Episodes
Episodes
Thursday Jul 11, 2024
Thursday Jul 11, 2024
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)
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Thursday Jun 27, 2024
Advanced Optical Imaging in 3D Nuclear Organisation (Lothar Schermelleh)
Thursday Jun 27, 2024
Thursday Jun 27, 2024
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)
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Thursday Jun 13, 2024
DNA Replication, Transcription and R-loops (Stephan Hamperl)
Thursday Jun 13, 2024
Thursday Jun 13, 2024
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
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Thursday May 30, 2024
Mutations of Gene Regulatory Elements in Human Disease (Nadav Ahituv)
Thursday May 30, 2024
Thursday May 30, 2024
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)
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Thursday May 16, 2024
Thursday May 16, 2024
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)
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Thursday May 02, 2024
The Impact of Sequence Variation on Transcription Factor Binding (Sven Heinz)
Thursday May 02, 2024
Thursday May 02, 2024
In this episode of the Epigenetics Podcast, we talked with Sven Heinz from the University of California in San Diego about his work on the impact of sequence variation on transcription factor binding affinities and genetic diversity.
Sven Heinz talks about a landmark study published in Nature that examined the impact of sequence variation on transcription factor binding affinities and downstream effects on gene expression. Modifying genetic sequences to understand the influence of different motifs provided valuable insights into how genetic variation shapes cellular responses and gene expression patterns, underscoring the importance of genetic diversity.
Methodological approaches using inducible systems to observe changes in transcription factor binding patterns highlight the critical role of motif variation and redundancy in transcription factor families. These studies provide essential insights into the complex network of transcriptional regulation and chromatin dynamics, revealing the nuanced mechanisms that control gene expression and chromatin organization. In addition, he is investigating how small nucleotide changes can significantly affect transcription factor binding in macrophages from different mouse strains, shedding light on the intricate effects of genetic variation on transcription factor binding.
Sven's career path from project scientist to assistant professor at UC San Diego and the Salk Institute reflects a journey marked by serendipitous opportunities and a collaborative, innovative research environment. The podcast delves into the effects of influenza virus infection on chromosomal territories, gene transcription, and chromatin structure, unraveling the sophisticated interplay between viral infection and host cell transcriptional regulation.
References
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular cell, 38(4), 576–589. https://doi.org/10.1016/j.molcel.2010.05.004
Heinz, S., Romanoski, C. E., Benner, C., Allison, K. A., Kaikkonen, M. U., Orozco, L. D., & Glass, C. K. (2013). Effect of natural genetic variation on enhancer selection and function. Nature, 503(7477), 487–492. https://doi.org/10.1038/nature12615
Texari, L., Spann, N. J., Troutman, T. D., Sakai, M., Seidman, J. S., & Heinz, S. (2021). An optimized protocol for rapid, sensitive and robust on-bead ChIP-seq from primary cells. STAR protocols, 2(1), 100358. https://doi.org/10.1016/j.xpro.2021.100358
Related Episodes
Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret)
Multiple Challenges in ChIP (Adam Blattler)
The Role of Pioneer Factors Zelda and Grainyhead at the Maternal-to-Zygotic Transition (Melissa Harrison)
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Thursday Apr 18, 2024
Comparing CUT&Tag to ENCODE ChIP-Seq in Alzheimer's Disease Samples (Sarah Marzi)
Thursday Apr 18, 2024
Thursday Apr 18, 2024
In this episode of the Epigenetics Podcast, we talked with Sarah Marzi from the UK Dementia Research Institute at Imperial College London about her work on epigenetic changes in Alzheimer's Disease, and comparing CUT&Tag to ENCODE ChIP-Seq using limited cell samples.
The interview discusses Sarah Marzi's work on ChIP-Seq experiments and their significance in understanding Alzheimer's disease from an epigenetic perspective. The discussion touches on the widespread dysregulation and changes in acetylation, particularly in genes associated with Alzheimer's risk, providing insights into potential links between epigenetic insults and disease onset.
Moving on to the technical aspects of the study, the interview examines the strategic use of CUT&Tag. It explores the challenges and optimizations involved in accurately profiling limited cell samples. The dialogue also compares CUT&Tag to ENCODE ChIP-Seq, highlighting the complexities of peak calling and data interpretation across different methodologies.
References
Kumsta, R., Marzi, S., Viana, J. et al. Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1. Transl Psychiatry 6, e830 (2016). https://doi.org/10.1038/tp.2016.95
Marzi, S. J., Schilder, B. M., Nott, A., Frigerio, C. S., Willaime‐Morawek, S., Bucholc, M., Hanger, D. P., James, C., Lewis, P. A., Lourida, I., Noble, W., Rodriguez‐Algarra, F., Sharif, J., Tsalenchuk, M., Winchester, L. M., Yaman, Ü., Yao, Z., The Deep Dementia Phenotyping (DEMON) Network, Ranson, J. M., & Llewellyn, D. J. (2023). Artificial intelligence for neurodegenerative experimental models. Alzheimer’s & Dementia, 19(12), 5970–5987. https://doi.org/10.1002/alz.13479
Marzi, S. J., Leung, S. K., Ribarska, T., Hannon, E., Smith, A. R., Pishva, E., Poschmann, J., Moore, K., Troakes, C., Al-Sarraj, S., Beck, S., Newman, S., Lunnon, K., Schalkwyk, L. C., & Mill, J. (2018). A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nature Neuroscience, 21(11), 1618–1627. https://doi.org/10.1038/s41593-018-0253-7
Hu, D., Abbasova, L., Schilder, B. M., Nott, A., Skene, N. G., & Marzi, S. J. (2022). CUT&Tag recovers up to half of ENCODE ChIP-seq peaks in modifications of H3K27 [Preprint]. Genomics. https://doi.org/10.1101/2022.03.30.486382
Related Episodes
When is a Peak a Peak? (Claudio Cantù)
Development of Integrative Machine Learning Tools for Neurodegenerative Diseases (Enrico Glaab)
DNA Methylation Alterations in Neurodegenerative Diseases (Paula Desplats)
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Thursday Apr 04, 2024
The Role of Hat1p in Chromatin Assembly (Mark Parthun)
Thursday Apr 04, 2024
Thursday Apr 04, 2024
In this episode of the Epigenetics Podcast, we talked with Mark Parthun from Ohio State University about his work on the role of Hat1p in chromatin assembly.
Mark Parthun shares insights into his pivotal paper in 2004 that explored the link between type B histone acetyltransferases and chromatin assembly, setting the stage for his current research interests in epigenetics. He highlights the role of HAT1 in acetylating lysines on newly synthesized histones, its involvement in double-strand break repair, and the search for phenotypes associated with HAT1 mutations.
The discussion expands to a collaborative research project between two scientists uncovering the roles of HAT1 and NASP as chaperones in chromatin assembly. Transitioning from yeast to mouse models, the team investigated the effects of HAT1 knockout on mouse phenotypes, particularly in lung development and craniofacial morphogenesis. They also explored the impact of histone acetylation on chromatin dynamics and its influence on lifespan, aging processes, and longevity.
References
Parthun, M. R., Widom, J., & Gottschling, D. E. (1996). The Major Cytoplasmic Histone Acetyltransferase in Yeast: Links to Chromatin Replication and Histone Metabolism. Cell, 87(1), 85–94. https://doi.org/10.1016/S0092-8674(00)81325-2
Kelly, T. J., Qin, S., Gottschling, D. E., & Parthun, M. R. (2000). Type B histone acetyltransferase Hat1p participates in telomeric silencing. Molecular and cellular biology, 20(19), 7051–7058. https://doi.org/10.1128/MCB.20.19.7051-7058.2000
Ai, X., & Parthun, M. R. (2004). The nuclear Hat1p/Hat2p complex: a molecular link between type B histone acetyltransferases and chromatin assembly. Molecular cell, 14(2), 195–205. https://doi.org/10.1016/s1097-2765(04)00184-4
Nagarajan, P., Ge, Z., Sirbu, B., Doughty, C., Agudelo Garcia, P. A., Schlederer, M., Annunziato, A. T., Cortez, D., Kenner, L., & Parthun, M. R. (2013). Histone acetyl transferase 1 is essential for mammalian development, genome stability, and the processing of newly synthesized histones H3 and H4. PLoS genetics, 9(6), e1003518. https://doi.org/10.1371/journal.pgen.1003518
Agudelo Garcia, P. A., Hoover, M. E., Zhang, P., Nagarajan, P., Freitas, M. A., & Parthun, M. R. (2017). Identification of multiple roles for histone acetyltransferase 1 in replication-coupled chromatin assembly. Nucleic Acids Research, 45(16), 9319–9335. https://doi.org/10.1093/nar/gkx545
Popova, L. V., Nagarajan, P., Lovejoy, C. M., Sunkel, B. D., Gardner, M. L., Wang, M., Freitas, M. A., Stanton, B. Z., & Parthun, M. R. (2021). Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones. Nucleic Acids Research, 49(21), 12136–12151. https://doi.org/10.1093/nar/gkab1044
Related Episodes
Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni)
Effects of Non-Enzymatic Covalent Histone Modifications on Chromatin (Yael David)
scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)
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