Epigenetics Podcast

DNase Hypersensitive Sites and Chromatin Remodeling Enzymes (Carl Wu)

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
 
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Epigenetic Mechanisms of Mammalian Germ Cell Development (Mitinori Saitou)

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
 
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Malaria Chromatin Structure and its Transcriptional Regulation (Karine Le Roch)

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
 
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Epigenetics in Human Malaria Parasites (Elena Gómez-Diaz)
 
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Characterizing Chromatin at the Nuclear Lamina (Bas van Steensel)

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
 
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Nucleosome Positioning in Cancer Diagnostics (Vladimir Teif)

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
 
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The Effect of Histone Demethylases on Gene Expression and Cancer Cell Stability (Johnathan Whetstine)

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
 
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Stem Cell Transcriptional Regulation in Naive vs. Primed Pluripotency (Christa Buecker)

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
 
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Gene Expression Control and Intricacies of X-chromosome Inactivation (Claire Rougeulle)

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
 
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