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- 2 weeks ago39 min
DPPA2 and DPPA4 as Chromatin Priming Factors (Melanie Eckersley-Maslin)
In this episode of the Epigenetics Podcast, we talked with Melanie Eckersley-Maslin from the Peter McCallum Cancer Center about her work on DPPA2 and DPPA4 as Chromatin Priming Factors. During her PhD in David Spector’s lab at Cold Spring Harbor Laboratory, Eckersley-Maslin studied monoallelic expression of autosomal genes. She developed an allele-specific RNA-sequencing screen to identify genes expressed differently from their two copies, then examined nuclear positioning, chromatin marks and DNA methylation. The work revealed associations between expression and chromatin state, but did not establish which changes caused the other. For her postdoctoral work in Wolf Reik’s lab in the UK, she investigated epigenetic regulation of zygotic genome activation, when an embryo begins transcribing its own genome. Using mouse embryonic stem cells that can enter a two-cell-like state, her research identified DPPA2 and DPPA4 as regulators of MERVL- and Zscan4-associated transcription. This work led her to consider how early-acting proteins may prime chromatin for later cell-fate decisions, even when their loss causes effects only much later in development. Then, Eckersley-Maslin discusses the importance of allowing researchers time to read, think and develop questions, as well as recognizing when to pause projects that are not progressing. She also describes moving from developmental biology into cancer research, bringing questions about cell identity and epigenetic regulation to a cancer-focused research environment. Her lab now studies DPPA2 and DPPA4 in cancer, including non-small-cell lung cancer. In that context, the proteins associate with chromatin domains marked by H3K4 trimethylation and H2AK119 ubiquitination, rather than the canonical bivalent combination studied in embryos. The function of these domains, including why they lack H3K27 trimethylation despite PRC2 recruitment, remains under investigation. She describes DPPA proteins as possible scaffolds that help recruit or coordinate chromatin machinery, rather than enzymes themselves. The conversation also covers sequential ChIP, which the lab refined to study the co-occurrence of histone modifications with limited cell numbers. Eckersley-Maslin notes that newer single-cell co-profiling methods may offer greater resolution. Looking ahead, her lab aims to identify other epigenetic priming factors and understand how chromatin states are established at particular genomic regions in particular cell types. References Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL. Random monoallelic gene expression increases upon embryonic stem cell differentiation. Dev Cell. 2014 Feb 24;28(4):351-65. doi: 10.1016/j.devcel.2014.01.017. PMID: 24576421; PMCID: PMC3955261. Eckersley-Maslin MA, Svensson V, Krueger C, Stubbs TM, Giehr P, Krueger F, Miragaia RJ, Kyriakopoulos C, Berrens RV, Milagre I, Walter J, Teichmann SA, Reik W. MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs. Cell Rep. 2016 Sep 27;17(1):179-192. doi: 10.1016/j.celrep.2016.08.087. PMID: 27681430; PMCID: PMC5055476. Related Episodes The Role of lncRNAs in Tumor Growth and Treatment (Sarah Diermeier) The Discovery of Genomic Imprinting (Azim Surani) Epigenetic Reprogramming During Mammalian Development (Wolf Reik) 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
- 4 weeks ago38 min
How Chromatin Marks Shape Transcription Factor Function (Luke Isbel)
In this episode we speak with Luke Isbell, Senior Research Fellow and group leader at Adelaide University and the South Australian immunoGENomics Cancer Institute. We discuss his work on transcription factors, chromatin, and how epigenetic marks on histones can influence transcription factor binding and function, with a focus on p53 and chromatin-based ways its activity can be silenced in cancer cells. We also talk about how he became interested in biology, starting from growing up in rural Australia and later being introduced to epigenetics through Professor Emma Whitelaw. He describes how that experience shaped his path through honours and PhD training, and how his interest in biology developed into a long-term focus on chromatin and gene regulation. He explains his PhD work on mouse mutagenesis screens and the transcriptional repressor WIS, which was identified in a screen for genes with epigenetic function. We discuss how that work connected WIS to regulation of clustered genes in the brain and showed the value of forward genetic screening in mice. We then turn to his postdoctoral work in Switzerland with Dirk Schübeler, where he moved toward more mechanistic and reductionist chromatin biology. He describes the value of combining wet-lab and dry-lab work, and how that approach helps connect data generation with hypothesis testing. Finally, we discuss his current lab in Adelaide, where he studies p53 cofactors, transcription factors, and how cofactors may help interpret chromatin marks in a tissue-specific way. He also reflects on the use of AI in science and on the importance of critical thinking, and closes by emphasizing the need to be kinder to people in academia. References Luke Isbel, Lexie Prokopuk, Haoyu Wu, Lucia Daxinger, Harald Oey, Alex Spurling, Adam J Lawther, Matthew W Hale, Emma Whitelaw (2016) Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse eLife 5:e15082. https://doi.org/10.7554/eLife.15082 Michael, A. K., Grand, R. S., Isbel, L., Cavadini, S., Kozicka, Z., Kempf, G., Bunker, R. D., Schenk, A. D., Graff-Meyer, A., Pathare, G. R., Weiss, J., Matsumoto, S., Burger, L., Schübeler, D., & Thomä, N. H. (2020). Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science, 368 (6498), 1460–1465. https://doi.org/10.1126/science.abb0074 Related Episodes Effects of DNA Methylation on Chromatin Structure and Transcription (Dirk Schübeler) Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret) The Impact of Sequence Variation on Transcription Factor Binding (Sven Heinz) 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
- Sep 24, 202640 min
CpG Islands, Polycomb, and the Regulation of Transcription (Rob Klose)
In this episode we speak with Rob Klose, Professor of Genetics at the University of Oxford, about how CpG islands help control gene expression and chromatin regulation during development. We discuss how his lab connected CpG islands to histone modifications and chromatin regulation. He describes how KDM2A and KDM2B were found to recognize CpG islands, how this led to the study of H3K36 methylation at promoters, and how BioCAP was developed to isolate non-methylated DNA. He also explains how this work showed that CpG islands are conserved across vertebrates. We also talk about the unexpected link between CpG islands, PRC1, and PRC2. He outlines how PRC1-dependent H2A ubiquitylation can recruit PRC2 and promote H3K27 trimethylation, and how his lab tested these pathways with ectopic tethering experiments. He further discusses what is known about H2A ubiquitylation, how it may affect access of the pre-initiation complex, and why the exact mechanism is still not fully understood. Another major theme is how CpG islands may help maintain gene expression states. We cover how SET1 at CpG islands helps prevent premature transcription termination at a subset of genes, especially those that are lowly transcribed, and how Polycomb can help lock genes in an off state. He also explains how the plus-one nucleosome and other early elongation barriers fit into this framework. Finally, we discuss the value of combining bulk genomics with live-cell imaging. He describes how single-cell approaches reveal stochastic, burst-like transcription that is hidden by ensemble measurements, and why his lab is now building synthetic systems and mathematical models to test how CpG islands, enhancers, and core promoters work together to shape transcription. References Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell. 2010 Apr 23;38(2):179-90. doi: 10.1016/j.molcel.2010.04.009. PMID: 20417597; PMCID: PMC3098377. Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LLP, Ito S, Cooper S, Kondo K, Koseki Y, Ishikura T, Long HK, Sheahan TW, Brockdorff N, Kessler BM, Koseki H, Klose RJ. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell. 2014 Jun 5;157(6):1445-1459. doi: 10.1016/j.cell.2014.05.004. Epub 2014 May 22. PMID: 24856970; PMCID: PMC4048464. Long HK, King HW, Patient RK, Odom DT, Klose RJ. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res. 2016 Aug 19;44(14):6693-706. doi: 10.1093/nar/gkw258. Epub 2016 Apr 15. PMID: 27084945; PMCID: PMC5001583. Huseyin, M.K., Klose, R.J. Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy. Nat Commun 12, 887 (2021). https://doi.org/10.1038/s41467-021-21130-6 Related Episodes Polycomb and Three-Dimensional Genome Organisation (Oliver Bell) Polycomb Proteins, Gene Regulation, and Genome Organization in Drosophila (Giacomo Cavalli) CpG Islands, DNA Methylation, and Disease (Sir Adrian Bird) Contact Epigenetics Podcast on Mastodon Epigenetics Podcast on Bluesky Dr. Stefan Dillinger on LinkedIn Active Motif on LinkedIn Active Motif on Bluesky Email: podcast@activem
- Sep 10, 202646 min
Epigenetics of the Cannabinoid System (Onder Albayram)
In this episode of the Epigenetics Podcast, we talked with Onder Albayram from the Medical University of South Carolina about the role of the endocannabinoid system in brain aging and neuroprotection. A major part of the conversation focuses on the endocannabinoid system. We talk about CB1 receptors, the endogenous ligands anandamide and 2-AG, and the enzymes involved in making and breaking them down. Dr. Albayram explains that this signaling system is widespread in the brain and is important for neuroimmune regulation and neuronal communication. We then cover his aging studies in the hippocampus. He reports that endocannabinoid tone declines with age, with reduced 2-AG and related biosynthetic machinery in old hippocampus, without a compensatory increase in receptor expression. He also describes experiments showing that deleting CB1 receptors improves learning in young animals but impairs performance in old animals. Another key topic is low-dose THC treatment in old mice. He reports that prolonged low-dose THC improved learning and memory in old animals, while reducing performance in young animals. After washout, the older animals still showed improved behavior, along with changes in synaptic proteins and gene expression patterns that shifted toward a younger profile. We also discuss the epigenetic findings. He says THC increased histone acetylation at promoters of anti-aging genes such as BDNF and Klotho after treatment had ended, suggesting longer-lasting regulation. He is now focusing on GABAergic neurons in the hippocampus to identify the specific epigenetic mechanisms involved and how they may relate to age-dependent neurodegenerative disorders. References Albayram, O., Alferink, J., Pitsch, J., Piyanova, A., Neitzert, K., Poppensieker, K., Mauer, D., Michel, K., Legler, A., Becker, A., Monory, K., Lutz, B., Zimmer, A., & Bilkei-Gorzo, A. (2011). Role of CB1 cannabinoid receptors on GABAergic neurons in brain aging. Proceedings of the National Academy of Sciences of the United States of America, 108(27), 11256–11261. https://doi.org/10.1073/pnas.1016442108 Related Episodes Long-Term Maintenance of Neuronal Identity (Tomohisa Toda) The Role of Histone Dopaminylation and Serotinylation in Neuronal Plasticity (Ian Maze) How BRD4 and H2BE Influence Neuronal Activity (Erica Korb) 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
- Aug 27, 202645 min
Chromatin State Reprogramming in Cancer Progression (Kunal Rai)
In this episode of the Epigenetics Podcast, we talked with Kunal Rai from MD Anderson Cancer Center about his work on chromatin state reprogramming in cancer progression. A major part of the conversation covers his postdoctoral work on active DNA demethylation. He describes how he identified an AID-MBD4-based mechanism, later supported by GAD45, and how this work showed a role for DNA demethylation in early neuronal differentiation and in colon cancer initiation. We then discuss his move into his own lab and his work on melanoma progression. He explains how he used broad epigenomic profiling, chromatin state analysis, and 3D chromatin methods to study enhancers and chromatin organization, and how these approaches helped reveal changes linked to cancer progression. Another topic is his work on epigenetic regulators such as RNF2 and KMT2D. He describes findings on polycomb and trithorax-related factors, including tumor-suppressive roles for KMT2D in melanoma and lung cancer, and how KMT2D loss affects cell phenotype and metabolism. Finally, we talk about lab organization, collaboration, and newer technologies. He says his group works across multiple cancer types and increasingly includes immunology, single-cell methods, spatial epigenomics, and clinical translation, while still using ChIP-seq, CUT&RUN, and CUT&Tag where appropriate. References Fiziev, P., Akdemir, K. C., Miller, J. P., Keung, E. Z., Samant, N. S., Sharma, S., Natale, C. A., Terranova, C. J., Maitituoheti, M., Amin, S. B., Martinez-Ledesma, E., Dhamdhere, M., Axelrad, J. B., Shah, A., Cheng, C. S., Mahadeshwar, H., Seth, S., Barton, M. C., Protopopov, A., Tsai, K. Y., … Rai, K. (2017). Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell reports, 19(4), 875–889. https://doi.org/10.1016/j.celrep.2017.03.078 Terranova, C. J., Tang, M., Maitituoheti, M., Raman, A. T., Ghosh, A. K., Schulz, J., Amin, S. B., Orouji, E., Tomczak, K., Sarkar, S., Oba, J., Creasy, C., Wu, C. J., Khan, S., Lazcano, R., Wani, K., Singh, A., Barrodia, P., Zhao, D., Chen, K., … Rai, K. (2021). Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell reports, 36(3), 109410. https://doi.org/10.1016/j.celrep.2021.109410 Related Episodes Epigenetic Signatures During Aging and Cancer (Alena van Bömmel) Epigenetic Mechanisms in Breast Cancer (Luca Magnani) The Effect of Histone Demethylases on Gene Expression and Cancer Cell Stability (Johnathan Whetstine) 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
- Aug 13, 202654 min
Statistical Physics Approaches to DNA Methylation and Aging (Steffen Rulands)
In this episode of the Epigenetics Podcast, we talked with Steffen Rulands from the Ludwig Maximilian University of Munich about how methods from statistical physics can be used to study collective phenomena in biology. We discuss his path from physics into stem cell biology and epigenetics, and how this background shapes the questions he asks in his work. We talk about his lab’s focus on quantitative and mechanistic modeling rather than wet lab experiments. He explains that he uses single-cell genomics and other datasets to understand how cells make decisions, with interests ranging from development and regeneration to aging and rejuvenation. A major topic is DNA methylation during embryonic development. We discuss how he and his collaborators found surprisingly simple, self-similar patterns in methylation over time and along the genome, and how they explained these patterns with a feedback loop between chromatin conformation and methylation deposition. We also cover his collaboration on social insect colonies, where he examines how DNA methylation and gene regulation help explain stable social roles and flexibility when the queen is removed. In that system, interactions across the whole nest shape the regulation of queen- and worker-associated genes. Later in the conversation, we turn to aging. We discuss his recent work on temporal hierarchies in epigenetic aging and on collective dynamics of DNA methylation, where we ask how molecular-scale events can combine to produce the long timescale of organismal aging. We close by talking about rejuvenation, general principles in aging, and the role of physics in identifying what is generic versus what is specifically regulated in biology. References Rulands, S., Lee, H. J., Clark, S. J., Angermueller, C., Smallwood, S. A., Krueger, F., Mohammed, H., Dean, W., Nichols, J., Rugg-Gunn, P., Kelsey, G., Stegle, O., Simons, B. D., & Reik, W. (2018). Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency. Cell systems, 7(1), 63–76.e12. https://doi.org/10.1016/j.cels.2018.06.012 Olmeda, F., Lohoff, T., Kafetzopoulos, I. et al. Scaling and self-similarity in the formation of the embryonic epigenome. Nat. Phys. 22, 931–940 (2026). https://doi.org/10.1038/s41567-026-03263-x Related Episodes Biophysical Modeling of 3-D Genome Organization (Leonid Mirny) The Interplay of Nutrition, Metabolic Pathways, and Epigenetic Regulation (Ferdinand von Meyenn) Epigenetic Reprogramming During Mammalian Development (Wolf Reik) 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
- Jul 30, 202644 min
From GAL4 to targeted DAM-ID: Tools for Studying Gene Expression In Vivo (Andrea Brand)
In this episode, we speak with Andrea Brand, Chair of the Department of Cell Biology at NYU Grossman School of Medicine and Director of the Regenerative Medicine Institute. We discuss her scientific path from yeast gene regulation to Drosophila neurobiology, and how early interests in DNA and microscopy shaped her career. We talk about the development of the GAL4 system with Norbert Perrimon and how it enabled targeted gene expression in specific tissues and cells. Andrea explains why this approach has remained useful across decades, including its applications in Drosophila and beyond, while noting that no experimental system is perfect and results should be cross-checked with other methods. We also discuss targeted DAM-ID and chromatin DAM-ID, methods developed in her lab to study protein-DNA interactions and chromatin marks in vivo without removing cells from their normal tissue environment. Andrea describes how these tools helped her lab analyze neural stem cells in their niche and investigate changes in chromatin during quiescence and reactivation. A major theme of the conversation is neural stem cell quiescence. We cover how her lab found that quiescent stem cells can show unexpectedly open chromatin, express neuronal genes, and adopt neuron-like features, including long projections and interactions with neurons. We also discuss the link to metabolism, including feeding signals, the fat body, blood-brain barrier glia, insulin-like peptides, and TGF-beta signaling. Finally, we talk about Andrea’s recent move toward human brain organoids and the goal of connecting model organism work to human biology and patient data. We discuss ongoing work on quiescent cells, TRIB family genes, and cancer–neuron interactions, as well as the need to better distinguish quiescence from senescence in vivo. References Brand, A. H., & Perrimon, N. (1993). Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development (Cambridge, England), 118(2), 401–415. https://doi.org/10.1242/dev.118.2.401 Southall, T. D., Gold, K. S., Egger, B., Davidson, C. M., Caygill, E. E., Marshall, O. J., & Brand, A. H. (2013). Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Developmental cell, 26(1), 101–112. https://doi.org/10.1016/j.devcel.2013.05.020 Tang, J. L. Y., Hakes, A. E., Krautz, R., Suzuki, T., Contreras, E. G., Fox, P. M., & Brand, A. H. (2022). NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system. Developmental cell, 57(9), 1193–1207.e7. https://doi.org/10.1016/j.devcel.2022.04.008 Cheetham, S. W., & Brand, A. H. (2018). RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nature structural & molecular biology, 25(1), 109–114. https://doi.org/10.1038/s41594-017-0006-4 Cheetham, S. W., Gruhn, W. H., van den Ameele, J., Krautz, R., Southall, T. D., Kobayashi, T., Surani, M. A., & Brand, A. H. (2018). Targeted DamID reveals differential binding of mammalian pluripotency factors. Development (Cambridge, England), 145(20), dev170209. https://doi.org/10.1242/dev.170209 Related Episodes scDamID, EpiDamID and Lamina Associated Domains (Jop Kind) Characterizing Chromatin at the Nuclear Lamina (Bas van Steensel) 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
- Jul 16, 202652 min
Antibodies, Automation, and the Fight for Reproducibility (Alon Goren)
In this episode we speak with Alon Goren from UC San Diego about his work at the intersection of genomic technology development and chromatin biology. We discuss how his lab studies how the epigenome is regulated, how disruption of that regulation contributes to disease, and how technology can be improved to make results more robust and reproducible. We talk about his early interest in biology, how that developed through medical research training, and how a molecular biology lab shaped the direction of his career. He explains how curiosity about how cells and organisms work led him toward genomics and chromatin research. We then discuss several methods from his career, including early direct sequencing approaches for small amounts of DNA and RNA, ChIP-based methods for chromatin regulators, and work on improving ChIP-seq workflows. He explains why antibody choice matters, why monoclonal antibodies can improve reproducibility, and how automation helped scale the process. We also cover his work on spike-in normalization, including the risks of using exogenous chromatin incorrectly and the need for better safeguards in genome-wide comparisons. He describes a newer approach that uses two spike-ins to provide multiple checks on normalization. Finally, we discuss his work on short tandem repeats, zebrafish heart regeneration, and SIRT6-related polymerase pausing, as well as a newer platform that converts molecular interactions into sequencing-readable barcodes. He closes by stressing the importance of validation, careful protocol design, and methods that can be used reliably by multiple people. References Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., Durham, T., Zhang, X., Donaghey, J., Epstein, C. B., Regev, A., & Bernstein, B. E. (2011). Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell, 147(7), 1628–1639. https://doi.org/10.1016/j.cell.2011.09.057 Busby, M., Xue, C., Li, C., Farjoun, Y., Gienger, E., Yofe, I., Gladden, A., Epstein, C. B., Cornett, E. M., Rothbart, S. B., Nusbaum, C., & Goren, A. (2016). Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq. Epigenetics & chromatin, 9, 49. https://doi.org/10.1186/s13072-016-0100-6 Patel, L. A., Cao, Y., Mendenhall, E. M., Benner, C., & Goren, A. (2024). The Wild West of spike-in normalization. Nature biotechnology, 42(9), 1343–1349. https://doi.org/10.1038/s41587-024-02377-y Ben-Yair, R., Butty, V. L., Busby, M., Qiu, Y., Levine, S. S., Goren, A., Boyer, L. A., Burns, C. G., & Burns, C. E. (2019). H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration. Development (Cambridge, England), 146(19), dev178632. https://doi.org/10.1242/dev.178632 Related Episodes Taking ChIP from Yeast to ENCODE to Enable Genome-Wide Regulatory Protein Mapping (Peggy Farnham) Comparing CUT&Tag to ENCODE ChIP-Seq in Alzheimer's Disease Samples (Sarah Marzi) Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff) 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
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