Epigenetic Reprogramming During Mammalian Development (Wolf Reik)
In this episode of the Epigenetics Podcast, we caught up with Dr. Wolf Reik, Director at the Babraham Institute in Cambridge, UK, to talk about his work on the role of epigenetic factors in cellular reprogramming. In this interview, we discuss the story behind how Dr. Wolf Reik almost discovered 5-hmC and how he later moved into developing single-cell methods like scRRBS and single-cell multi-omics approaches.
In Vivo Nucleosome Structure and Dynamics (Srinivas Ramachandran)
In this episode of the Epigenetics Podcast, we caught up with Dr. Srinivas Ramachandran, Assistant Professor at the University of Colorado, Anschutz Medical Campus, to talk about his work on in vivo nucleosome structure and dynamics. We discuss the story behind how Dr. Ramachandran found his way into chromatin research, what it was like to start a wet lab postdoc with a bioinformatics background, and what he is working on now to unravel nucleosomal structure and dynamics in his own lab.
Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret)
In this episode of the Epigenetics Podcast, we caught up with Dr. Ken Zaret, Professor in the Department of Cell and Developmental Biology at the Perelman School of Medicine, University of Pennsylvania, to talk about his work on pioneer transcription factors and their influence on chromatin structure. We discuss the story behind how Dr. Zaret discovered pioneer transcription factors like FoxA, how these factors are influenced by the chromatin environment, and how they function.
The Role of Small RNAs in Transgenerational Inheritance in C. elegans (Oded Rechavi)
In this episode of the Epigenetics Podcast, we caught up with Dr. Oded Rechavi, Professor at the University of Tel Aviv, to talk about his work on the role of small RNAs in transgenerational inheritance in C. elegans. In this interview, we cover how Dr. Rechavi chose C. elegans as a model organism, discuss his first major discoveries in the field of transgenerational effects of starvation, and what role small RNAs and other epigenetic factors play in this process.
Development of Site-Specific ChIP Technologies (Hodaka Fujii)
In this episode of the Epigenetics Podcast, we caught up with Dr. Hodaka Fujii, Professor of Biochemistry and Genome Biology at Hirosaki University Graduate School of Medicine and School of Medicine, to talk about his work on the development of locus-specific ChIP technologies. We also discuss the story behind how Dr. Fujii got into the field of epigenetics, how he developed iChIP, and how the method was improved over the years. Furthermore, we discuss the development of enChIP and how this method can be used as an alternative to Hi-C.
Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni)
Geneviève Almouzni is a leader in the field of epigenetics, and we are excited to welcome her as a guest on our Epigenetics Podcast. She discovered multiple histone chaperones and is working on unraveling the mechanisms responsible for nucleosome assembly as well as the links between chromatin structure at centromeres and cancer. In this interview, we sat down with Dr. Almouzni to learn about the stories behind her discoveries, what she’s focusing on now, how she got started in science (hint: it involves tadpoles!), and much more.
How the "Fragile Nucleosome" Science Community Came to Life (Christine Cucinotta, Melvin Noe Gonzalez)
In this episode of the Epigenetics Podcast, we caught up with Dr. Christine Cucinotta and Dr. Melvin Noe Gonzalez, members of the organizing committee for the independent "Fragile Nucleosome" scientific community, to talk about how they brought the #fragilenucleosome seminar series and Discord channel to life. In this interview, Christine and Melvin share the story of how the Fragile Nucleosome community got started, what has happened so far, and what the future plans are for the #fragilenucleosome.
Epigenetic Influence on Memory Formation and Inheritance (Isabelle Mansuy)
In this episode of the Epigenetics Podcast, we caught up with Professor Isabelle Mansuy, Ph.D. from the University of Zürich and the ETH Zürich, to talk about her work on epigenetic influences on memory formation and inheritance. Check out this interview to learn more about the challenges and obstacles that needed to be overcome to create a novel experimental approach to tackle the questions of whether and which epigenetic factors might influence transgenerational epigenetic inheritance.
Influence of Dynamic RNA Methylation on Gene Expression (Chuan He)
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. In this interview, we discuss the story of 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.
How to Publish in Nature: Lessons from the ENCODE Consortium (Michelle Trenkmann, Senior Editor at Nature)
In this episode of the Epigenetics Podcast, we caught up with Dr. Michelle Trenkmann, Senior Editor at Nature. We discussed her work as an editor at Nature and how she contributed to the ENCODE 3 publications, which are the results of the third phase of the ENCODE project. Dr. Trenkmann also talked about how to get your research published in Nature and what it’s like to review high profile scientific articles.
The Role of Non-Histone Proteins in Chromosome Structure and Function During Mitosis (Bill Earnshaw)
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.
In this interview, we discuss the story on how centromeric proteins were first identified using sera from human scleroderma patients, how the chromosomal passenger complex was discovered, how condensin I and II work together in chromatin loop formation, and much more!
Effects of DNA Methylation on Chromatin Structure and Transcription (Dirk Schübeler)
In this episode of the Epigenetics Podcast, we caught up with Dr. Dirk Schübeler, Director of the Friedrich Miescher Institute in Basel, Switzerland, to talk about his work on the effects of DNA methylation on chromatin structure and transcription.
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.
CpG Islands, DNA Methylation, and Disease (Sir Adrian Bird)
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.
In this interview, podcast host Stefan Dillinger and Adrian Bird discuss the discovery of the methyl-CpG-binding protein MeCP2, which is almost as abundant as histones in neurons. MeCP2 deficiencies in children can cause serious neurological diseases such as the autism spectrum disorder Rett Syndrome. Adrian Bird talks about how his research on MeCP2 may potentially lead to the discovery of a treatment for Rett Syndrome.
Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)
In this episode of the Epigenetics Podcast, we caught up with Leonid Mirny, Ph.D., from Massachusetts Institute of Technology to talk about his work on biophysical modeling of the 3-D structure of chromatin.
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.
From Nucleosome Structure to Function (Karolin Luger)
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.
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.
Identification of Functional Elements in the Genome (Bing Ren)
In this episode of the Epigenetics Podcast, we caught up with Bing Ren, Ph.D., from the University of California, San Diego and the Ludwig Institute for Cancer Research to talk about his work on identifying functional elements in the genome and higher order genome structure.
Dr. Ren’s lab invented an approach for finding cis-elements that involves the identification of transcription factor binding sites and chromatin modification status genome-wide using chromatin immunoprecipitation-based methods. His group demonstrated that this is an effective approach for genome-wide mapping of cis-elements, and their approach has now been widely adopted in the field. Among many other distinctions, Bing Ren's group was also a major contributor to the ENCODE Project.
In this interview, we discuss the path Bing Ren has taken so far on scientific career, his role in the ENCODE Project and Roadmap Epigenome Consortia, and the discovery of topologically associating domains (TADs).
Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden)
In this episode of the Epigenetics Podcast, we caught up with Erez Lieberman Aiden, Ph.D. from Baylor College of Medicine and Rice University in Houston to talk about his work on developing Hi-C and investigating the three-dimensional structure of the genome. He was the first author on a publication in the journal Science titled "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome" which was the paper that first introduced the Hi-C method in 2009 and he has continued studying the structure of the chromosome ever since.
Erez Liebermann Aiden is currently an Assistant Professor in both the Department of Genetics at the Baylor College of Medicine, where he directs the newly-established Center for Genome Architecture, and in the Department of Computer Science and Computational and Applied Mathematics at Rice University across the street.
In this interview, we discuss the road that Erez Liebermann Aiden went down to optimize the Hi-C protocol, the hurdles he had to overcome, and how Hi-C made it possible to probe the three-dimensional structure of the genome.
Chromatin Structure and Dynamics at Ribosomal RNA Genes (Tom Moss)
In this episode of the Epigenetics Podcast, we caught up with Professor Tom Moss from Université Laval in Québec City, Canada to talk about his work on the chromatin structure and dynamics at ribosomal RNA genes.
Dr. Tom Moss has been a member of the Department of Molecular Biology, Medical Biochemistry, and Pathology at the Laval University School of Medicine since he was recruited from the University of Portsmouth in the United Kingdom in 1986. Since then he focused on the ribosomal transcription factor Upstream Binding Factor (UBF) and how it regulates the chromatin structure at ribosomal RNA genes (rDNA).
UBF binds to the rDNA as a dimer where it leads to six in-phase bends and induces the formation of the ribosomal enhanceosome. This enhanceosome is required for the initial step in formation of an RNA polymerase I initiation complex, and therefore plays an important role in regulating the expression of ribosomal RNA genes.
In this interview, we discuss the function of UBF on the rDNA, how UBF impacts the chromatin landscape at rRNA genes, the role of DNA methylation in this process, and how UBF influences the structure of the nucleolus.
Epigenetic Origins Of Heterogeneity And Disease (Andrew Pospisilik)
In this episode of the Epigenetics Podcast, we caught up with Dr. Andrew Pospisilik from the Van Andel Institute in Grand Rapids, Michigan to talk about his work on the epigenetic origins of heterogeneity and disease.
Dr. Andrew Pospisilik worked at the Max Planck Institute for Epigenetics in Freiburg for 8 years and in 2018 he joined the Van Andel Institute as the director of its Center for Epigenetics. At the Van Andel Institute his research focuses on diabetes, neurodegenerative diseases, cancer, and obesity. The goal of the Pospisilik Laboratory is to better understand epigenetic mechanisms of these diseases and the roles of epigenetics in disease susceptibility and heterogeneity.
These areas of medicine are among the most important public health challenges, with the latest estimates suggesting that they impact more than 1 billion people worldwide. Although these diverse conditions are all very different, they are now thought to be caused, at least partially, from alterations in the epigenetic mechanisms that regulate gene expression and metabolism.
This podcast interview covers recent work from the Pospisilik lab on the epigenetics of these complex diseases.
PIXUL: On the Leading Edge of Chromatin Shearing (Karol Bomsztyk and Tom Matula)
In this episode of the Epigenetics Podcast, we caught up with Karol Bomsztyk, M.D. and Tom Matula, Ph.D. from the University of Washington and Matchstick Technologies to talk about their work on DNA and chromatin sonication.
During his career, Karol's research has focused on improving ChIP protocols to make them faster, easier, and higher throughput. First, to make ChIP assays faster, Karol and his lab developed Fast ChIP. More recently, he adjusted this protocol to improve throughput and Matrix ChIP was born. Tom is an expert in the field of ultrasound physics and cavitation and the Director of the Center for Industrial and Medical Ultrasound at the University of Washington.
To further improve and speed up the 96-well Matrix ChIP protocol, Karol and Tom teamed up and co-founded Matchstick Technologies to develop a sonication device that would be able to processes each and every well of a 96-well microplate consistently and quickly. The result of this cooperation is the PIXUL Multi-Sample Sonicator that is now available for order from Active Motif.
PIXUL is an ultrasound-based sample preparation platform that was designed completely from the ground up to provide researchers with an easy-to-use tool that is simple to set up, simple to use, and generates consistent results day in and day out. No other sample preparation platform out there can match the power and convenience of PIXUL.
PIXUL was conceived by an epigenetics researcher and designed and built by ultrasound engineers to take the guesswork out of sample preparation. With PIXUL, sample preparation is no longer an art form, but instead a simple and predictable part of experiments that works every single time.
This interview goes into the mechanism behind sonication-based shearing of DNA and chromatin and highlights how PIXUL is different from existing sonication instruments.
Influence of Histone Variants on Chromatin Structure and Metabolism (Marcus Buschbeck)
In this episode of the Epigenetics Podcast, we sat down with Marcus Buschbeck, Group Leader at the Josep Carreras Leukaemia Research Institute in Barcelona, to talk about his work on the histone variant macroH2A, its role in metabolism, and how it contributes to the regulation of chromatin structure.
Histone variants equip chromatin with unique properties and show a specific genomic distribution. The histone variant macroH2A is unique in having a tripartite structure consisting of a N-terminal histone-fold, an intrinsically unstructured linker domain, and a C-terminal macro domain. Recent discoveries show that macroH2A proteins have a major role in nuclear organization, which has the potential to explain how these proteins can act as tumor suppressors, promoters of differentiation, and barriers to somatic cell reprogramming.
We discuss these topics, the mission of the Josep Carreras Leukaemia Research Institute, and much more in this episode.
Epigenetic Mechanisms of Aging and Longevity (Shelley Berger)
In this episode of the Epigenetics Podcast, we sat down with Dr. Shelley Berger, Director of the Epigenetics Institute and Daniel S. Och Professor of Cell and Developmental Biology at the University of Pennsylvania School of Medicine, and Keynote Speaker at the EMBO | EMBL Symposium: Metabolism Meets Epigenetics, to talk about her work on epigenetic mechanisms of aging and longevity. We also discussed how cytoplasmic chromatin fragments are involved in these processes, how alcohol has an effect on histone PTMs in the brain, and how ants became her favorite model organism.
Epigenetics & Glioblastoma: New Approaches to Treat Brain Cancer (Lucy Stead)
In this episode of the Epigenetics Podcast our guest Dr. Lucy Stead, Head of Glioma Genomics at the University of Leeds, discusses her recent work on intratumor heterogeneity in glioblastoma brain tumors. Her research involves a true multidisciplinary approach, including computational genomics, in silico modeling, and functional genomics. She uses this experimental strategy to test whether treatment-resistant cancer cells emerge in recurrent tumors and characterizes them in clinically relevant ways in multiple patients.
And this is just a glimpse of the conversation. Listen to the podcast episode to learn more about this fascinating topic and potential new ways to treat brain cancer.
The Past, Present, and Future of Epigenetics (Joe Fernandez, founder of Active Motif)
Joe Fernandez, the founder of Active Motif, has played a significant role in the evolution of the biotechnology industry. He’s seen where the industry has been, and he has a good idea where it’s going.
Prior to founding Active Motif in 1999, Joe was a co-founder of Invitrogen where he helped revolutionize molecular cloning with the TOPO TA kit. Joe’s passion for disrupting established workflows by making them easier and more efficient didn’t stop there. With Active Motif, he launched the first ever ChIP kit in 2003, and the company now offers the most complete portfolio of ChIP kits for different workflows and sample types, the highest quality ChIP-validated antibodies, and the most comprehensive and most cited end-to-end Epigenetic Services.
In this interview, we sat down with Joe to learn how he got started in science, what he’s currently excited about, and what he thinks will be the next big thing in epigenetics research.
Check out our blog post to learn more.
The Interchromatin Network Model (Ana Pombo)
There are many levels of control that contribute to regulating the levels of gene expression. One major mechanism of gene regulation involves organization of the genome within the nucleus. In this episode of the Epigenetics Podcast, our guest Professor Ana Pombo from the Max-Delbrück-Center in Berlin provides insight into her work on the interplay between gene regulation and genome architecture.
Dr. Pombo and her team use different state-of-the-art methods in their research, including cryo-sectioning, to unravel this regulatory network. In 2006, they proposed the "Interchromatin Network Model" of chromosome organization which postulates that chromosome folding is driven by contacts between different genomic regions and chromatin and nuclear landmarks, such as the nuclear lamina. They also used polymer physics modeling to study those mechanisms, which lead to the development of the "Strings and Binders Switch" model of chromatin organization.
Listen to the podcast episode to learn more about this fascinating topic.
Dosage Compensation in Drosophila (Asifa Akhtar)
For many organisms, from fruit flies to humans, sex is determined by the number of X chromosomes. Females often have two copies of the X and males have one, creating an imbalance in the number of X chromosome genes present in each sex. Different organisms have evolved different strategies for how to cope with this imbalance. For example, in humans, one of the two X chromosomes in every female cell is randomly inactivated, leaving both males and females with one active X chromosome each. However, in Drosophila, the balance is achieved by males overexpressing the genes on their single X chromosome two-fold to bring up the levels of gene expression to match expression from the two X chromosomes in females. Essentially the same end result is achieved in both humans and Drosophila, balanced levels of X chromosome transcription in both males and females, but using two extremely different mechanisms.
In this episode, our guest Dr. Asifa Akhtar, Senior Group Leader and Director at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany, discussed her lab's recent work on dosage compensation in Drosophila melanogaster. Dr. Akhtar talked about how the MSL complex, and the histone acetyltransferase MOF in particular, contributes to the regulation of the dosage compensation process. Furthermore, she also talked about some potential functions of the conserved MSL proteins in humans and how they are similar to and different from their fruit fly counterparts.
Check out our blog post to learn more.
Spatial Organization of the Human Genome (Wendy Bickmore)
In recent years it has become more and more evident that genome organization the nucleus plays a pivotal role in the regulation of gene expression. In this episode of our podcast we spoke with Professor Wendy Bickmore, Director of the MRC Human Genetics Unit at the University of Edinburgh, about her work on the spatial organization of the human genome. Professor Bickmore and her team use visual methods like fluorescence in situ hybridization (FISH) to study the organization of human and mouse chromosomes and investigate how organization of the genome contributes to transcriptional regulation. Dr. Bickmore's research group also studies how this organization changes during aging, development, and disease.
Check out our blog post to learn more.
Heterochromatin and Phase Separation (Gary Karpen)
Heterochromatin plays a pivotal role in organizing our genome in the nucleus and is probably most well known for marking inactive genomic regions. In this podcast episode our guest Gary Karpen from UC Berkeley sits down with us to talk about the regulation of this heterochromatin and how DNA repair mechanisms function in this densely packed nuclear compartment. We also discuss how phase separation might be an important part of the way that heterochromatin domains are formed.
Check out our blog post to learn more.
Diabetes and Epigenetics (Jean-Sébastien Annicotte)
Type 2 Diabetes (T2D) is a chronic metabolic disease that is caused by the failure of beta-cells in the pancreas and insulin resistance in peripheral tissue, and is characterized by high glucose levels in the blood. 382 million people suffer from diabetes worldwide, which makes up >8% of the global population.
Due to this high proportion of people affected, it is of high interest to find a cure for this disease and tremendous efforts have been made on deciphering epigenetic regulations that control metabolic tissue function.
For several years, the research team led by Dr. Jean-Sebastien Annicotte have dissected the molecular links between insulin producing cells, insulin target tissues, and T2D/obesity development. Their research has specifically been focused on the role of cell cycle regulators and their transcriptional co-regulators in the control of metabolic homeostasis, T2D and obesity.
In this podcast episode, we caught up with Dr. Jean-Sebastien Annicotte to discuss his views on type 2 diabetes and the roles of epigenetic mechanisms in regulating this disease.
Check out our blog post to learn more.
Epigenetics and X-Inactivation (Edith Heard)
In this episode of our Epigenetics Podcast, we sat down with Professor Edith Heard, the Director General of the European Molecular Biology Laboratory (EMBL), to talk about the challenges and goals of her new position as DG of the EMBL and her research on X-inactivation and dosage compensation.
Chromatin Organization (Susan Gasser)
In this episode of our Epigenetics Podcast, we caught up with Professor Susan Gasser, director of the Friedrich Miescher Institute in Basel, to talk about her research on heterochromatin, its localization in the nucleus and factors that are involved in the anchoring genomic regions at the nuclear periphery.
Epigenomics (Henk Stunnenberg)
In this episode of our Epigenetics Podcast, we chatted with Professor Henk Stunnenberg, head of the Department of Molecular Biology at the Radboud University in Nijmegen, to discuss his scientific work which led him to epigenetics research. Topics include his establishment of the BLUEPRINT and Human Cell Atlas consortia, a European collaborative database of at least 100 reference epigenomes of blood cells from healthy donors and their malignant counterparts, and his feelings about his recent knighthood.
Aging and Epigenetics (Peter Tessarz)
In this episode of our Epigenetics Podcast, we were joined by Dr. Peter Tessarz from the Max Planck Institute for Biology of Ageing in Cologne, and discussed the factors that influence the aging process in humans, how epigenetics comes into play, and how Peter's research can lead to a longer and healthier life.
Cancer and Epigenetics (David Jones)
In this episode of our Epigenetics Podcast, we visited Dr. David Jones at the DKFZ in Heidelberg to talk about the implications of epigenetics in cancer. We also talked about David's contributions to the field of pediatric brain tumors and the role of large consortia in doing science today and in the future.
The Nucleosome: From Atoms to Genomes (Ada and Don Olins)
In this episode of our Epigenetics Podcast we sat down with Ada and Don Olins at the EMBO meeting on "The Nucleosome: From Atoms to Genomes" to talk about their outstanding scientific journey together as a married couple and their perspectives on the future of the chromatin field.
Multiple Challenges in ChIP (Adam Blattler)
In this first episode of the Active Motif Epigenetics Podcast we chatted with Dr. Adam Blattler from the R&D team at Active Motif and discussed the multiple challenges of ChIP, the critical points of the ChIP protocol, as well as possible pitfalls.
Chromatin immunoprecipitation has become a very powerful method to study protein-DNA interactions, identify the binding profiles of DNA binding proteins, and determine whether specific proteins are associated with specific genomic regions. However, the workflow is complicated and involves many steps, so extensive experience and optimization are often required to achieve the best results.
Check out our Guide to Generating the Best ChIP Data on our blog for more details.