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Discover the stories behind the science.

Epigenetics Podcast from Active Motif

Discover the stories behind the science.

Active Motif's Epigenetics Podcast is a lively discussion about the latest tips and techniques for epigenetics research. Podcast host Dr. Stefan Dillinger chats with experts from different fields within epigenetics about the latest research findings, the hottest epigenetics applications, and how to overcome the many challenges of ChIP and other epigenetic assays.









& Disease

Paula Desplats headshot

DNA Methylation Alterations in Neurodegenerative Diseases (Paula Desplats)

Episode 101

June 1, 2023

In this episode of the Epigenetics Podcast, we caught up with Paula Desplats from the University of California, San Diego to talk about her work on DNA methylation alterations in neurodegenerative diseases.

The Desplats lab focuses on decoding the role of epigenetic mechanisms, in particular DNA methylation, on the onset and progression of neurodegenerative diseases like Parkinson’s and Alzheimer’s. One of the goals of the Desplats team is to develop a biomarker panel, based on quantification of DNA methylation of selected genes, that may be able to discriminate Parkison's Disease patients from healthy subjects in a simple blood test. More recently, the team also focused on the role of the circadian rhythm on neurodegenerative diseases and exploring whether interventions can help in managing the disease.

Sarah Kimmins headshot

The Epigenetics of Human Sperm Cells (Sarah Kimmins)

Episode 95

March 8, 2023

In this episode of the Epigenetics Podcast, we caught up with Sarah Kimmins from Université de Montreal to talk about her work on the epigenetics of human sperm cells.

The focus of Sarah Kimmins and her lab is how sperm and offspring health is impacted by the father's environment. The core of this is the sperm epigenome, which has been implicated in complex diseases such as infertility, cancer, diabetes, schizophrenia and autism. The Kimmins lab is interested which players play a role in this and came across the Histone post-translational modification H3K4me3. In this interview we talk about how the father's life choices can impact offspring health, which can also be inherited transgenerationally and how this can be used to develop intervention strategies to improve child and adult health.

Karen Arndt headshot

Transcription Elongation Control by the Paf1 Complex (Karen Arndt)

Episode 93

February 8, 2023

In this episode of the Epigenetics Podcast, we caught up with Karen Arndt from the University of Pittsburgh to talk about her work on transcription elongation control by the Paf1 complex.

Karen Arndt and her lab investigate the process of transcriptional elongation and how RNA polymerase II overcomes obstacles like nucleosomes. One of the proteins that helps overcome those obstacles is the Paf1 complex. This complex associates with the transcribing polymerase and helps in modifying the chromatin template by ubiquitinating Histone H2B and methylating Histone H3.

Karim-Jean Armache headshot

Molecular Mechanisms of Chromatin Modifying Enzymes (Karim-Jean Armache)

Episode 92

January 25, 2023

In this episode of the Epigenetics Podcast, we caught up with Karim-Jean Armache from New York University - Grossman School of Medicine to talk about his work on the structural analysis of Polycomb Complex Proteins.

Karim-Jean Armache started his research career with the structural characterization of the 12-subunit RNA Polymerase II. After starting his own lab he used this knowledge in x-ray crystallography and electron microscopy to study how gene silencing complexes like the PRC complex act on chromatin and influence transcription. Further work in the Armache Lab focused on the Dot1, a histone H3K79 methyltransferase, and how it acts on chromatin, as well as how it is regulated by Histone-Histone crosstalk.

Sarah Kinkley headshot

The Role of PHF13 in Chromatin and Transcription (Sarah Kinkley)

Episode 91

January 11, 2023

In this episode of the Epigenetics Podcast, we caught up with Sarah Kinkley from the Max Planck Institute of Molecular Genetics to talk about her work on PHF13 and its role in chromatin and transcription.

The Kinkley laboratory focuses mainly on unraveling the mechanism of action of the transcription factor PHF13 (PHC Finger Protein 13). PHF13 is a reader of the epigenetic mark H3K4 trimethylation which influences higher chromatin order, transcriptional regulation, and differentiation. The lab has shown that PHF13 plays a crucial role in phase separation and mitotic chromatin compaction.

Melissa Harrison headshot

The Role of Pioneer Factors Zelda and Grainyhead at the Maternal-to-Zygotic Transition (Melissa Harrison)

Episode 89

November 30, 2022

In this episode of the Epigenetics Podcast, we caught up with Melissa Harrison from the University of Wisconsin-Madison to talk about her work on the “Pioneer” Transcription Factors - Zelda and Grainyhead - and their role at the maternal-to-zygotic transition.

The Harrison lab studies how differentiation and development are driven by coordinated changes in gene expression. To do this, the targets of choice are the transcription factors Zelda and Grainyhead that bind to the genome at specific and crucial points in development and differentiation. These specialised transcription factors have the ability to bind to DNA in the context of nucleosomes which defines regulatory elements and leads to subsequent binding of additional classical transcription factors. These properties allow pioneer factors to act at the top of gene regulatory networks and control developmental transitions.

Elena Gómez-Diaz headshot

Epigenetics in Human Malaria Parasites (Elena Gómez-Diaz)

Episode 88

November 16, 2022

In this episode of the Epigenetics Podcast, we caught up with Elena Gomez-Diaz from the Institute of Parasitology and Biomedicine López-Neyra at the Spanish National Research Council. She shared with us her work on the Epigenetics in Human Malaria Parasites.

Elena Gómez-Díaz and her team are focusing on understanding how epigenetic processes are implicated in host-parasite interactions by regulating gene expression in the model of malaria. The team has started to investigate and uncover layers of chromatin regulation that control developmental transitions in Plasmodium falciparum, especially in the parts of the life cycle that take place in the mosquito. Furthermore, the lab has investigated epigenetic changes that are present in malaria-infected Anopheles mosquitos, this led to the identification of cis-regulatory elements and enhancer-promoter networks in response to infection.

Marco Trizzino headshot

Transposable Elements in Gene Regulation and Evolution (Marco Trizzino)

Episode 84

September 22, 2022

In this episode of the Epigenetics Podcast, we caught up with Marco Trizzino from Thomas Jefferson University to talk about his work on transposable elements in gene regulation and evolution.

Marco Trizzino and his team focus on characterising transposable elements and how they affect gene regulation, evolution and ageing in primates. They could show that transposable elements that integrated into the genome turned into regulatory elements in the genome, like enhancers. They then contribute to regulation of processes like development or ageing, which could be among those factors that lead to increased brain development or longevity in great apes.

John Rinn headshot

The Effect of lncRNAs on Chromatin and Gene Regulation (John Rinn)

Episode 78

June 30, 2022

In this episode of the Epigenetics Podcast, we caught up with John Rinn from the University of Colorado in Boulder to talk about his work on the role of lncRNAs in gene expression and nuclear organization.

The Rinn Lab pioneered the approach of screening the human genome for long noncoding RNAs (lncRNAs). More recently, the lab has shifted focus from measuring the number of lncRNAs to finding lncRNAs that have a distinct biological function in human health and disease. One example of such a lncRNA is FIRRE, which is present in all animals, however the sequence is not conserved, except for in primates. FIRRE contains many interesting features, such as repeat sequences and CTCF binding sites. In absence of FIRRE, defects in the immune system can be observed and also some brain defects may also be observed.

Jan Żylicz headshot

Epigenetic and Metabolic Regulation of Early Development (Jan Żylicz)

Episode 76

June 9, 2022

In this episode of the Epigenetics Podcast, we caught up with Jan Żylicz from the Novo Nordisk Foundation Center for Stem Cell Medicine to talk about his work on epigenetic and metabolic regulation of early development.

The focus of the Żylicz Lab is studying early development and how this process is influenced by epigenetic factors. In more detail, the team focuses on the function of chromatin modifiers in this process. Primed pluripotent epiblasts in vivo show a distinct chromatin landscape that is characterized by high levels of histone H3 lysine 9 dimethylation (H3K9me2) and rearranged Polycomb-associated histone H3 lysine 27 trimethylation (H3K27me3) at thousands of genes along the genome. However, the function of only about 100 loci is impaired. The Żylicz Lab tries to understand this process behind and also the cause of this discrepancy.

Ian Maze headshot

The Role of Histone Dopaminylation and Serotinylation in Neuronal Plasticity (Ian Maze)

Episode 74

May 12, 2022

In this episode of the Epigenetics Podcast, we caught up with Ian Maze from Ichan School of Medicine at Mount Sinai and a Howard Hughes Medical Institute (HHMI) Investigator to talk about his work on the role of histone dopaminylation and serotinylation in neuronal plasticity.

The Maze group focuses on understanding the complex interplay between chromatin regulatory mechanisms in brain and neuronal plasticity. The lab places an emphasis on psychiatric disorders associated with monoaminergic (e.g., serotonin, dopamine, etc.) dysfunction, such as major depressive disorder and drug addiction. In particular the Maze team has investigated cocaine addiction and its effect on chromatin by serotonylation and dopaminylation of Histone H3 Tails.

Erna Magnúsdóttir headshot

The Role of Blimp-1 in Immune-Cell Differentiation (Erna Magnúsdóttir)

Episode 73

April 28, 2022

In this episode of the Epigenetics Podcast, we caught up with Erna Magnúsdóttir from the University of Iceland to talk about her work on the role of Blimp-1 in immune-cell differentiation.

The Magnúsdóttir Lab is interested in how the mammalian genome is interpreted in a context dependent manner, leading to different cellular states, by using mouse primordial germ cells as well as mouse and human B-cells as model systems. More specifically, the team is interested in the Transcription Factor Blimp-1 and its effect on immune cell differentiation. Next to its function in immune cells, Blimp-1 also plays a role in Waldenström’s macroglobulinemia. The lab hopes to reveal the intricacies in disease progression and alteration in cellular states to increasingly aggressive tumor behavior.

Eleni Tomazou headshot

Epigenome-based Precision Medicine (Eleni Tomazou)

Episode 69

March 9, 2022

In this episode of the Epigenetics Podcast, we caught up with Eleni Tomazou from St. Anna Children's Cancer Research Institute in Vienna to talk about her work on Epigenome-based precision medicine.

The Tomazou lab studies Ewing sarcoma and the effects of Epigenetic factors on this disease. Ewing sarcoma is a type of cancer that affects bone and soft tissue of children and young adults, with a peak incidence at the age of 15. Ewing sarcoma is among the pediatric cancer types with the lowest survival rates and the development of novel therapies was obstructed by the limited understanding of the mechanisms behind the disease.

Work done in Eleni Tomazou's group identified an epigenetic signature of Ewing sarcoma which, ultimately, lead to the possibility to diagnose Ewing sarcoma from liquid biopsies. The team is now looking to find actionable targets like enhancers to develop therapies, finding biomarkers to enable disease monitoring, and to further characterize these tumors to decipher intra-tumor epigenetic heterogeneity and characterize the developmental stage of the cell of origin.

Yad Ghavi-Helm headshot

Enhancer-Promoter Interactions During Development (Yad Ghavi-Helm)

Episode 67

February 9, 2022

In this episode of the Epigenetics Podcast, we caught up with Yad Ghavi-Helm from the Institut de Génomique Functionnelle de Lyon to talk about her work on enhancer-promoter interactions during development.

The Laboratory of Yad Ghavi-Helm focuses on how developmental genes are regulated by enhancers. Their work shows that developmental genes are often regulated by more than one enhancer and that those enhancers can often be located many kilobases away on the linear chromosome. Furthermore, their research also indicates that the interactions between promoters and their respective enhancers are usually established before the expression of the target gene is switched on, and that those interactions are generally stable during embryogenesis. In addition, those stable interactions seem to coincide with paused RNA Pol II being located at those promoters before gene activation.

Folami Ideraabdullah headshot

The Effect of Vitamin D on the Epigenome (Folami Ideraabdullah)

Episode 66

January 26, 2022

In this episode of the Epigenetics Podcast, we caught up with Folami Ideraabdullah from the University of North Carolina at Chapel Hill to talk about her work on the environmental modulation of the epigenome during development.

The lab of Folami Ideraabdullah focuses on studying how environmental factors modulate the epigenome. In particular the team investigates how Vitamin D levels influence epigenetic processes and, hence, the susceptibility for diseases like adipositas. Folami Ideraabdullah started with a genome-wide screen of DNA Methylation patterns that are observed after Vitamin D depletion. This work was then followed up by investigating the impact of Vitamin D depletion on mouse sperm DNA methylation.

Emily Bernstein headshot

H3K4me3, SET Proteins, Isw1, and their Role in Transcription (Jane Mellor)

Episode 65

January 12, 2022

In this episode of the Epigenetics Podcast, we caught up with Jane Mellor from the University of Oxford to talk about her work on H3K4me3, SET proteins, Isw1 and their role in transcription.

Since the beginning of the century, Jane Mellor and her team have focused on H3K4 trimethylation and the factors that influence this mark. They discovered that H3K4me3 is an almost universal mark of the first nucleosome in every transcribed unit and all organisms. She could subsequently, together with the Tony Kouzarides lab, identify SetD1, the enzyme that is responsible for writing this modification. Later on, the team characterized Isw1, a chromatin remodeler which “reads” H3K4me3. More recently the lab focuses on how the polymerase transcribes throughout the first nucleosomes of the transcribed region at the +2 nucleosome, with the help of Spt4.

Emily Bernstein headshot

The Role of DNA Methylation in Epilepsy (Katja Kobow)

Episode 64

December 15, 2021

In this episode of the Epigenetics Podcast, we caught up with Katja Kobow from the Universitätsklinikum Erlangen to talk about her work on the role of DNA methylation in Epilepsy.

Katja Kobow started studying the role of Epigenetics in Epilepsy by doing a genome wide Bisulfite-Sequencing screen that revealed a typical DNA methylation signature of epileptic patients versus healthy controls. After these initial results in human patient samples, she switched to an animal model to investigate this further. Now the focus of the Kobow Lab is to look for the same DNA methylation signature in blood samples, using this as a basis for the development of a potential prognostic marker for Epilepsy.

Jane Skok headshot

Spatio-Temporal Alterations in Chromosome Dynamics (Jane Skok)

Episode 62

November 17, 2021

In this episode of the Epigenetics Podcast, we caught up with Jane Skok from New York University School of Medicine to talk about her work on spatio-temporal alterations in chromosome dynamics.

Studies demonstrating that nuclear organization and long-range chromatin interactions play essential roles in gene regulation have been the focus of the Skok Lab, where the team has played a leading role. Their initial studies focused on lymphocyte development and the control of V(D)J recombination, a key part of generating the diverse repertoire of B-cell antibodies and T-cell receptors. The Skok Lab was among the first to demonstrate the possibility of chromatin forming dynamic loops which lead to the formation of reversible intra-locus loops in the immunoglobulin and T-cell receptor loci and to a profound impact on the ability of B and T cells to generate receptor diversity.

Marieke Oudelaar headshot

Chromatin Organization During Development and Disease (Marieke Oudelaar)

Episode 61

November 10, 2021

In this episode of the Epigenetics Podcast, we caught up with Marieke Oudelaar from the Max Planck Institute for Biophysical Chemistry to talk about her work on chromatin organization during development and disease.

Marieke Oudelaar and her team focus on on developing high-resolution Chromosome Conformation Capture (3C) based techniques, like low-input Capture-C, Tri-C, and Tiled-C. Those techniques are then used in combination with other genomic techniques, genetic perturbations, and computational approaches to investigate the 3D structure of chromatin in development and disease. The team focused on the interplay between genome organisation and regulation during mammalian differentiation, and how perturbations in these processes contribute to human disease, including cancer.

Camila dos Santos headshot

Enhancers and Chromatin Remodeling in Mammary Gland Development (Camila dos Santos)

Episode 60

October 28, 2021

In this episode of the Epigenetics Podcast, we caught up with Camila dos Santos from Cold Spring Harbor Laboratories to talk about her work on enhancers and chromatin remodeling in mammary gland development.

The lab of Camila dos Santos focuses on epigenetic regulation of normal and malignant mammary gland development. After puberty, the next significant phase in mammary gland development occurs in pregnancy, including changes in cellular function, and tissue reorganization. A different and as significant change in mammary glands occurs in the development breast cancer.

Camila dos Santos and her lab were recently able to show that the reaction of mammary glands to a second pregnancy is different than to a first one, which is accompanied by changes in the DNA methylome of the cells. Furthermore, the lab studies the connection of pregnancy-induced epigenetic changes of chromatin and the risk of cancer development.

Marnie Blewitt headshot

The Role of SMCHD1 in Development and Disease (Marnie Blewitt)

Episode 59

October 14, 2021

In this episode of the Epigenetics Podcast, we caught up with Marnie Blewitt from the Walter and Eliza Hall Institute of Medical Research to talk about her work on the role of SMCHD1 in Development and Disease.

The Laboratory of Marnie Blewitt focuses finding inhibitors or activators for the epigenetic regulator SMCHD1. Marnie Blewitt identified and characterized this protein during her PhD and the findings were published in 2008 in Nature Genetics. Since then, she and her team were able to investigate the function of this protein further. By doing so, they showed the involvement of SMCHD1 in cancer and several other diseases. Currently the lab is screening for small molecules that can act as inhibitors or activators of SMCHD1 the former as potential treatments for facioscapulohumeral muscular dystrophy, the latter for Prader Willi and Schaaf-Yang syndromes, both of which have no current targeted treatments.

Efrat Shema headshot

Single-Molecule Imaging of the Epigenome (Efrat Shema)

Episode 58

September 30, 2021

In this episode of the Epigenetics Podcast, we caught up with Efrat Shema from the Weizmann Institute of Science to talk about her work on Single Molecule Imaging of chromatin, and the analysis of nucleosomes circulating in plasma.

In ChIP-Seq experiments the peak you get as a read out represents an average over, most often, millions of cells. Furthermore, one often does not know if that peak represents one or more than one nucleosome. If you then want to study multiple marks at the same time, the question remains: do those modifications occur at the same time, in the same cell?

The Laboratory of Efrat Shema works on answering those questions by developing methods to study the modification patterns on single nucleosomes with single molecule imaging. With that it is possible to study single nucleosomes in a high throughout manner to identify the modifications they are decorated with. A subsequent sequencing step makes it possible to identify the genomic location of that nucleosome.

Serena Sanulli headshot

Heterochromatin Protein 1 and its Influence on the Structure of Chromatin (Serena Sanulli)

Episode 57

September 16, 2021

In this episode of the Epigenetics Podcast, we caught up with Serena Sanulli from Stanford University to talk about her work on Heterochromatin Protein 1 (HP1), the structure of chromatin on the atomic-scale and the meso-scale, and phase separation.

The Laboratory of Serena Sanulli is interested in finding connections between changes that happen on the nucleosomal level and the resulting impact on chromatin conformation on the meso-scale. They combine methods like NMR and Hydrogen-Deuterium Exchange-MS with Cell Biology and Genetics. This enables them to dissect how cells use the diverse biophysical properties of chromatin to regulate gene expression across length and time scales.

A second focus of the lab is HP1, which interacts with the nucleosome and changes its conformation, enabling the compaction of the genome into heterochromatin, effectively silencing genes in that region. A high concentration of HP1 leads to the phenomenon of phase separation in the nucleus, which the Sanulli lab is now investigating.

Catherine J. Peña headshot

The Effects of Early Life Stress on Mammalian Development (Catherine J. Peña)

Episode 56

September 2, 2021

In this episode of the Epigenetics Podcast, we caught up with Catherine Jensen Peña from Princeton University to talk about her work on early life stress and its effects on behavior.

The Peña lab focuses on how early life experiences are encoded and maintained into adulthood, with a long-lasting impact on behavior. Recent work shows that child maltreatment and other forms of early life stress increase the lifetime risk of depression and other mood, anxiety, and drug disorders by 2-4 fold. The Peña lab uses genome wide approaches to investigate key brain regions with a two-hit stress model.

Using RNA-Seq, the Peña Lab has shown that depression-like gene expression patterns are programmed by early life stress, similar to observations in mice exhibiting depression-like behavior after adult stress and are visible even before behavioral changes. Furthermore, latent and unique transcriptional responses to adult stress among a subset of genes is programmed by early life stress. The role of chromatin modifications in regulating these processes are investigated using state of the art technologies like Mod-Spec or ATAC-Seq.

Yael David headshot

Effects of Non-Enzymatic Covalent Histone Modifications on Chromatin (Yael David)

Episode 54

August 5, 2021

In this episode of the Epigenetics Podcast, we caught up with Yael David from Memorial Sloan Kettering Cancer Center in New York to talk about her work on Effects of Non-Enzymatic Covalent Histone Modifications on Chromatin.

The David lab studies on non-enzymatic covalent modifications of Histones, including Histone glycation and citrullination. These modifications recognize metabolites that are produced in the cell and aid as a sensor for chromatin to quickly adapt to cellular changes. These unique modifications do not have a so-called erasing enzyme, which makes them terminal, rendering these sites inaccessible for further modifications such as methylation or acetylation.

A second area of research in the David lab is Histone H1. The lab has developed a new method to purify Histone H1, superior to the commonly used method of acid extraction which leads to degradation of Histone H1. This purification method enabled the lab to purify and characterize the functional properties of all Histone H1 variants.

Karmella Haynes headshot

Synthetic Chromatin Epigenetics (Karmella Haynes)

Episode 52

July 8, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Karmella Haynes from Emory University to talk about her work on synthetic chromatin epigenetics, specifically on the design of synthetic chromatin sensor proteins. The first one of its kind, the Polycomb Transcription Factor (PcTF), senses H3K27me3 and recruits effector proteins to the sites of this modification. This sensor can be brought into cancer cells to activate hundreds of silenced genes. The lab hopes to characterize these effects genome wide and seeks to find a way to deliver those sensor into cancer cells, without affecting healthy cells.

In this Episode we discuss how Karmella Haynes got into the field of Epigenetics and the way she came to learn how important the right control experiments are. In the end we also discuss her activities to promote diversity and inclusion in science.

Enrico Glaab headshot

Development of Integrative Machine Learning Tools for Neurodegenerative Diseases (Enrico Glaab)

Episode 51

June 24, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Enrico Glaab from the University of Luxembourg to talk about his work on the development of integrative machine learning tools for neurodegenerative diseases. The work of Dr. Enrico Glaab focuses on neurodegenerative disorders like Parkinson’s and Alzheimer’s disease. In his group his team works on the development of software tools to analyze molecular, clinical and neuroimaging data for those diseases that can be used and applied easily by scientists and deliver publication ready figures. More recently, Enrico Glaab's group got interested in the influence of Epigenetics in Parkinson's and Alzheimer's disease.

Diane Dickel headshot

Ultraconserved Enhancers and Enhancer Redundancy (Diane Dickel)

Episode 50

June 10, 2021

In our 50th episode of the Epigenetics Podcast, we caught up with Dr. Diane Dickel from Lawrence Berkeley National Laboratory to talk about her work on ultraconserved enhancers and enhancer redundancy. We discuss how Diane Dickel and her team try to identify and characterize enhancers at a genomic scale and use CRISPR/CAS9 to mutate enhancer sequences in order to understand sequence dependent functional relevance. In addition, we chat about what ultraconservation actually means, how enhancer redundancy works and how Diane Dickel dealt with a failed PhD project.

Sandra Hake headshot

Variants of Core Histones: Modulators of Chromatin Structure and Function (Sandra Hake)

Episode 49

May 27, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Sandra Hake from the Justus Liebig University in Giessen to talk about her work on variants of core histones and their role as modulators of chromatin structure and function. In addition to discussing her approach to the characterization and identification of novel histone variants like H3.3, H3.X and H3.Y, we talk about what it's like to work in a small field like histone variants and what is coming up next for the Hake lab.

Charlotte Ling headshot

Effects of DNA Methylation on Diabetes (Charlotte Ling)

Episode 45

April 1, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Charlotte Ling from Lund University in Sweden, to talk about her work on the role of DNA methylation in diabetes. The Ling lab investigates how differently methylated DNA is associated with diabetes risk, with its successful treatment, and how it can change with exercise. We discuss how Charlotte Ling ended up in the field of diabetes and how the results of her work are now used to develop blood-based biomarkers.

Monica Dus headshot

Nutriepigenetics: The Effects of Diet on Behavior (Monica Dus)

Episode 44

March 18, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Monica Dus from the University of Michigan to talk about her work on nutriepigenetics and the effects of diet on behavior. The Dus lab is attempting to understand why animals are more likely to overeat if they consume foods rich in sugar, salt, and fat. We discuss how the sensory neurons of fruit flies can be reprogrammed with a high sugar diet, affecting both the taste and amount of they eat.

Céline Vallot headshot

Investigating the Dynamics of Epigenetic Plasticity in Cancer with Single Cell Technologies (Céline Vallot)

Episode 43

March 3, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Céline Vallot from L'Institut Curie in Paris to discuss her work on investigating the dynamics of epigenetic plasticity in cancer with single cell technologies. We discuss how she had her once-in-a-lifetime scientific eureka-moment, when, during her postdoc, she first saw XACT coating the whole X-Chromosome in humans and then how she pivoted when starting her own lab and focuses now on single-cell epigenomics in cancer.

Keji Zhao headshot

Genome-Wide Investigation of Epigenetic Marks and Nucleosome Positioning (Keji Zhao)

Episode 41

February 4, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Keji Zhao from the National Heart, Lung, and Blood Institute at the National Institutes of Health in Bethesda, MD, to talk about his work on the genome-wide investigation of epigenetic marks and nucleosome positioning. We also discuss the story behind how Dr. Keji Zhao was one of the pioneers of the chromatin immunoprecipitation technology, how he discovered the genomic locations of HATs and HDACs, and in the end he shares some tips and tricks on how to get the best results in ChIP-Seq assays.

Sarah Diermeier headshot

The Role of lncRNAs in Tumor Growth and Treatment (Sarah Diermeier)

Episode 40

January 20, 2021

In this episode of the Epigenetics Podcast, we caught up with Dr. Sarah Diermeier from the University of Otago in New Zealand to talk about her work on the role of long non-coding RNAs in tumor growth and treatment. This episode also tells the stories behind how Dr. Sarah Diermeier ended up in New Zealand, how her childhood influenced her career path, the role of lncRNAs in cancer, and how she deals with being a young PI and a mother at the same time.

Sandra Atlante & Carlo Gaetano headshot

The Epigenetics of COVID-19 (Sandra Atlante & Carlo Gaetano)

Episode 37

December 3, 2020

In this episode of the Epigenetics Podcast, we caught up with Dr. Sandra Atlante and Dr. Carlo Gaetano from the Istituti Clinici Scientifici Maugeri in Pavia, Italy, to talk about the roles epigenetic mechanisms play in COVID-19. In this episode we discuss how Dr. Atlante and Dr. Gaetano set up studies to investigate the epigenetic response to a SARS-CoV-2 infection, which epigenetic factors play a role in COVID-19 disease progression, and what we can expect from mutations of the virus in the future.

Srinivas Ramachandran headshot

In Vivo Nucleosome Structure and Dynamics (Srinivas Ramachandran)

Episode 35

November 18, 2020

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.

Ken Zaret headshot

Pioneer Transcription Factors and Their Influence on Chromatin Structure (Ken Zaret)

Episode 34

November 4, 2020

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.

Hodaka Fujii headshot

Development of Site-Specific ChIP Technologies (Hodaka Fujii)

Episode 32

October 1, 2020

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.

Christine Cucinotta & Melvin Noe Gonzalez headshots

How the "Fragile Nucleosome" Science Community Came to Life (Christine Cucinotta, Melvin Noe Gonzalez)

Episode 30

September 10, 2020

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.

Isabelle Mansuy headshot

Epigenetic Influence on Memory Formation and Inheritance (Isabelle Mansuy)

Episode 29

September 3, 2020

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.

Chuan He headshot

Influence of Dynamic RNA Methylation on Gene Expression (Chuan He)

Episode 28

August 20, 2020

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.

Michelle Trenkmann headshot

How to Publish in Nature: Lessons from the ENCODE Consortium (Michelle Trenkmann, Senior Editor at Nature)

Episode 27

August 6, 2020

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.

Bill Earnshaw headshot

The Role of Non-Histone Proteins in Chromosome Structure and Function During Mitosis (Bill Earnshaw)

Episode 26

July 23, 2020

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!

Leonid Mirny headshot

Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)

Episode 23

June 4, 2020

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.

Bing Ren headshot

Identification of Functional Elements in the Genome (Bing Ren)

Episode 21

May 7, 2020

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).

Tom Moss headshot

Chromatin Structure and Dynamics at Ribosomal RNA Genes (Tom Moss)

Episode 19

March 24, 2020

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.

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Epigenetic Origins Of Heterogeneity And Disease (Andrew Pospisilik)

Episode 18

February 19, 2020

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.

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PIXUL: On the Leading Edge of Chromatin Shearing (Karol Bomsztyk and Tom Matula)

Episode 17

January 28, 2020

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.

Marcus Buschbeck headshot

Influence of Histone Variants on Chromatin Structure and Metabolism (Marcus Buschbeck)

Episode 16

December 16, 2019

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.

Lucy Stead headshot

Epigenetics & Glioblastoma: New Approaches to Treat Brain Cancer (Lucy Stead)

Episode 14

October 15, 2019

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.

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The Interchromatin Network Model (Ana Pombo)

Episode 12

August 12, 2019

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.

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Dosage Compensation in Drosophila (Asifa Akhtar)

Episode 11

July 16, 2019

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.

Jean-Sebastien Annicotte

Diabetes and Epigenetics (Jean-Sébastien Annicotte)

Episode 8

April 4, 2019

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.

Edith Heard headshot

Epigenetics and X-Inactivation (Edith Heard)

Episode 7

November 21, 2018

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.

Susan Gasser headshot

Chromatin Organization (Susan Gasser)

Episode 6

October 15, 2018

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.

Henk Stunnenberg headshot

Epigenomics (Henk Stunnenberg)

Episode 5

September 12, 2018

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.

Peter Tessarz headshot

Aging and Epigenetics (Peter Tessarz)

Episode 4

January 3, 2018

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.

David Jones headshot

Cancer and Epigenetics (David Jones)

Episode 3

October 31, 2017

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.

Ada and Don Olins headshots

The Nucleosome: From Atoms to Genomes (Ada and Don Olins)

Episode 2

September 11, 2017

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.