A lively discussion about the latest tips and techniques for epigenetics research.
In this episode of the Epigenetics Podcast, we caught up with Geneviève Almouzni, Ph.D., Research Director at the CNRS at Institut Curie in Paris, to talk about her work on the regulation of chromatin organization by histone chaperones. Geneviève Almo
In this episode of the Epigenetics Podcast, we caught up with Geneviève Almouzni, Ph.D., Research Director at the CNRS at Institut Curie in Paris, to talk about her work on the regulation of chromatin organization by histone chaperones.
Erschienen: 17.09.2020
Dauer: 38:43
In this episode of the Epigenetics Podcast, we caught up with Dr. Christine Cucinotta and Dr. Melvin Noe Gonzalez to talk about how they brought the #fragilenucleosome seminar series and Discord channel to life. Christine Cucinotta and Melvin Noe Gon
In this episode of the Epigenetics Podcast, we caught up with Dr. Christine Cucinotta and Dr. Melvin Noe Gonzalez to talk about how they brought the #fragilenucleosome seminar series and Discord channel to life. Christine Cucinotta and Melvin Noe Gonzales are part of the organizing committee of the independent scientific community "Fragile Nucleosome." This community consists of a Discord channel with more than 1,000 members, a biweekly seminar series, a mentoring program, and a journal club series. The Fragile Nucleosome is organized exclusively by early-career scientists, without external sponsors or under the roof of a single graduate program or university. In this interview, Christine and Melvin share the story on how the Fragile Nucleosome community got started, what has happened so far, and what the future plans are for the #fragilenucleosome. References #fragilenucleosome on Twitter Fragile Nucleosome Discord Channel Fragile Nucleosome on generegulation.org Christine Cucinotta on Twitter Melvin Noe Gonzalez on Twitter Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com
Erschienen: 10.09.2020
Dauer: 41:20
In this episode of the Epigenetics Podcast, we caught up with Prof. Isabelle Mansuy, Ph.D., from the University and the ETH in Zürich, to talk about her work on epigenetic influences on memory formation and inheritance. Dr. Mansuy received her PhD f
In this episode of the Epigenetics Podcast, we caught up with Prof. Isabelle Mansuy, Ph.D., from the University and the ETH in Zürich, to talk about her work on epigenetic influences on memory formation and inheritance.
Erschienen: 03.09.2020
Dauer: 38:50
In this episode of the Epigenetics Podcast, we caught up with Dr. Chuan He, John T. Wilson Distinguished Service Professor at the University of Chicago, to talk about his work on the influence of dynamic RNA methylation on gene expression. More than 150
In this interview, we discuss the story on how the He lab discovered the members of the family of proteins that read, write, and erase RNA modifications and the mechanisms of how those RNA modifications act in the field of epigenetics.
Erschienen: 20.08.2020
Dauer: 41:22
Podcast-Webseite: Episode "Influence of Dynamic RNA Methylation on Gene Expression (Chuan He)"
In this episode of the Epigenetics Podcast, we caught up with Dr. Michelle Trenkmann, Senior Editor at Nature, to talk about her work as an Editor at Nature and also how she contributed in the final phase of publishing the results of the third Phase of
In this episode of the Epigenetics Podcast, we caught up with Dr. Michelle Trenkmann, Senior Editor at Nature, to talk about her work as an Editor at Nature and also how she contributed in the final phase of publishing the results of the third Phase of the ENCODE Project. ENCODE References Immersive ENCODE Website Perspectives on ENCODE Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com
Erschienen: 06.08.2020
Dauer: 35:08
In this episode of the Epigenetics Podcast, we caught up with Professor Bill Earnshaw, Wellcome Trust Principal Research Fellow at the University of Edinburgh, to talk about his work on the role of non-histone proteins in chromosome structure and functi
In this episode of the Epigenetics Podcast, we caught up with Professor Bill Earnshaw, Wellcome Trust Principal Research Fellow at the University of Edinburgh, to talk about his work on the role of non-histone proteins in chromosome structure and function during mitosis.
Erschienen: 23.07.2020
Dauer: 01:04:51
In this episode of the Epigenetics Podcast, we caught up with Dr. Dirk Schübeler, Director of the Friedrich Miescher Institute (FMI) in Basel, Switzerland, to talk about his work on the effects of DNA methylation on chromatin structure and transcriptio
In this episode of the Epigenetics Podcast, we caught up with Dr. Dirk Schübeler, Director of the Friedrich Miescher Institute (FMI) in Basel, Switzerland, to talk about his work on the effects of DNA methylation on chromatin structure and transcription. Dirk Schübeler was born in Germany and started his scientific career in Braunschweig, Germany. After his postdoc at the Fred Hutchinson Cancer Research Center in Seattle, he joined the FMI in 2003 and never left. He was recently appointed as the Director of the FMI in March 2020. Dirk Schübeler’s research focuses on DNA methylation and its effects on chromatin and transcription. It is widely known that DNA methylation leads to gene silencing, but many of the mechanisms and regulatory factors involved in this process remain understudied. Therefore, Dirk Schübeler and his team set out to characterize the DNA methylation profiles in normal human somatic cells and compare them with the methylation profiles in transformed human cells. More recent work in his lab led by postdoc Tuncay Baubec focused on factors that bind to methylated DNA regions and modify chromatin structure. The factors they studied include the MBD protein family and also proteins like DNMT3B. In this interview, we discuss the impact of DNA methylation on chromatin states, how CpG-binding factors influence those processes, and we also talk about his new role as Director of the Friedrich Miescher Institute. References Tuncay Baubec, Daniele F. Colombo, … Dirk Schübeler (2015) Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation (Nature) DOI: 10.1038/nature14176 Paul Adrian Ginno, Lukas Burger, … Dirk Schübeler (2018) Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape (Nature Communications) DOI: 10.1038/s41467-018-06007-5 Michael B. Stadler, Rabih Murr, … Dirk Schübeler (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions (Nature) DOI: 10.1038/nature10716 Silvia Domcke, Anaïs Flore Bardet, … Dirk Schübeler (2015) Competition between DNA methylation and transcription factors determines binding of NRF1 (Nature) DOI: 10.1038/nature16462 Florian Lienert, Christiane Wirbelauer, … Dirk Schübeler (2011) Identification of genetic elements that autonomously determine DNA methylation states (Nature Genetics) DOI: 10.1038/ng.946 Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com
Erschienen: 02.07.2020
Dauer: 36:13
In this episode of the Epigenetics Podcast, we caught up with Sir Adrian Bird, Buchanan Professor of Genetics at the University of Edinburgh to talk about his work on CpG islands, DNA methylation, and the role of DNA methylation in human diseases. Ad
In this episode of the Epigenetics Podcast, we caught up with Sir Adrian Bird, Buchanan Professor of Genetics at the University of Edinburgh to talk about his work on CpG islands, DNA methylation, and the role of DNA methylation in human diseases. Adrian Bird has been a pioneer in studying the CpG dinucleotide sequence. The CpG dinucleotide is distributed genome-wide and has several properties expected of a genomic signaling module. The extent to which CpG signaling is involved in development, differentiation, and disease is only just beginning to emerge. Adrian Bird's work indicates that proteins that bind methylated CpGs recruit chromatin modifying enzymes to reinforce gene silencing, whereas proteins that bind unmethylated CpGs promote the formation of active chromatin. These results suggest that CpG acts as a global modulator of genome activity. One of the best-studied methyl-CpG binding proteins is MeCP2, which is almost as abundant as histones in neurons. MeCP2-deficient children acquire serious neurological disorders, in particular the autism spectrum disorder Rett Syndrome. Due to its monogenic origin, Rett Syndrome has become one of the most experimentally accessible of such disorders and studies of MeCP2 offer a golden opportunity to understand its complex pathology at a molecular level. Adrian Bird created a mouse model of Rett Syndrome which has accelerated the understanding of this disorder, most notably by demonstrating that advanced Rett-like symptoms in mice can be “cured” by reintroducing a functional MeCP2 gene. In this interview, podcast host Stefan Dillinger and Adrian discuss CpG islands, DNA methylation, and how the discovery of MeCP2 lead to the discovery of a possible treatment of Rett Syndrome. References S. Lindsay, A. P. Bird (1987) Use of restriction enzymes to detect potential gene sequences in mammalian DNA (Nature) DOI: 10.1038/327336a0 R. R. Meehan, J. D. Lewis, … A. P. Bird (1989) Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs (Cell) DOI: 10.1016/0092-8674(89)90430-3 R. R. Meehan, J. D. Lewis, A. P. Bird (1992) Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA (Nucleic Acids Research) DOI: 10.1093/nar/20.19.5085 Eric U. Selker, Nikolaos A. Tountas, … Michael Freitag (2003) The methylated component of the Neurospora crassa genome (Nature) DOI: 10.1038/nature01564 Robert J. Klose, Shireen A. Sarraf, … Adrian P. Bird (2005) DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG (Molecular Cell) DOI: 10.1016/j.molcel.2005.07.021 Jacky Guy, Jian Gan, … Adrian Bird (2007) Reversal of neurological defects in a mouse model of Rett syndrome (Science (New York, N.Y.)) DOI: 10.1126/science.1138389 Daniel H. Ebert, Harrison W. Gabel, … Michael E. Greenberg (2013) Activity-dependent phosphorylation of MeCP2 threonine 308 regulates interaction with NCoR (Nature) DOI: 10.1038/nature12348 Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com
Erschienen: 18.06.2020
Dauer: 47:10
Podcast-Webseite: Episode "CpG Islands, DNA Methylation, and Disease (Adrian Bird)"
In this episode of the Epigenetics Podcast, we caught up with Leonid Mirny, Ph.D., from MIT to talk about his work on biophysical modeling of the 3-D structure of chromatin. Leonid Mirny was part of the initial Hi-C paper titled "Comprehensive Mapping o
In this episode of the Epigenetics Podcast, we caught up with Leonid Mirny, Ph.D., from MIT to talk about his work on biophysical modeling of the 3-D structure of chromatin. Leonid Mirny was part of the initial Hi-C paper titled "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome" that was published in 2009 in the journal Science. Since then, technology has evolved and Dr. Mirny's group has developed a method called Micro-C that improves the Hi-C protocol by using MNase digestion to increase the resolution to nucleosomal level. This led to the visualization of interactions that were already predicted by his previous biophysical models. Furthermore, Leonid Mirny worked on finding the mechanism by which chromatin loops are formed. He and his team proposed that loop extrusion underlies TAD formation. In this process, factors like cohesin and CTCF form progressively larger loops but stall at TAD boundaries due to interactions of CTCF with TAD boundaries. He used polymer simulations to show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. In this interview, we chatted with Dr. Mirny about the details of Hi-C, the development of Micro-C and how it compares to Hi-C, and how biophysical modeling helps to unravel the mechanisms behind loop extrusion. References Grigory Kolesov, Zeba Wunderlich, … Leonid A. Mirny (2007) How gene order is influenced by the biophysics of transcription regulation (Proceedings of the National Academy of Sciences) DOI: 10.1073/pnas.0700672104 Erez Lieberman-Aiden, Nynke L. van Berkum, … Job Dekker (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome (Science (New York, N.Y.)) DOI: 10.1126/science.1181369 Geoffrey Fudenberg, Maxim Imakaev, … Leonid A. Mirny (2016) Formation of Chromosomal Domains by Loop Extrusion (Cell Reports) DOI: 10.1016/j.celrep.2016.04.085 Johannes Nuebler, Geoffrey Fudenberg, … Leonid A. Mirny (2018) Chromatin organization by an interplay of loop extrusion and compartmental segregation (Proceedings of the National Academy of Sciences) DOI: 10.1073/pnas.1717730115 Martin Falk, Yana Feodorova, … Leonid A. Mirny (2019) Heterochromatin drives compartmentalization of inverted and conventional nuclei (Nature) DOI: 10.1038/s41586-019-1275-3 Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com
Erschienen: 04.06.2020
Dauer: 41:49
Podcast-Webseite: Episode "Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)"
In this episode of the Epigenetics Podcast, we caught up with Karolin Luger, Ph.D., from the University of Colorado in Boulder to talk about her work on solving the crystal structure of the nucleosome and on how histone chaperones like FACT act on chrom
In this episode of the Epigenetics Podcast, we caught up with Karolin Luger, Ph.D., from the University of Colorado in Boulder to talk about her work on solving the crystal structure of the nucleosome and on how histone chaperones like FACT act on chromatin. During her postdoc with Timothy Richmond at the Swiss Federal Institute of Technology in Zürich, Karolin Luger was the first author on an all-time classic paper called "Crystal structure of the nucleosome core particle at 2.8 A resolution" which was published in Nature. This article was published more than 20 years ago now and it has been cited about 9000 times. After completing her postdoc, she moved to Colorado to set up her own lab where she continued to work on the structure of the nucleosome and the factors that influence their structure. The most recent Nature paper published by her lab investigated how the FACT complex promotes both disassembly and reassembly of nucleosomes during gene transcription, DNA replication, and DNA repair. In this interview, we discuss the efforts that went into solving the crystal structure of the nucleosome back in 1997, her work on histone chaperones, and her recent work on how FACT keeps nucleosomes intact after gene transcription. References K. Luger, A. W. Mäder, … T. J. Richmond (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution (Nature) DOI: 10.1038/38444 Yang Liu, Keda Zhou, … Karolin Luger (2020) FACT caught in the act of manipulating the nucleosome (Nature) DOI: 10.1038/s41586-019-1820-0 Contact Active Motif on Twitter Epigenetics Podcast on Twitter Active Motif on Linked-In Active Motif on Facebook eMail: podcast@activemotif.com
Erschienen: 19.05.2020
Dauer: 36:27
Podcast-Webseite: Episode "From Nucleosome Structure to Function (Karolin Luger)"
