Taking ChIP from Yeast to ENCODE to Enable Genome-Wide Regulatory Protein Mapping (Peggy Farnham)

In this episode of the Epigenetics Podcast, we talked with Peggy Farnham from the Keck School of Medicine at USC about her work on establishing the ChIP Method in mammalian cells. In this episode, we dive into the relationship between transcription factors, chromatin dynamics, and gene expression with Professor Peggy Farnham from the Keck School of Medicine at USC. Professor Farnham shares her profound insights into how her groundbreaking research has reshaped our understanding of gene regulation and its implications in cancer. We explore how she has been a pioneer in mapping the genome-wide landscape of regulatory proteins, illuminating the molecular logic behind transcriptional control and its disruption in cancer biology. The interview starts with her instrumental role in adapting chromatin immunoprecipitation (ChIP) technology from yeast to human cells. Professor Farnham reflects on the technical challenges she faced during this transition, such as the quest for visibility of signals in mammalian systems. Her ability to innovate and troubleshoot challenges led to significant advancements in techniques that allow for the rapid identification of transcription factor binding sites, fundamentally changing the landscape of epigenetic research. As the discussion progresses, we learn about Professor Farnham's active involvement in the ENCODE project, where she contributed to high-resolution mapping of transcription factors and regulatory elements in human cells. She articulates her appreciation for collaborative efforts in science, highlighting how working within a consortium harnesses the collective expertise of diverse research groups. This collaboration not only bolstered the credibility of the data produced but also propelled the field forward in understanding the complexity of gene regulation. Through her participation in various projects, such as the Psyc-ENCODE consortium and the Roadmap Epigenome Mapping Consortium, Professor Farnham shares insights into her investigation of epigenetic variations, particularly in relation to complex disorders like schizophrenia. Her findings underscore the nuances of enhancer variability among individuals and the implications for understanding disease mechanisms, thereby advancing our knowledge of genetic regulation and its contributions to diverse biological outcomes. Moreover, the episode highlights Professor Farnham's reflective understanding of emerging technologies in the field. She discusses the evolution of methods that allow researchers to investigate gene regulation at single-cell resolution, recognizing the significant implications these innovations have for our comprehension of cellular differentiation and the transcriptional landscape. References Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Molecular and Cellular Biology. 2001 Oct;21(20):6820-6832. DOI: 10.1128/mcb.21.20.6820-6832.2001. PMID: 11564866; PMCID: PMC99859. Wells J, Farnham PJ. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods (San Diego, Calif.). 2002 Jan;26(1):48-56. DOI: 10.1016/s1046-2023(02)00007-5. PMID: 12054904. Rhie SK, Schreiner S, Witt H, et al. Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Science Advances. 2018 Dec;4(12):eaav8550. DOI: 10.1126/sciadv.aav8550. PMID: 30555922; PMCID: PMC6292713. Tak YG, Hung Y, Yao L, et al. Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Nucleic Acids Research. 2016 May;44(9):4123-4133. DOI: 10.1093/nar/gkv1530. PMID: 26743005; PMCID: PMC4872074. Related Episodes The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn) CpG Islands, DNA Methylation, and Disease (Sir Adrian Bird) The Future of Protein–DNA Mapping (Mitch Guttman) MLL Proteins in Mixed-Lineage Leukemia (Yali Dou) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Will Wang from Sanford Burnham Prebys about his work on muscle stem cell repair, regeneration, and aging, exploring spatial-omics and machine learning. We begin our conversation by exploring the traditional concepts of spatial biology and how they have evolved to play a critical role in disease research. Dr. Wang recounts his journey from a young student in a family of academics to becoming a leading figure in regenerative biology, highlighting how his early interests in life sciences, natural problem-solving abilities, and inspirations from mentorship set the stage for his current research trajectory. Throughout the discussion, we uncover key insights on how muscle stem cells transition from a quiescent state to a proliferative state in response to injury and how this dynamic process is governed by the epigenetic landscape and various signalling pathways. Dr. Wang emphasises the impact of external factors—be it microenvironment conditions or metabolic cues—on the fate and function of these stem cells, reflecting on the methodologies used to investigate these processes throughout his career. He shares fascinating findings from his PhD work, where he explored the regulatory role of transcription factors like PAX-7 in muscle stem cell activation, and how subsequent research developed in his postdoc at Stanford further illuminated the relationship between metabolism and histone acetylation. This pivotal work not only demonstrated how metabolic states dictate epigenetic modifications but also offered potential therapeutic insights for muscle degeneration and repair. As we move into more recent projects, Dr. Wang discusses the advances in multiplexed spatial proteomics and the insights garnered from a single-cell spatiotemporal atlas of muscle regeneration, which highlight the cellular heterogeneity in muscle tissue. He describes the use of novel computational tools, including neural networks, to uncover the regulatory mechanisms underlying stem cell function, particularly how prostaglandin signalling informs the regeneration process and how age impacts stem cell efficacy. The episode then wraps up with an engaging dialogue about the future implications of Dr. Wang’s work in addressing age-related muscle degradation and broader applications in regenerative medicine. References Yucel, N., Wang, Y. X., Mai, T., Porpiglia, E., Lund, P. J., Markov, G., Garcia, B. A., Bendall, S. C., Angelo, M., & Blau, H. M. (2019). Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function. Cell Reports, 27(13), 3939-3955.e6. https://doi.org/10.1016/j.celrep.2019.05.092 Wang, Y. X., Palla, A. R., Ho, A. T. V., Robinson, D. C. L., Ravichandran, M., Markov, G. J., Mai, T., Still, C., Balsubramani, A., Nair, S., Holbrook, C. A., Yang, A. V., Kraft, P. E., Su, S., Burns, D. M., Yucel, N. D., Qi, L. S., Kundaje, A., & Blau, H. M. (2025). Multiomic profiling reveals that prostaglandin E2 reverses aged muscle stem cell dysfunction, leading to increased regeneration and strength. Cell Stem Cell, 32(7), 1154-1169.e9. https://doi.org/10.1016/j.stem.2025.05.012 Related Episodes Stem Cell Transcriptional Regulation in Naive vs. Primed Pluripotency (Christa Buecker) The Effect of Mechanotransduction on Chromatin Structure and Transcription in Stem Cells (Sara Wickström) Epigenetic Regulation of Stem Cell Self-Renewal and Differentiation (Peggy Goodell) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Will Wang from Sanford Burnham Prebys about his work on muscle stem cell repair, regeneration, and aging, exploring spatial-omics and machine learning. We begin our conversation by exploring the traditional concepts of spatial biology and how they have evolved to play a critical role in disease research. Dr. Wang recounts his journey from a young student in a family of academics to becoming a leading figure in regenerative biology, highlighting how his early interests in life sciences, natural problem-solving abilities, and inspirations from mentorship set the stage for his current research trajectory. Throughout the discussion, we uncover key insights on how muscle stem cells transition from a quiescent state to a proliferative state in response to injury and how this dynamic process is governed by the epigenetic landscape and various signalling pathways. Dr. Wang emphasises the impact of external factors—be it microenvironment conditions or metabolic cues—on the fate and function of these stem cells, reflecting on the methodologies used to investigate these processes throughout his career. He shares fascinating findings from his PhD work, where he explored the regulatory role of transcription factors like PAC-7 in muscle stem cell activation, and how subsequent research developed in his postdoc at Stanford further illuminated the relationship between metabolism and histone acetylation. This pivotal work not only demonstrated how metabolic states dictate epigenetic modifications but also offered potential therapeutic insights for muscle degeneration and repair. As we move into more recent projects, Dr. Wang discusses the advances in multiplexed spatial proteomics and the insights garnered from a single-cell spatiotemporal atlas of muscle regeneration, which highlight the cellular heterogeneity in muscle tissue. He describes the use of novel computational tools, including neural networks, to uncover the regulatory mechanisms underlying stem cell function, particularly how prostaglandin signalling informs the regeneration process and how age impacts stem cell efficacy. The episode then wraps up with an engaging dialogue about the future implications of Dr. Wang’s work in addressing age-related muscle degradation and broader applications in regenerative medicine. References Yucel, N., Wang, Y. X., Mai, T., Porpiglia, E., Lund, P. J., Markov, G., Garcia, B. A., Bendall, S. C., Angelo, M., & Blau, H. M. (2019). Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function. Cell Reports, 27(13), 3939-3955.e6. https://doi.org/10.1016/j.celrep.2019.05.092 Wang, Y. X., Palla, A. R., Ho, A. T. V., Robinson, D. C. L., Ravichandran, M., Markov, G. J., Mai, T., Still, C., Balsubramani, A., Nair, S., Holbrook, C. A., Yang, A. V., Kraft, P. E., Su, S., Burns, D. M., Yucel, N. D., Qi, L. S., Kundaje, A., & Blau, H. M. (2025). Multiomic profiling reveals that prostaglandin E2 reverses aged muscle stem cell dysfunction, leading to increased regeneration and strength. Cell Stem Cell, 32(7), 1154-1169.e9. https://doi.org/10.1016/j.stem.2025.05.012 Related Episodes Stem Cell Transcriptional Regulation in Naive vs. Primed Pluripotency (Christa Buecker) The Effect of Mechanotransduction on Chromatin Structure and Transcription in Stem Cells (Sara Wickström) Epigenetic Regulation of Stem Cell Self-Renewal and Differentiation (Peggy Goodell) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Mitch Guttman from Caltec about ChIP-DIP (ChIP-Done In Parallel). ChIP-DIP is a newly developed approach for high-resolution protein–DNA interaction mapping. The method uses antibody-guided isolation of denaturant-insoluble protein–DNA complexes, resulting in substantially improved specificity and peak definition compared with conventional ChIP-seq. We explore why denaturation resistance is central to the workflow, how the method performs across transcription factors, chromatin regulators, and histone marks, and what experimental parameters determine its success. The conversation also covers current limitations, practical adoption details, and perspectives on how ChIP-DIP fits into the broader landscape of chromatin profiling technologies. References Perez, A. A., Goronzy, I. N., Blanco, M. R., Yeh, B. T., Guo, J. K., Lopes, C. S., Ettlin, O., Burr, A., & Guttman, M. (2024). ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements. Nature genetics, 56(12), 2827–2841. https://doi.org/10.1038/s41588-024-02000-5 Ramani, V. Split-pool barcoding serves up an epigenomic smorgasbord. Nat Genet 56, 2596–2597 (2024). https://doi.org/10.1038/s41588-024-01980-8 Related Episodes Split-Pool Recognition of Interactions by Tag Extension (SPRITE) (Mitch Guttman) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Fides Zenk from the École polytechnique fédérale de Lausanne about her work on transgenerational inheritance in Drosophila and brain organoids for human development insights. Dr. Zenk begins by sharing her journey into the field of biology, revealing her childhood fascination with nature and the intricate details of plant development. Her transition from an interest in ecology to a deep dive into molecular biology and gene regulation lays the groundwork for understanding her current research focus. We explore how her early experiences continue to shape her scientific curiosity, particularly her passion for studying cellular changes over time during embryonic development. As the conversation progresses, Dr. Zenk paints a vivid picture of her work at EPFL, where she combines functional genomics, chromatin profiling, and molecular biology techniques. She elaborates on her initial research during her PhD with Nicola Iovino, where she investigated the transgenerational inheritance of histone modifications in Drosophila. This discussion includes fascinating insights into how histone modifications can carry information across generations and their implications in gene expression regulation during early embryonic stages. Dr. Zenk also provides a glimpse into her postdoctoral work with Barbara Treutlein, where she shifted focus to human models and quantitative analysis using brain organoids. This segment of the episode reveals her commitment to translating molecular mechanisms to human health, especially in understanding the intricacies of brain development and neurogenesis. She describes how her team mapped dynamic changes in histone modifications during critical developmental stages, integrating various data modalities to build an intricate developmental atlas.   References Zenk F, Loeser E, Schiavo R, et al. Germ line-inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. Science (New York, N.Y.). 2017 Jul;357(6347):212-216. DOI: 10.1126/science.aam5339. PMID: 28706074. Zenk F, Zhan Y, Kos P, et al. HP1 drives de novo 3D genome reorganization in early Drosophila embryos. Nature. 2021 May;593(7858):289-293. DOI: 10.1038/s41586-021-03460-z. PMID: 33854237; PMCID: PMC8116211. Zenk F, Fleck JS, Jansen SMJ, et al. Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems. Nature Neuroscience. 2024 Jul;27(7):1376-1386. DOI: 10.1038/s41593-024-01652-0. PMID: 38914828; PMCID: PMC11239525. Related Episodes The Role of Small RNAs in Transgenerational Inheritance in C. elegans (Oded Rechavi) Mapping the Epigenome: From Arabidopsis to the Human Brain (Joseph Ecker) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Anders Sejr Hansen from MIT about his work on the impact of 3D genome structures on gene expression, the roles of proteins like CTCF and cohesin, and advanced techniques like Region Capture Micro-C for mapping genome organisation. Dr. Sejr Hansen introduces his research focusing on the relationship between three-dimensional genome structure and function, specifically how these structures can influence gene expression. He elaborates on the importance of transcription factors and the role of looping structures in gene regulation, emphasizing the implications of his work for understanding gene functionality in the context of both development and disease. The conversation then shifts to discussing loop extrusion and the factors affecting loop stability, primarily CTCF and cohesin. Dr. Sejr Hansen highlights the dynamics of these proteins' binding interactions and how their speeds challenge the notion of stable looping structures in the genome. With a keen interest in CTCF's role, he explains how the protein interacts with DNA and the mechanistic aspects of transcription factor movement, alluding to research findings that reveal that CTCF and cohesin tend to form clusters which may play vital roles in establishing chromatin structure. As the interview progresses, Dr. Sejr Hansen details his transition to leading his own lab at MIT, emphasizing the continuation of his earlier work while expanding into new methodologies for studying chromatin. He underscores the importance of understanding not just the static structures of DNA interactions, but the dynamic nature of these relationships and how they influence gene expression. His lab's recent focus has included using advanced imaging techniques to assess the dynamics of chromatin interactions more precisely. The discussion then touches on specific findings from Dr. Sejr Hansen's lab regarding the relationship between genome organization and double-strand break repair mechanisms. He emphasizes how the repair machinery can affect chromatin structure and underscores the essential role of cohesin in facilitating effective double-strand break repair by keeping broken DNA ends in proximity. He suggests that loop extrusion might help prevent genetic material from diffusing too far apart and improve the efficiency of repair. Dr. Sejr Hansen also discusses innovations in genome mapping techniques, particularly the development of Region Capture Micro-C, which facilitates deeper insights into the three-dimensional organization of the genome. This method allows researchers to achieve significantly higher resolution in their analyses compared to traditional 3D genomics techniques like Hi-C. He outlines the technical process and the implications of their findings, especially regarding enhancer-promoter interactions and the surprisingly promiscuous nature of these relationships. References Anders S Hansen, Iryna Pustova, Claudia Cattoglio, Robert Tjian, Xavier Darzacq (2017) CTCF and cohesin regulate chromatin loop stability with distinct dynamics eLife 6:e25776 https://doi.org/10.7554/eLife.25776 Claudia Cattoglio, Iryna Pustova, Nike Walther, Jaclyn J Ho, Merle Hantsche-Grininger, Carla J Inouye, M Julius Hossain, Gina M Dailey, Jan Ellenberg, Xavier Darzacq, Robert Tjian, Anders S Hansen (2019) Determining cellular CTCF and cohesin abundances to constrain 3D genome models eLife 8:e40164 https://doi.org/10.7554/eLife.40164 Goel, V.Y., Huseyin, M.K. & Hansen, A.S. Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. Nat Genet 55, 1048–1056 (2023). https://doi.org/10.1038/s41588-023-01391-1 Related Episodes Biophysical Modeling of 3-D Genome Organization (Leonid Mirny) Unraveling Mechanisms of Chromosome Formation (Job Dekker) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Vincent Pasque from KU Leuven about his work on the reprogramming of cell identity through epigenetic mechanisms, particularly during early development and cellular reprogramming. We begin by tracing Vincent's journey into biology, sparked by early childhood experiences in nature and meaningful encounters with inspiring teachers. His fascination with the complexities of biology crystallized during a pivotal moment while listening to a radio segment on epigenetics in the late '90s, which led him to pursue studies in genetics and biochemistry. This formative path brought him to leading institutions, including the prestigious lab of John Gurdon, where he explored the phenomenon of nuclear reprogramming. Vincent recounts his early experiments that led to the discovery of macro H2A as a barrier to reprogramming, emphasizing the core challenge of erasing somatic cell identity. As the conversation unfolds, Vincent introduces us to critical findings from his research. He shares how the inactive X chromosome serves as a compelling model to investigate epigenetic regulation, revealing that the dynamics of reprogramming and differentiation are far from simple reversals of development. He highlights the significant differences between male and female iPSCs and how X-linked genes influence DNA methylation and differentiation rates in these cells. The implications of these findings extend beyond developmental biology to inform our understanding of diseases, particularly cancer. Transitioning to his current work, Vincent describes pioneering advances in characterizing the chromatin-associated proteome during the differentiation of human pluripotent stem cells. The surprising discovery of elevated histone modifications in naïve cells leads to intriguing questions about the barriers to cellular plasticity and the mechanisms by which cells resist alternative fate conversions. The potential applications of this research could reshape our approach to regenerative medicine and therapeutic interventions. References Pasque V, Gillich A, Garrett N, Gurdon JB. Histone variant macroH2A confers resistance to nuclear reprogramming. The EMBO Journal. 2011 May;30(12):2373-2387. DOI: 10.1038/emboj.2011.144. PMID: 21552206; PMCID: PMC3116279. Jullien, J., Miyamoto, K., Pasque, V., Allen, G. E., Bradshaw, C. R., Garrett, N. J., Halley-Stott, R. P., Kimura, H., Ohsumi, K., & Gurdon, J. B. (2014). Hierarchical Molecular Events Driven by Oocyte-Specific Factors Lead to Rapid and Extensive Reprogramming. Molecular Cell, 55(4), 524–536. https://doi.org/10.1016/j.molcel.2014.06.024 Pasque V, Tchieu J, Karnik R, et al. X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency. Cell. 2014 Dec;159(7):1681-1697. DOI: 10.1016/j.cell.2014.11.040. PMID: 25525883; PMCID: PMC4282187. Zijlmans DW, Talon I, Verhelst S, et al. Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction. Nature Cell Biology. 2022 Jun;24(6):858-871. DOI: 10.1038/s41556-022-00932-w. PMID: 35697783; PMCID: PMC9203278. Related Episodes The Discovery of Genomic Imprinting (Azim Surani) Gene Expression Control and Intricacies of X-chromosome Inactivation (Claire Rougeulle) Epigenetics and X-Inactivation (Edith Heard) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Ryan Corces from the Gladstone Institutes about his work on the impact of chromatin architecture on Alzheimer's and Parkinson's Disease. The discussion begins in discussing he start of Dr. Corces research career and he shares his groundbreaking findings in acute myeloid leukemia (AML), demonstrating how mutations occurring in hematopoietic stem cells lead to the evolution of this disease. He emphasizes the pivotal role of epigenetic modifiers and how these insights steered his focus towards epigenetic research. As the conversation progresses, Dr. Corces covers his transition to a postdoctoral role, emphasizing his collaborative work employing the ATAC-seq technique. He details how refinements to this protocol not only improved data quality but also paved the way for more expansive research within the fields of hematology and cancer genetics. Additionally, he discusses his excitement for developing new computational tools for single-cell analysis, aiming to address the critical challenge of distinguishing between cellular states effectively. The episode also explores the fascinating intersection of Alzheimer’s and Parkinson’s diseases. Dr. Corces explains the rationale for studying both conditions simultaneously, shedding light on the shared and divergent pathological features that emerge in patients. He argues for the importance of understanding mixed pathologies, which reflect the reality for many individuals diagnosed with these neurodegenerative diseases. References Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., Kathiria, A., Cho, S. W., Mumbach, M. R., Carter, A. C., Kasowski, M., Orloff, L. A., Risca, V. I., Kundaje, A., Khavari, P. A., Montine, T. J., … Chang, H. Y. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods, 14(10), 959–962. https://doi.org/10.1038/nmeth.4396 Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., Satpathy, A. T., Mumbach, M. R., Hoadley, K. A., Robertson, A. G., Sheffield, N. C., Felau, I., Castro, M. A. A., Berman, B. P., Staudt, L. M., Zenklusen, J. C., … Chang, H. Y. (2018). The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.), 362(6413), eaav1898. https://doi.org/10.1126/science.aav1898 Corces, M. R., Trevino, A. E., Hamilton, E. G., Greenside, P. G., Sinnott-Armstrong, N. A., Vesuna, S., Satpathy, A. T., Rubin, A. J., Montine, K. S., Wu, B., Kathiria, A., Cho, S. W., Mumbach, M. R., Carter, A. C., Kasowski, M., Orloff, L. A., Risca, V. I., Kundaje, A., Khavari, P. A., Montine, T. J., … Chang, H. Y. (2017). An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature methods, 14(10), 959–962. https://doi.org/10.1038/nmeth.4396 Sant, C., Mucke, L., & Corces, M. R. (2025). CHOIR improves significance-based detection of cell types and states from single-cell data. Nature genetics, 57(5), 1309–1319. https://doi.org/10.1038/s41588-025-02148-8 Related Episodes ATAC-Seq, scATAC-Seq and Chromatin Dynamics in Single-Cells (Jason Buenrostro) Multiple challenges of ATAC-Seq, Points to Consider (Yuan Xue) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]

In this episode of the Epigenetics Podcast, we talked with Mo Motamedi from the Center for Cancer Research at Massachusetts General Hospital about his work on RNA-mediated epigenetic regulation. The Interview starts with Dr. Motamedi sharing his personal journey into the realm of biology, sparked by a familial inclination towards science and a challenge to excel in a field that initially felt daunting. His passion was ignited during a genetics class, as he recognized the quantitative nature of the discipline amidst the evolution of modern techniques like qPCR and high-throughput sequencing. Dr. Motamedi goes on to articulate the importance of understanding the interplay between genetics and broader biological systems, emphasizing that an insightful grasp of evolution is vital for decoding cellular mechanisms. He reflects on his time in a postdoctoral lab under Danesh Moazed, investigating RNA interference (RNAi) and its unexpected nuclear roles, contributing significantly to the understanding of how RNAi is involved in gene silencing via chromatin interaction. As his narrative unfolds, Dr. Motamedi provides deep insights into his own lab's work, which focuses on the establishment and maintenance of epigenetic states and their implications in cancer epigenetics. He discusses groundbreaking discoveries related to RNAi and heterochromatin, detailing experiments that unveil how specific proteins contribute to transcriptional and post-transcriptional gene silencing. A pivotal theme emerges: the complex dynamics of genome evolution and chromatin organization can be reshaped under various biological contexts, including the quiescent state of cells under stress. Moreover, the discussion traverses recent publications from Dr. Motamedi's lab, revealing how they identify long non-coding RNAs that function as silencers at centromeres, an essential mechanism that aids in the establishment of heterochromatin independently of RNAi. His findings advocate for the idea that well-structured genome organization can lead to more efficient gene regulation, which can also be crucial in therapeutic contexts for various cancers. References Motamedi, M. R., Hong, E. J., Li, X., Gerber, S., Denison, C., Gygi, S., & Moazed, D. (2008). HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms. Molecular cell, 32(6), 778–790. https://doi.org/10.1016/j.molcel.2008.10.026 Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Hoi Sui SJ, Sadreyev RI, Aryee MJ, and Motamedi M. Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by argonaute-associated small RNAs. † Mol Cell. 2016; 64: 1088-1101. J. S. Khanduja, R. I. Joh, M. M. Perez, J. A. Paulo, C. M. Palmieri, J. Zhang, A. O. D. Gulka, W. Haas, S.P. Gygi, M. Motamedi. RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly. Cell 2024. 187: 3262-3283. *Equal contributions R. I. Joh, M. S. Lawrence, M. J. Aryee, M. Motamedi. Gene clustering drives the transcriptional coherence of disparate biological pathways in eukaryotes. bioRxiv 2023. doi: 10.1101/2021.04.17.440292 *co-corresponding authors. J. S. Khanduja, M. Motamedi. Protocol for the development and use of spike-in control for chromatin immunoprecipitation (ChIP) of chromatin-binding proteins. Star Protocol 2025. 6: 104007. J. S. Khanduja, M. Motamedi. Protocol for chromatin immunoprecipitation of chromatin-binding proteins in Schizosaccharomyces pombe using a dual-crosslinking approach. Star Protocol 2025. 6: 103695. Related Episodes Evolutionary Forces Shaping Mammalian Gene Regulation (Emily Wong) Chromatin Evolution (Arnau Sebé-Pedrós) The Role of lncRNAs in Tumor Growth and Treatment (Sarah Diermeier) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]  

In this episode of the Epigenetics Podcast, we talked with Emily Wong from the University of New South Wales in Sydney about her work on how evolution shapes mammalian genes. As the head of the Regulatory Systems Lab at the Victor Chang Cardiac Research Institute and an associate professor at UNSW, Emily’s research centers on gene control and enhancers. We delve into her pivotal 2017 publication in Nature Communications, where she investigated transcription factor binding in liver-specific contexts, shedding light on the regulatory mechanisms at play in mammals. Emily elaborates on her postdoctoral work at the European Bioinformatics Institute and the innovative hybrid systems she used to dissect genetic variation effects, which allowed her to differentiate between cis-regulatory and trans-regulatory influences. By employing techniques like ChIP-seq, she was able to illustrate the combinatorial effects of transcription factors on gene expression, paving the way for her collaborative efforts across disciplines and organisms. We also examine Emily's findings regarding enhancer function through comparative studies between zebrafish and marine sponges. Using historical data on conserved genetic sequences, she and her team identified enhancer regions that displayed activity in specific vertebrate cell types, despite their evolutionary divergence from sponges. This unexpected result suggests deeper insights into how enhancers can be co-opted for new functions as species evolve. Furthermore, we dive into Emily's latest ventures involving advanced methodologies such as chromatin accessibility profiling with ATAC-seq and how these insights can elucidate the genomic landscape of metazoan embryogenesis. She highlights significant correlations between enhancer turnover and DNA replication timing, suggesting evolutionary implications that should be taken into account in future genomic studies.   References Wong, E. S., Zheng, D., Tan, S. Z., Bower, N. I., Garside, V., Vanwalleghem, G., Gaiti, F., Scott, E., Hogan, B. M., Kikuchi, K., McGlinn, E., Francois, M., & Degnan, B. M. (2020). Deep conservation of the enhancer regulatory code in animals. Science, 370(6517), eaax8137. https://doi.org/10.1126/science.aax8137 Cornejo-Páramo, P., Petrova, V., Zhang, X. et al. Emergence of enhancers at late DNA replicating regions. Nat Commun 15, 3451 (2024). https://doi.org/10.1038/s41467-024-47391-5   Related Episodes Ultraconserved Enhancers and Enhancer Redundancy (Diane Dickel) Enhancer Communities in Adipocyte Differentiation (Susanne Mandrup) Enhancer-Promoter Interactions During Development (Yad Ghavi-Helm)   Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: [email protected]