNA-binding proteins, including DSP-1 and GAGA factor, in this intricate regulatory landscape. He emphasizes the evolution of our understanding of Polycomb recruitment, illustrating the multifactorial nature of this biological puzzle. As the conversation progresses, we explore Dr. Cavalli's fascinating research into the three-dimensional organization of the genome. He explains his contributions to mapping chromosomal interactions within Drosophila and the distinctions observed when performing similar studies in mammalian systems. Key findings regarding topologically associated domains (TADs) and their association with gene expression are presented, alongside the implications for our understanding of gene regulation in development and disease.   References Déjardin, J., Rappailles, A., Cuvier, O., Grimaud, C., Decoville, M., Locker, D., & Cavalli, G. (2005). Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1. Nature, 434(7032), 533–538. https://doi.org/10.1038/nature03386 Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012). Three-dimensional folding and functional organization principles of the Drosophila genome. Cell, 148(3), 458–472. https://doi.org/10.1016/j.cell.2012.01.010 Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J. P., Tanay, A., & Cavalli, G. (2017). Multiscale 3D Genome Rewiring during Mouse Neural Development. Cell, 171(3), 557–572.e24. https://doi.org/10.1016/j.cell.2017.09.043 Szabo, Q., Donjon, A., Jerković, I., Papadopoulos, G. L., Cheutin, T., Bonev, B., Nora, E. P., Bruneau, B. G., Bantignies, F., & Cavalli, G. (2020). Regulation of single-cell genome organization into TADs and chromatin nanodomains. Nature genetics, 52(11), 1151–1157. https://doi.org/10.1038/s41588-020-00716-8   Related Episodes BET Proteins and Their Role in Chromosome Folding and Compartmentalization (Kyle Eagen) Long-Range Transcriptional Control by 3D Chromosome Structure (Luca Giorgetti) Epigenetic Landscapes During Cancer (Luciano Di Croce)   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 Ferdinand von Meyenn from ETH Zürich about his work on the interplay of nutrition, metabolic pathways, and epigenetic regulation. To start Dr. Meyenn recounts his pivotal research on DNA methylation in naive embryonic stem cells during his time with Wolf Reick. He explains the dynamics of global demethylation in naive stem cells, revealing the key enzymes involved and the unexpected findings surrounding UHF1—its role in maintaining DNA methylation levels and influencing the methylation landscape during early embryonic development. Dr. Meyenn then shares his perspective on the scientific transition to establishing his own lab at ETH. He reflects on his ambitions to merge the fields of metabolism and epigenetics, which is a recurring theme throughout his research. By investigating the interplay between metabolic changes and epigenetic regulation, he aims to uncover how environmental factors affect cellular dynamics across various tissues. This leads to a discussion of his recent findings on histone lactylation and its implications in cellular metabolism, as well as the intricacies of epigenetic imprinting in stem cell biology. Last but not least we touch upon Dr. Meyenn’s most recent study, published in Nature, investigating the epigenetic effects of obesity. He provides a detailed overview of how adipose tissue undergoes transcriptional and epigenetic rearrangements during weight fluctuations. The conversation highlights the notion of epigenetic memory in adipocytes, showing how obesity is not just a temporary state but leaves lasting cellular changes that can predispose individuals to future weight regain after dieting. This exploration opens avenues for potential therapeutic interventions aimed at reversing adverse epigenetic modifications.   References von Meyenn, F., Iurlaro, M., Habibi, E., Liu, N. Q., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., Kroeze, L. I., Nesterova, T. B., Jansen, J. H., Xie, H., He, C., Reik, W., & Stunnenberg, H. G. (2016). Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Molecular cell, 62(6), 848–861. https://doi.org/10.1016/j.molcel.2016.04.025 Galle, E., Wong, C. W., Ghosh, A., Desgeorges, T., Melrose, K., Hinte, L. C., Castellano-Castillo, D., Engl, M., de Sousa, J. A., Ruiz-Ojeda, F. J., De Bock, K., Ruiz, J. R., & von Meyenn, F. (2022). H3K18 lactylation marks tissue-specific active enhancers. Genome biology, 23(1), 207. https://doi.org/10.1186/s13059-022-02775-y Agostinho de Sousa, J., Wong, C. W., Dunkel, I., Owens, T., Voigt, P., Hodgson, A., Baker, D., Schulz, E. G., Reik, W., Smith, A., Rostovskaya, M., & von Meyenn, F. (2023). Epigenetic dynamics during capacitation of naïve human pluripotent stem cells. Science advances, 9(39), eadg1936. https://doi.org/10.1126/sciadv.adg1936 Bonder, M. J., Clark, S. J., Krueger, F., Luo, S., Agostinho de Sousa, J., Hashtroud, A. M., Stubbs, T. M., Stark, A. K., Rulands, S., Stegle, O., Reik, W., & von Meyenn, F. (2024). scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood. Nature communications, 15(1), 7567. https://doi.org/10.1038/s41467-024-51833-5 Hinte, L. C., Castellano-Castillo, D., Ghosh, A., Melrose, K., Gasser, E., Noé, F., Massier, L., Dong, H., Sun, W., Hoffmann, A., Wolfrum, C., Rydén, M., Mejhert, N., Blüher, M., & von Meyenn, F. (2024). Adipose tissue retains an epigenetic memory of obesity after weight loss. Nature, 636(8042), 457–465. https://doi.org/10.1038/s41586-024-08165-7   Related Episodes Nutriepigenetics: The Effects of Diet on Behavior (Monica Dus) Epigenetic and Metabolic Regulation of Early Development (Jan Żylicz) Effects of Environmental Cues on the Epigenome and Longevity (Paul Shiels)   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 Vijay Ramani from the Gladstone Institute about his work on Single-Molecule Adenine Methylated Oligonucleosome Sequencing Assay (SAMOSA). Our discussion starts with Vijay Ramani's impactful contributions to the field during his time in Jay Shendure's lab, where he worked on several innovative methods, including RNA proximity ligation. This project was conceived during his graduate studies, aiming to adapt techniques from DNA research to investigate RNA structures—a largely unexplored area at the time. We delved into the nuances of his experiences in graduate school, emphasizing how critical it was to have mentors who provided room for creativity and autonomy in experimental design. Dr. Ramani then shares insights about his foray into developing more refined methodologies, such as in-situ DNA Hi-C, a revolutionary protocol tailored for three-dimensional genomic mapping. He explained the rationale behind his projects, comparing the outcomes with contemporaneous advancements in methods like Micro-C. The discussion highlighted the importance of understanding enzyme bias in chromatin studies and the need for meticulous experimental design to ensure the validity of biological interpretations. We further explored exciting advancements in single-cell genomics, specifically Ramani's work on developing sci-Hi-C. This innovative technique leverages combinatorial indexing to allow high-resolution mapping of chromatin architecture at the single-cell level, a significant leap forward in understanding the complexities of gene regulation. As we progress, Ramani detailed his transition from graduate student to independent investigator starting his own lab. He elaborated on the challenges and excitements associated with establishing his research focus in chromatin structure and function using advanced sequencing technologies. Employing various strategies, including the innovative SAMOSA assay, his research seeks to elucidate the mechanisms by which chromatin structure influences transcriptional regulation. We also discussed the heterogeneity of chromatin and its implications for gene expression. Ramani provided a fascinating perspective on how variations in chromatin structure could affect gene activity, highlighting potential avenues for future research that aims to untangle the complex dynamics at play in both healthy and diseased states.   References Ramani, V., Cusanovich, D., Hause, R. et al. Mapping 3D genome architecture through in situ DNase Hi-C. Nat Protoc 11, 2104–2121 (2016). https://doi.org/10.1038/nprot.2016.126 Nour J Abdulhay, Colin P McNally, Laura J Hsieh, Sivakanthan Kasinathan, Aidan Keith, Laurel S Estes, Mehran Karimzadeh, Jason G Underwood, Hani Goodarzi, Geeta J Narlikar, Vijay Ramani (2020) Massively multiplex single-molecule oligonucleosome footprinting eLife 9:e59404. https://doi.org/10.7554/eLife.59404 Abdulhay, N.J., Hsieh, L.J., McNally, C.P. et al. Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. Nat Struct Mol Biol 30, 1571–1581 (2023). https://doi.org/10.1038/s41594-023-01093-6 Nanda, A.S., Wu, K., Irkliyenko, I. et al. Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. Nat Genet 56, 1300–1309 (2024). https://doi.org/10.1038/s41588-024-01748-0   Related Episodes Epigenetic Mechanisms in Genome Regulation and Developmental Programming (James Hackett) Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff) Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman)   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 Maxim Greenberg from the Institute Jacob Monot about his work on epigenetic consequences of DNA methylation in development. In this interview we explore how Dr. Greenberg’s work at UCLA involved pioneering experiments on DNA methylation mechanisms and how this period was marked by significant collaborative efforts within a highly competitive yet supportive lab environment that ultimately lead to publications in high impact journals. His transition to a postdoctoral position at the Institut Curie with Deborah Bourc'his harnessed his expertise in mammalian systems, examining chromatin changes and the implications for embryonic development. Dr. Greenberg explained the nuances of his research, particularly how chromatin modifications during early development can influence gene regulatory mechanisms later in life, providing a compelling narrative about the potential long-term impacts of epigenetic changes that occur in utero. Throughout our conversation, we examined the intricate relationship between DNA methylation and Polycomb repression, discussing how these epigenetic mechanisms interact and the functional outcomes of their regulation. Dr. Greenberg's insights into his recent studies reveal a commitment to unraveling the complexities of enhancer-promoter interactions in the context of epigenetic regulation.   References Greenberg, M. V., Ausin, I., Chan, S. W., Cokus, S. J., Cuperus, J. T., Feng, S., Law, J. A., Chu, C., Pellegrini, M., Carrington, J. C., & Jacobsen, S. E. (2011). Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics, 6(3), 344–354. https://doi.org/10.4161/epi.6.3.14242 Greenberg, M. V., Glaser, J., Borsos, M., Marjou, F. E., Walter, M., Teissandier, A., & Bourc'his, D. (2017). Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. Nature genetics, 49(1), 110–118. https://doi.org/10.1038/ng.3718 Greenberg, M., Teissandier, A., Walter, M., Noordermeer, D., & Bourc'his, D. (2019). Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency. eLife, 8, e44057. https://doi.org/10.7554/eLife.44057 Monteagudo-Sánchez, A., Richard Albert, J., Scarpa, M., Noordermeer, D., & Greenberg, M. V. C. (2024). The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation. Nucleic acids research, 52(18), 10934–10950. https://doi.org/10.1093/nar/gkae724 Richard Albert, J., Urli, T., Monteagudo-Sánchez, A., Le Breton, A., Sultanova, A., David, A., Scarpa, M., Schulz, M., & Greenberg, M. V. C. (2024). DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency. Nature structural & molecular biology, 10.1038/s41594-024-01405-4. Advance online publication. https://doi.org/10.1038/s41594-024-01405-4   Related Episodes DNA Methylation and Mammalian Development (Déborah Bourc'his) Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon) Epigenetic Mechanisms in Genome Regulation and Developmental Programming (James Hackett)   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 Natalia Gromak from the University of Oxford about her work on R-Loop biology in health and disease. In this interview Dr. Gromak delves into her significant research on transcription and RNA biology, particularly focusing on the molecular mechanisms involved at transcriptional pause sites. She describes her early work in understanding transcription termination and how her team investigated the role of specific RNA and DNA structures, including R-loops, that could influence polymerase progression. This exploration into R-loops—complexes formed by RNA and DNA interactions—was a key turning point in her research, as she and her colleagues identified their regulatory functions within the human genome. Discussion transitions into her findings regarding the implications of R-loops in diseases like Friedrich's ataxia and Fragile X syndrome. Dr. Gromak then elucidates how the pathological expansion of repeat sequences in these conditions interferes with normal gene expression, and how R-loops exacerbate transcriptional silencing. Throughout her reflection on these discoveries, she emphasizes the importance of studying R-loops beyond merely being a transcriptional byproduct, but as players in gene regulation and potential contributors to disease pathology. The episode also covers her innovative work in characterizing the R-loop interactome through various experimental techniques. She highlights the complexity of R-loop dynamics, including the discovery of protein factors that interact with R-loops and could influence their stability and regulatory functions. Furthermore, she discusses the exciting intersection of RNA modifications, such as m6A, which plays a role in R-loop regulation and presents new avenues for research, particularly pertaining to how disease-specific modifications might alter R-loop behavior.   References Cristini, A., Groh, M., Kristiansen, M. S., & Gromak, N. (2018). RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage. Cell reports, 23(6), 1891–1905. https://doi.org/10.1016/j.celrep.2018.04.025 Abakir, A., Giles, T. C., Cristini, A., Foster, J. M., Dai, N., Starczak, M., Rubio-Roldan, A., Li, M., Eleftheriou, M., Crutchley, J., Flatt, L., Young, L., Gaffney, D. J., Denning, C., Dalhus, B., Emes, R. D., Gackowski, D., Corrêa, I. R., Jr, Garcia-Perez, J. L., Klungland, A., … Ruzov, A. (2020). N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nature genetics, 52(1), 48–55. https://doi.org/10.1038/s41588-019-0549-x   Related Episodes DNA Replication, Transcription and R-loops (Stephan Hamperl)   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 Yadira Soto-Feliciano from MIT about her work on the Menin-MLL complex and the effect of small molecules on its stability in leukemia. We explore the pivotal moments that led her to cancer biology during her graduate studies, where her work included ground-breaking research on the role of the plant homeodomain Finger protein-6 (PHF-6) in leukemia. This work bridged the realms of chromatin accessibility, transcription factors, and cancer cell lineage, providing critical evidence for the concept of lineage plasticity in cancer biology—a topic that has gained significant traction in recent years. Dr. Soto-Feliciano discusses how advances in techniques like CRISPR and ChIP-sequencing have shaped her research, enabling deeper insights into the mechanisms underlying cancer cell identity. As our discussion transitions, Dr. Soto-Feliciano shares her experience in David Allis's lab, illustrating how the collaboration across diverse scientific disciplines enhanced her understanding of chromatin biology and generated significant insights into the mechanics of epigenetic regulation. Highlighting a recent 2023 publication, we unpack her findings related to the conserved molecular switch between MLL1 and MLL3 complexes. These discoveries revealed how the application of small-molecule inhibitors of the menin-MLL interaction can alter gene expression and affect leukemia cells’ responses to treatments. We also touch on the operational dynamics within her lab at MIT, established during challenging times marked by the pandemic. Yadira is dedicated to fostering a collaborative and respectful environment among her team, comprised of PhD candidates and research technicians, all sharing a commitment to unraveling the complexities of chromatin regulation. She emphasizes the significance of understanding chromatin scaffold proteins and their role in regulating gene expression and genome organization.   References Soto-Feliciano, Y. M., Bartlebaugh, J. M. E., Liu, Y., Sánchez-Rivera, F. J., Bhutkar, A., Weintraub, A. S., Buenrostro, J. D., Cheng, C. S., Regev, A., Jacks, T. E., Young, R. A., & Hemann, M. T. (2017). PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes & development, 31(10), 973–989. https://doi.org/10.1101/gad.295857.117 Soto-Feliciano, Y. M., Sánchez-Rivera, F. J., Perner, F., Barrows, D. W., Kastenhuber, E. R., Ho, Y. J., Carroll, T., Xiong, Y., Anand, D., Soshnev, A. A., Gates, L., Beytagh, M. C., Cheon, D., Gu, S., Liu, X. S., Krivtsov, A. V., Meneses, M., de Stanchina, E., Stone, R. M., Armstrong, S. A., … Allis, C. D. (2023). A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin-MLL Inhibition. Cancer discovery, 13(1), 146–169. https://doi.org/10.1158/2159-8290.CD-22-0416 Zhu, C., Soto-Feliciano, Y. M., Morris, J. P., Huang, C. H., Koche, R. P., Ho, Y. J., Banito, A., Chen, C. W., Shroff, A., Tian, S., Livshits, G., Chen, C. C., Fennell, M., Armstrong, S. A., Allis, C. D., Tschaharganeh, D. F., & Lowe, S. W. (2023). MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer. eLife, 12, e80854. https://doi.org/10.7554/eLife.80854   Related Episodes MLL Proteins in Mixed-Lineage Leukemia (Yali Dou) Targeting COMPASS to Cure Childhood Leukemia (Ali Shilatifard)   Contact Epigenetics Podcast on Instagram 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 Mary Anne Jelinek Associate Director of R&D at Active Motif about writing and reviewing grants in academia and industry. Learn from Dr. Jelinek’s years of experience writing and reviewing grants and get her best advice and insight for success. Hear about similarities and differences in preparing grants in academia vs. biotech or other industry settings. Key insights include: Finding Grant opportunities that exist for different sectors and countries, from the familiar ones like NIH and NSF in the United States grant funding offered by NATO for member countries.  Learn about grants targeted to small businesses and specific allocation of resources intended to foster and promote innovation and entrepreneurship and how to navigate confidentiality when writing grants in industry, being mindful of conflict of interest and best practices.  Coming up with ideas is easy – but how do you find institutes interested in funding those research areas? Get tips on how to submit a 1-page inquiry for feedback and guidance at early stages that will help your grant be robust and successful.  Think you can go from idea to funding in 4 weeks? She has and discusses the best strategy to do this - collaboration is key and you’ll learn why. Get tips on wording and writing for reviewers who may not be experts in your field and how to “paint a picture” that makes it both clear and persuasive, including your writing style and use of diagrams and figures for those complex concepts. Hear all of Dr. Jelinek’s “best advice” and encouragement for dealing with stress and frustration that can be part of the process.  Finally, as a co-developer for the first commercially available ChIP Kit, Dr. Jelinek tells the story of how this assay developed and became a gold-standard method for epigenetics. Tune in to this in depth and very helpful episode!   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 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

In this episode of the Epigenetics Podcast, we talked with Mitinori Saitou from Kyoto University about his work on germ cell development, focusing on proteins like BLIMP1 and PRDM14, reprogramming iPSCs, and his vision to address infertility and genetic disorders through epigenetic insights. To start our discussion, Dr. Saitou shares the foundation of his research, which centers on the mechanisms of germ cell development across various species, including mice, non-human primates, and humans. He provides insight into his early work examining the roles of two key proteins: BLIMP1 and PRDM14. These proteins are essential for germline specification in mammals, and their functions are unveiled through detailed exploration of knockout models. In particular, Dr. Saitou elucidates the critical events in germ cell specification, highlighting how disruptions to the functions of these proteins lead to significant impairments in development. As the conversation deepens, we discuss Dr. Saitou’s groundbreaking advances in human-induced pluripotent stem cells (iPSCs). He elaborates on the processes involved in reprogramming these cells to form primordial germ cell-like cells, emphasizing the significance of understanding various cellular contexts and transcriptional regulation. Dr. Saitou then details how overexpression of certain factors in embryonic stem cells can induce these germline characteristics, presenting the promise of innovation in regenerative medicine and reproductive biology. We end our talk with the exploration of chromatin remodeling that occurs during germ cell development, including fascinating details about DNA and histone modification dynamics. Dr. Saitou articulates how the epigenetic landscape shifts during the transition from pluripotent states to germ cell specification, providing a detailed comparison between mouse and human systems. This highlights the complexity of gene regulation and the importance of specific epigenetic markers in establishing and maintaining cellular identity.   References Yamaji, M., Seki, Y., Kurimoto, K. et al. Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat Genet 40, 1016–1022 (2008). https://doi.org/10.1038/ng.186 Katsuhiko Hayashi et al., Offspring from Oocytes Derived from in Vitro Primordial Germ Cell–like Cells in Mice. Science 338, 971-975 (2012). DOI: 10.1126/science.1226889 Nakaki, F., Hayashi, K., Ohta, H. et al. Induction of mouse germ-cell fate by transcription factors in vitro. Nature 501, 222–226 (2013). https://doi.org/10.1038/nature12417 Nakamura, T., Okamoto, I., Sasaki, K. et al. A developmental coordinate of pluripotency among mice, monkeys and humans. Nature 537, 57–62 (2016). https://doi.org/10.1038/nature19096 Murase, Y., Yokogawa, R., Yabuta, Y. et al. In vitro reconstitution of epigenetic reprogramming in the human germ line. Nature 631, 170–178 (2024). https://doi.org/10.1038/s41586-024-07526-6   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 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

In this episode of the Epigenetics Podcast, we caught up with Vladimir Teif from the University of Essex to talk about his work on nucleosome positioning in development and disease. Vladimir's research has been pivotal in understanding nucleosome positioning and its implications for cell differentiation, particularly in embryonic stem cells and cancer. We discuss his groundbreaking studies that first mapped nucleosome positions in various cell types and how these findings led to uncovering the intricate relationships between nucleosome stability, transcription factors, and DNA modifications such as methylation. This understanding has immense significance for cancer diagnostics, where knowing the spatial arrangement of nucleosomes could influence how aggressive a cancer type might be, or how a patient might respond to treatment. Transitioning from foundational research to clinical applications, Vladimir elaborates on his exciting work with liquid biopsies. By analyzing cell-free DNA from blood plasma, researchers can infer the nucleosome positioning and, ultimately, the presence of cancer without the need for invasive tissue biopsies. We explore how this new approach holds potential for earlier detection of cancers and more effective patient stratification, demonstrating a profound shift in how we leverage epigenetic data in clinical settings.   References Vladimir B. Teif, Karsten Rippe, Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities, Nucleic Acids Research, Volume 37, Issue 17, 1 September 2009, Pages 5641–5655, https://doi.org/10.1093/nar/gkp610 Teif, V., Vainshtein, Y., Caudron-Herger, M. et al. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol 19, 1185–1192 (2012). https://doi.org/10.1038/nsmb.2419 Beshnova DA, Cherstvy AG, Vainshtein Y, Teif VB (2014) Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions. PLoS Comput Biol 10(7): e1003698. https://doi.org/10.1371/journal.pcbi.1003698 Shtumpf, M., Piroeva, K.V., Agrawal, S.P. et al. NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA. Chromosoma 131, 19–28 (2022). https://doi.org/10.1007/s00412-021-00766-9   Related Episodes Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon) Epigenome-based Precision Medicine (Eleni Tomazou)   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 Johnathan Whetstine from Fox Chase Cancer Center about his work on how histone demethylases affect gene expression and cancer cell stability. The Interview start by discussing a pivotal paper from Jonathan's lab in 2010, where they identified a role for the KDM4A histone demethylase in replication timing and cell cycle progression. They elaborate on the discoveries made regarding the link between histone marks, replication timing, and gene expression control. Jonathan explains the impact of microRNAs on regulating KDM4A and how protein turnover rates can influence cellular responses to treatments like mTOR inhibitors. Further, they explore the causal relationship between histone marks and replication timing, demonstrating how alterations in epigenetic regulation can affect genome stability. Jonathan shares insights from his latest research on H3K9 methylation balance at the MLL-KM2A locus, elucidating how these epigenetic modifications regulate amplifications and rearrangements in cancer cells. The episode concludes with a discussion on the establishment of the Cancer Epigenetics Institute at Fox Chase Cancer Center, aiming to bridge academia and industry to accelerate translational research in cancer epigenetics.   References Black, J. C., Allen, A., Van Rechem, C., Forbes, E., Longworth, M., Tschöp, K., Rinehart, C., Quiton, J., Walsh, R., Smallwood, A., Dyson, N. J., & Whetstine, J. R. (2010). Conserved antagonism between JMJD2A/KDM4A and HP1γ during cell cycle progression. Molecular cell, 40(5), 736–748. https://doi.org/10.1016/j.molcel.2010.11.008 Mishra, S., Van Rechem, C., Pal, S., Clarke, T. L., Chakraborty, D., Mahan, S. D., Black, J. C., Murphy, S. E., Lawrence, M. S., Daniels, D. L., & Whetstine, J. R. (2018). Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell, 174(4), 803–817.e16. https://doi.org/10.1016/j.cell.2018.06.018 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 Gray, Z. H., Chakraborty, D., Duttweiler, R. R., Alekbaeva, G. D., Murphy, S. E., Chetal, K., Ji, F., Ferman, B. I., Honer, M. A., Wang, Z., Myers, C., Sun, R., Kaniskan, H. Ü., Toma, M. M., Bondarenko, E. A., Santoro, J. N., Miranda, C., Dillingham, M. E., Tang, R., Gozani, O., … Whetstine, J. R. (2023). Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell, 186(21), 4528–4545.e18. https://doi.org/10.1016/j.cell.2023.09.009   Related Episodes The Impact of Chromatin Modifiers on Disease Development and Progression (Capucine van Rechem)   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 Christa Buecker from the Max Perutz Laboratories in Vienna about her work on transcriptional regulation during early embryonic development. Dr. Buecker unravels the differences between naive and primed pluripotency states, showcasing how OCT4 relocalization and enhancer chromatin landscapes play pivotal roles during this transition. The conversation delves into the intricate interplay of transcription factors like OCT4 and OTX2, shedding light on their collaborative efforts in regulating gene expression during differentiation. Dr. Buecker then shares insights from her study on enhancer elements controlling FGF5 expression and discusses the surprising revelation that individual enhancers show no intrinsic activity but work together in a super additive fashion. She also touches upon her research on IRF1's connection to the gene regulatory network and its role in protecting cells against viral infections. The conversation shifts to Dr. Buecker's current research endeavors, focusing on exploring the strength of enhancers and their impact on gene expression at different distances from promoters. She shares her vision for future experiments and the integration of enhancers to decipher their impact on transcription regulation.   References Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., Simeone, A., Tan, M., Swigut, T., & Wysocka, J. (2014). Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell stem cell, 14(6), 838–853. https://doi.org/10.1016/j.stem.2014.04.003 Thomas, H. F., Kotova, E., Jayaram, S., Pilz, A., Romeike, M., Lackner, A., Penz, T., Bock, C., Leeb, M., Halbritter, F., Wysocka, J., & Buecker, C. (2021). Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Molecular cell, 81(5), 969–982.e13. https://doi.org/10.1016/j.molcel.2020.12.047 Romeike, M., Spach, S., Huber, M., Feng, S., Vainorius, G., Elling, U., Versteeg, G. A., & Buecker, C. (2022). Transient upregulation of IRF1 during exit from naive pluripotency confers viral protection. EMBO reports, 23(9), e55375. https://doi.org/10.15252/embr.202255375   Related Episodes Enhancer Communities in Adipocyte Differentiation (Susanne Mandrup) Enhancer-Promoter Interactions During Development (Yad Ghavi-Helm) Enhancers and Chromatin Remodeling in Mammary Gland Development (Camila dos Santos) Ultraconserved Enhancers and Enhancer Redundancy (Diane Dickel)   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 Claire Rougeulle from the Epigenetics and Cell Fate Center at Université Paris City about her work on gene expression control, the intricacies of X-chromosome inactivation, and the potential of non-coding RNAs in this process. In this episode Claire Rougeulle explains her discoveries regarding the transcription regulation of XIST by factors like YY1 and the erosion of X-chromosome inactivation in human pluripotent stem cells. She shares the complexity of distinguishing between epigenetics and transcriptional regulation, highlighting the challenges in studying allelic expression of X-chromosomes at the single-cell level. The Episode further explores Claire's findings on the XACT locus regulation, evolution from retroviruses, and its potential role in preventing X-chromosome silencing. Claire also shares her future research focus on understanding X-inactivation establishment in humans and the transition from XIST attenuating to silencing X-chromosomes after implantation.   References Makhlouf, M., Ouimette, J. F., Oldfield, A., Navarro, P., Neuillet, D., & Rougeulle, C. (2014). A prominent and conserved role for YY1 in Xist transcriptional activation. Nature communications, 5, 4878. https://doi.org/10.1038/ncomms5878 Vallot, C., Ouimette, J. F., Makhlouf, M., Féraud, O., Pontis, J., Côme, J., Martinat, C., Bennaceur-Griscelli, A., Lalande, M., & Rougeulle, C. (2015). Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape. Cell stem cell, 16(5), 533–546. https://doi.org/10.1016/j.stem.2015.03.016 Casanova, M., Moscatelli, M., Chauvière, L. É., Huret, C., Samson, J., Liyakat Ali, T. M., Rosspopoff, O., & Rougeulle, C. (2019). A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans. Nature communications, 10(1), 5652. https://doi.org/10.1038/s41467-019-13551-1   Related Episodes Epigenetics and X-Inactivation (Edith Heard) Investigating the Dynamics of Epigenetic Plasticity in Cancer with Single Cell Technologies (Céline Vallot)   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 James Hackett from the EMBL in Rome about his work on epigenetic mechanisms in genome regulation and developmental programming. One of James Hackett's significant studies focused on DNA methylation and genome defense mechanisms in the germline, exploring the role of chromatin modifications in mammalian gene regulation. He delves into investigating the erasure of DNA methylation in the germline, highlighting the key role of the TET-enzymes in demethylation processes. Dr. Hackett shares insights from his research on pluripotent stem cells, where he mapped genome-wide DNA methylation and hydroxymethylation in different pluripotent states. He discusses the impact of extrinsic conditions on pluripotent states and the biases observed in lineage preferences. Furthermore, the discussion delves into the development of a CRISPR screening tool to study cell fate transitions, particularly focusing on the genetic factors contributing to germline specification. He also talks about his work on epigenetic inheritance, highlighting the importance of precise perturbations in understanding chromatin modifications and their functional implications. In a recent study, the Hackett lab focuses on systematic epigenome editing to investigate the context-dependent functions of chromatin modifications. We hear about this work, and the complexity of interactions between chromatin marks, DNA sequences, and transcription factors, shedding light on the nuanced effects of various chromatin modifications on gene expression.   References Hackett JA, Reddington JP, Nestor CE, et al. Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline. Development (Cambridge, England). 2012 Oct;139(19):3623-3632. DOI: 10.1242/dev.081661. PMID: 22949617; PMCID: PMC3436114. Hackett JA, Sengupta R, Zylicz JJ, et al. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science (New York, N.Y.). 2013 Jan;339(6118):448-452. DOI: 10.1126/science.1229277. PMID: 23223451; PMCID: PMC3847602. Hackett JA, Kobayashi T, Dietmann S, Surani MA. Activation of Lineage Regulators and Transposable Elements across a Pluripotent Spectrum. Stem Cell Reports. 2017 Jun;8(6):1645-1658. DOI: 10.1016/j.stemcr.2017.05.014. PMID: 28591649; PMCID: PMC5470235. Hackett JA, Huang Y, Günesdogan U, et al. Tracing the transitions from pluripotency to germ cell fate with CRISPR screening. Nature Communications. 2018 Oct;9(1):4292. DOI: 10.1038/s41467-018-06230-0. PMID: 30327475; PMCID: PMC6191455.   Related Episodes Epigenetic and Metabolic Regulation of Early Development (Jan Żylicz) H3K79 Methylation, DOT1L, and FOXG1 in Neural Development (Tanja Vogel) The Impact of Chromatin Modifiers on Disease Development and Progression (Capucine van Rechem)     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 Lothar Schermelleh from the University of Oxford about his work on advanced optical imaging in 3D nuclear organisation.  The interview starts by Lothar Schermelleh sharing his groundbreaking work in understanding chromatin organization using super-resolution microscopy techniques. He then delves into his past experiments, including his publication on imaging chromatin domains and X chromosome inactivation. His work showcases the power of structured illumination microscopy in overcoming diffraction limits, revealing insights into nuclear organization and regulation. Lothar also discusses refining methods for labeling chromosome territories and replication domains, as well as exploring structural and functional nuclear organization using advanced microscopy techniques. They touch on the potential of AI in microscopy, the importance of quality control in imaging, and Lothar's grant proposal for developing artifact-free, super-resolution imaging under cryo conditions with adaptive optics. The conversation emphasizes the intersection of technology development and biological applications, highlighting the importance of addressing specific biological questions through innovative imaging approaches.    References Schermelleh, L., Carlton, P. M., Haase, S., Shao, L., Winoto, L., Kner, P., Burke, B., Cardoso, M. C., Agard, D. A., Gustafsson, M. G., Leonhardt, H., & Sedat, J. W. (2008). Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science (New York, N.Y.), 320(5881), 1332–1336. https://doi.org/10.1126/science.1156947 Schermelleh, L., Heintzmann, R., & Leonhardt, H. (2010). A guide to super-resolution fluorescence microscopy. The Journal of cell biology, 190(2), 165–175. https://doi.org/10.1083/jcb.201002018 Smeets, D., Markaki, Y., Schmid, V. J., Kraus, F., Tattermusch, A., Cerase, A., Sterr, M., Fiedler, S., Demmerle, J., Popken, J., Leonhardt, H., Brockdorff, N., Cremer, T., Schermelleh, L., & Cremer, M. (2014). Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci. Epigenetics & chromatin, 7, 8. https://doi.org/10.1186/1756-8935-7-8 Ball, G., Demmerle, J., Kaufmann, R., Davis, I., Dobbie, I. M., & Schermelleh, L. (2015). SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy. Scientific reports, 5, 15915. https://doi.org/10.1038/srep15915   Related Episodes Long-Range Transcriptional Control by 3D Chromosome Structure (Luca Giorgetti) Analysis of 3D Chromatin Structure Using Super-Resolution Imaging (Alistair Boettiger)   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 Dr. Stephan Hamperl from the Helmholtz Zentrum Munich about his work on how conflicts between transcription, replication, and R-loop formation influence genome stability in human cells. During the early stages of his career Stephan studied conflicts between transcription and replication in human cells, particularly focusing on R-loop structures. In our discussion, he explains the formation of R-loops and their impact on genome stability, emphasizing the importance of the orientation of replication forks approaching R-loops in determining DNA damage outcomes. Stephan then delves into his work on the MATAC-Seq method, which analyzes chromatin domains at DNA replication origins to understand replication timing variability. The method involves methylating DNA linkers between nucleosomes and using nanopore sequencing for single-molecule readouts, revealing heterogeneity in chromatin structure at replication origins. Finally, Stephan discusses his automated image analysis pipeline for quantifying transcription and replication activity overlap in mammalian genomes, addressing the challenge of visualizing these processes simultaneously. The conversation concludes with insights into Stefan's future research directions, focusing on understanding transcription-replication conflicts' molecular basis and their potential implications in cancer cell transformation. References Hamperl, S., Brown, C. R., Garea, A. V., Perez-Fernandez, J., Bruckmann, A., Huber, K., Wittner, M., Babl, V., Stoeckl, U., Deutzmann, R., Boeger, H., Tschochner, H., Milkereit, P., & Griesenbeck, J. (2014). Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic acids research, 42(1), e2. https://doi.org/10.1093/nar/gkt891 Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T., & Cimprich, K. A. (2017). Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. Cell, 170(4), 774–786.e19. https://doi.org/10.1016/j.cell.2017.07.043 Chanou, A., Weiβ, M., Holler, K., Sajid, A., Straub, T., Krietsch, J., Sanchi, A., Ummethum, H., Lee, C. S. K., Kruse, E., Trauner, M., Werner, M., Lalonde, M., Lopes, M., Scialdone, A., & Hamperl, S. (2023). Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency. Nucleic acids research, 51(22), 12303–12324. https://doi.org/10.1093/nar/gkad1022   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 Nadav Ahituv from University of California, San Francisco about his work on mutations of gene regulatory elements in human disease. Using massively parallel experiments, his lab revolutionized functional genomics by studying the impact of transcription factor binding sites on gene expression. His groundbreaking technology deciphered the regulatory language of gene expression by exploring transcription factor combinations, spacing, and orientation. By delving into the influence of DNA shape and gene topology, Nadav Ahituv's research provides a comprehensive understanding of gene regulation at the molecular level, shedding light on the complexity of genetic interactions. The conversation delves into specific cases involving enhancers, gene sequencing, and 3D genomic structure, highlighting the impact of critical elements such as CTCF sites on gene expression. Discussions of haploid insufficiency and its implications for human health, using CRISPR technology to enhance gene expression, offer new possibilities for treating genetic diseases. Explorations of leptin-responsive regulatory elements in the hypothalamus and liver-associated transcription factors provide insights into metabolic regulation and gene expression networks in different tissues. The episode also explores the epigenomic landscape, the evolution of methods from bulk approaches to single-cell analyses, and the role of AI and machine learning in deciphering complex genetic patterns. The conversation transitions to a unique study of bat embryonic development, dietary differences, and their implications for understanding wing development and metabolism in different bat species.   References Ahituv, N., Zhu, Y., Visel, A., Holt, A., Afzal, V., Pennacchio, L. A., & Rubin, E. M. (2007). Deletion of ultraconserved elements yields viable mice. PLoS biology, 5(9), e234. https://doi.org/10.1371/journal.pbio.0050234 Matharu, N., Rattanasopha, S., Tamura, S., Maliskova, L., Wang, Y., Bernard, A., Hardin, A., Eckalbar, W. L., Vaisse, C., & Ahituv, N. (2019). CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency. Science (New York, N.Y.), 363(6424), eaau0629. https://doi.org/10.1126/science.aau0629 Ushiki, A., Zhang, Y., Xiong, C., Zhao, J., Georgakopoulos-Soares, I., Kane, L., Jamieson, K., Bamshad, M. J., Nickerson, D. A., University of Washington Center for Mendelian Genomics, Shen, Y., Lettice, L. A., Silveira-Lucas, E. L., Petit, F., & Ahituv, N. (2021). Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia. Nature communications, 12(1), 2282. https://doi.org/10.1038/s41467-021-22470-z Georgakopoulos-Soares, I., Deng, C., Agarwal, V., Chan, C. S. Y., Zhao, J., Inoue, F., & Ahituv, N. (2023). Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nature communications, 14(1), 2333. https://doi.org/10.1038/s41467-023-37960-5 Gordon, W. E., Baek, S., Nguyen, H. P., Kuo, Y. M., Bradley, R., Fong, S. L., Kim, N., Galazyuk, A., Lee, I., Ingala, M. R., Simmons, N. B., Schountz, T., Cooper, L. N., Georgakopoulos-Soares, I., Hemberg, M., & Ahituv, N. (2024). Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nature communications, 15(1), 12. https://doi.org/10.1038/s41467-023-44186-y   Related Episodes Ultraconserved Enhancers and Enhancer Redundancy (Diane Dickel) Enhancers and Chromatin Remodeling in Mammary Gland Development (Camila dos Santos) Enhancer-Promoter Interactions During Development (Yad Ghavi-Helm)   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 Ana Cvejic from the Biotech Research & Innovation Centre at the University of Copenhagen about her work on using sc-multiomics to characterise human developmental hematopoiesis. The conversation starts by delving into Ana's research on hematopoiesis, starting with her work on identifying novel genes controlling blood traits in zebrafish models. She explains her transition to single-cell methodologies and the application of single-cell RNA sequencing to study hematopoietic cells in zebrafish, focusing on thrombocyte lineage commitment and gene expression. The discussion progresses to her groundbreaking study on human fetal hematopoiesis, where she combined single-cell RNA-seq with single-cell ATAC-seq to understand chromatin accessibility and gene expression dynamics. Ana then shares insights into the identification of new cell surface markers and the priming of hematopoietic stem cells, particularly in conditions like Down syndrome. Furthermore, she then elaborates on the construction of a phylogenetic tree of blood development using whole-genome sequencing of single-cell-derived hematopoietic colonies from healthy human fetuses. She explains the motivation behind this study, highlighting the insights gained regarding stem cell quantities, developmental timelines, and mutations in blood development. References Bielczyk-Maczyńska, E., Serbanovic-Canic, J., Ferreira, L., Soranzo, N., Stemple, D. L., Ouwehand, W. H., & Cvejic, A. (2014). A loss of function screen of identified genome-wide association study Loci reveals new genes controlling hematopoiesis. PLoS genetics, 10(7), e1004450. https://doi.org/10.1371/journal.pgen.1004450 Athanasiadis, E. I., Botthof, J. G., Andres, H., Ferreira, L., Lio, P., & Cvejic, A. (2017). Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis. Nature communications, 8(1), 2045. https://doi.org/10.1038/s41467-017-02305-6 Ranzoni, A. M., Tangherloni, A., Berest, I., Riva, S. G., Myers, B., Strzelecka, P. M., Xu, J., Panada, E., Mohorianu, I., Zaugg, J. B., & Cvejic, A. (2021). Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell stem cell, 28(3), 472–487.e7. https://doi.org/10.1016/j.stem.2020.11.015   Related Episodes Single Cell Epigenomics in Neuronal Development (Tim Petros) ATAC-Seq, scATAC-Seq and Chromatin Dynamics in Single-Cells (Jason Buenrostro) Single-Cell Technologies using Microfluidics (Ben Hindson)   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