In this episode of the Epigenetics Podcast, we caught up with Margaret (“Peggy”) Goodell from Baylor College of Medicine in Houston, Texas to talk about her work on the epigenetic regulation of stem cell self-renewal and differentiation.

Dr. Margret Goodell's laboratory focuses on how differentiation and self-renewal is regulated in hematopoietic stem cells (HSC). In the early stages of her research career, however, Dr. Goodell was able to develop a new method to purify stem cells. This method was based on the characteristic of stem cells to pump out the Hoechst dye that was used for the purification.

In recent years, the focus of the lab has been to identify how HSCs decide whether to self-renew or differentiate. To get an answer to this question, the lab has performed genome-wide screens to find differentially expressed genes during the decision process. By doing that, they recently found that the DNA methyltransferase 3A (DNMT3A) was highly and specifically expressed in HSCs and that it is required for differentiation. When DNMT3A was knocked out in HSCs, the cell population expanded dramatically and the ability to differentiate was impaired. This finding led to further experiments in this area and to the discovery of so-called DNA methylation canyons in the genome, which are large regions of very low DNA methylation that harbor highly conserved regulator genes.

In this episode we discuss how Dr. Peggy Goodell described a new approach to isolate hematopoietic stem cells even though she was not looking for that, how she discovered DNMT3A as an important factor in stem cell decision making, and how she entered and approached new fields of research along the path of her research career. 

References

• M. A. Goodell, K. Brose, … R. C. Mulligan (1996) Isolation and functional properties of murine hematopoietic stem cells that are replicating in vivo (The Journal of Experimental Medicine) DOI: 10.1084/jem.183.4.1797

Related Episodes

• Epigenetic Reprogramming During Mammalian Development (Wolf Reik)

Contact

• Active Motif on Twitter

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.

Dr. Keji Zhao pioneered in the development of cutting-edge techniques in the field of epigenetics. Current methods at that time relied on DNA microarrays, however, Dr. Zhao wanted a more comprehensive and unbiased approach that would avoid the shortfalls of these array-based methods. Hence, he set out to develop new sequencing-based methods like ChIP-Seq and MNase-Seq with accompanying computational methods to analyze the huge amount of sequencing data that would be generated.

Using the above-mentioned techniques, Dr. Zhao was able to show that histone deacetylases (HDACs) and histone acetyltransferases (HATs) were found at inactive and active genes, respectively, as previously thought. Surprisingly, he was also able to show that HDACs were also located at active genes. Furthermore, both, HATs and HDACs can be found at low levels at silenced genes.

In this episode we 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.

References

• Artem Barski, Suresh Cuddapah, … Keji Zhao (2007) High-resolution profiling of histone methylations in the human genome (Cell) DOI: 10.1016/j.cell.2007.05.009

Related Episodes

• In Vivo Nucleosome Structure and Dynamics (Srinivas Ramachandran)

Contact

• Active Motif on Twitter

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.

Although only 1-2% of the human genome is transcribed into mRNAs that code for proteins, 75% of the genome is transcribed into non-coding RNAs. The function of these non-coding RNAs lie in the regulation of cellular processes and hence, offer the possibility of therapeutic intervention. Dr. Diermeier and her laboratory focus on a subset of these non-coding RNAs: the long non-coding RNAs (lncRNAs) that have been shown to play a role in breast and colorectal cancers.

This interview discusses how the Diermeier lab uses state-of-the-art techniques to both answer fundamental questions about biological mechanisms and also for translational research approaches. We also touch upon Dr. Diermeier becoming mother during her first years being a PI and the challenges and opportunities faced while raising a child and running a lab, and how the University of Otago and the State of New Zealand support young mothers in science.

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.

References

• R. Gualdi, P. Bossard, … K. S. Zaret (1996) Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control (Genes & Development) DOI: 10.1101/gad.10.13.1670

Related Episodes

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

Contact

• Active Motif on Twitter

In this episode of the Epigenetics Podcast, we caught up with Job Dekker from the University of Massachusetts Medical School to talk about his work on unraveling mechanisms of chromosome formation.

In 2002, during graduate school, Job Dekker was the first author on the paper describing the chromosome conformation capture (3C) method, which revolutionized the field of nuclear architecture. In the 3C protocol, chromatin is crosslinked using formaldehyde and then digested using a restriction enzyme. After ligating the digested blunt ends of crosslinked DNA fragments together they can be analyzed using qPCR. In the next couple of years 3C was further developed and methods like 4C, 5C, and Hi-C were published. This led to the generation of genome-wide contact maps which helped understand the 3-D organization of the nucleus.

Job Dekker’s research group is also part of the 4D Nucleome initiative, which is dedicated to understanding the structure of the human genome. More recent work of the lab includes analyzing interactions between and along sister chromatids with a method called SisterC and expanding their research to organisms like dinoflagellates to learn more about the basic organization principles of the genome.

In this episode, we discuss the story behind the idea of the chromosome conformation capture method, how close Job Dekker was to giving up on it, how the 3C methods evolved, the importance of data visualization, and we touch on parts of his current work on dinoflagellates.

References

• Job Dekker, Karsten Rippe, … Nancy Kleckner (2002) Capturing Chromosome Conformation (Science) DOI: 10.1126/science.1067799

Related Episodes

• Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden)

Contact

• Active Motif on Twitter

In this episode of the Epigenetics Podcast, we caught up with Dr. Danny Reinberg from the New York University School of Medicine to talk about his work on transcription and polycomb in inheritance and disease.

Dr. Danny Reinberg is a pioneer in the characterization of transcription factors for human RNA polymerase II. In his groundbreaking work in the 1990s, he purified the essential transcription factors and reconstituted the polymerase in vitro on both naked DNA and chromatin.  Dr. Reinberg next started focusing on the polycomb repressive complex 2 (PRC2), which is the only known methyltransferase for lysine 27 on histone H3. He biochemically characterized the PRC2 subunits EZH1 and EZH2. More recently, Dr. Reinberg has been investigating the role of PRC2 in neurons. 

This interview discusses the story behind how Dr. Danny Reinberg started his research career by identifying the essential RNA polymerase transcription factors, how he discovered and characterized the polycomb repressive complex 2 (PRC2), and what his research holds for the future.

References

• H. Lu, L. Zawel, … D. Reinberg (1992) Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II (Nature) DOI: 10.1038/358641a0

Contact

• Active Motif on Twitter

In this episode of the Epigenetics Podcast, we caught up with Dr. Sandra Atlante and Dr. Carlo Gaetano from the Instituti Clinici Scientifici Maugeri in Pavia, Italy, to talk about the roles epigenetic mechanisms play in COVID-19.

In early 2020 a novel coronavirus, SARS-CoV-2, emerged in Wuhan, China. This coronavirus causes the coronavirus disease 2019 (COVID-19) and rapidly spread all over the globe. In a worldwide effort, scientists and doctors tried to find drugs and looked for vaccines to help contain the spreading of the virus. It seems that an overreaction of the immune system, the so called "cytokine storm," could be one of the major complications of this disease. This reaction is not directly linked to the viral infection but is an overreaction of the body's own immune system. Therefore, small molecules that regulate gene expression via chromatin modifying enzymes might help keep the immune system in check.

In this episode we discuss how Dr. Gaetano and Dr. Atlante set up studies to investigate the epigenetic response to a SARS-CoV-2 infection, which epigenetic factors play a role in disease progression, and what we can expect from mutations of the virus in the future.

References

• Sandra Atlante, Alessia Mongelli, … Carlo Gaetano (2020) The epigenetic implication in coronavirus infection and therapy (Clinical Epigenetics) DOI: 10.1186/s13148-020-00946-x

Contact

• Active Motif on Twitter

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 the beginning of his research career, Dr. Wolf Reik worked on cellular reprogramming during embryogenesis. Epigenetic marks like DNA methylation or post-translational modifications of histone tails are removed and reprogrammed during embryogenesis, which can limit the amount of epigenetic information that can be passed on to future generations. However, this process is sometimes defective, which can lead to transgenerational epigenetic inheritance.

More recently, the laboratory of Dr. Wolf Reik has done pioneering work in the emerging field of single-cell experimental methods. The Reik lab developed a single-cell reduced representation bisulfite sequencing (scRRBS) approach to investigate DNA methylation at single-cell resolution. They also developed an integrated multi-omics approach called single-cell nucleosome, methylation, and transcription sequencing (scNMT-Seq) to map chromatin accessibility, DNA methylation, and RNA expression at the same time during the onset of gastrulation in mouse embryos.

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.

References

• W. Reik, A. Collick, … M. A. Surani (1987) Genomic imprinting determines methylation of parental alleles in transgenic mice (Nature) DOI: 10.1038/328248a0

Contact

• Active Motif on Twitter

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.

Dr. Srinivas Ramachandran studies the structure and dynamics of nucleosomes during cellular processes like transcription and DNA replication. During transcription, as the RNA polymerase transcribes along the DNA, it needs to pass nucleosomes. Dr. Ramachandran investigated the effect of nucleosomes on transcription and also studied how different histone variants affect this process. He found that the first nucleosome within a gene body is a barrier for the progression of RNA polymerase, and that presence of the histone variant H2A.Z in this first nucleosome lowers this barrier.

Furthermore, Dr. Ramachandran developed a method called mapping in vivo nascent chromatin using EdU and sequencing (MINCE-Seq), enabling the study of chromatin landscapes right after DNA replication. In MINCE-Seq, newly replicated DNA is labeled right after the replication fork has passed by with the nucleotide analog ethynyl deoxyuridine (EdU), which can then be coupled with biotin using click chemistry. After the purification of newly replicated DNA and MNase digestion, the chromatin landscape can be analyzed.

In this interview, 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.

References

• Christopher M. Weber, Srinivas Ramachandran, Steven Henikoff (2014) Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase (Molecular Cell) DOI: 10.1016/j.molcel.2014.02.014

Contact

• Active Motif on Twitter

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.

Embryonic development is a complex process that needs to be tightly regulated. Multiple regulatory factors contribute to proper development, including a family of specialized regulatory proteins called "pioneer factors." Our guest Dr. Ken Zaret found that these pioneer factors are among the first proteins to bind to chromatin during development and that they can prime important regulatory genes for activation at a later developmental stage. Furthermore, he and his team showed that there might be a "pre-pattern" that exists in cells that determines their developmental fate.

Pioneer factors are not only important in embryonic development, they can also help restart transcription after mitosis. Dr. Zaret and his colleagues demonstrated that FoxA stays bound to chromosomes during mitosis, leading to a rapid reactivation of essential genes at the exit of mitosis.

In this interview, 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.

References

• R. Gualdi, P. Bossard, … K. S. Zaret (1996) Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control (Genes & Development) DOI: 10.1101/gad.10.13.1670

Contact

• Active Motif on Twitter

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.

The most prominent example of transgenerational inheritance is the Dutch famine of 1944 during World War II. Effects of this famine could be observed in the grandchildren of people that lived through this hunger winter, but the molecular mechanisms involved remain largely unknown. The guest of this podcast episode, Dr. Rechavi, has taken on the challenge to unravel parts of this puzzle by studying transgenerational epigenetics in C. elegans.

It was already known that small RNA molecules could play a role in passing on information from one generation to the next, but it was not clear what exactly was being inherited. Was it RNAs? Or chromatin modifications? Or something else?

Dr. Rechavi made several important discoveries in his journey to answer these questions. He started out by showing that RNAi provides an antiviral protection mechanism in C. elegans that can be passed on over multiple generations. He then went on to show that starvation in one generation leads to changes in the lifespan of future generations, and investigate how long this memory could last. Simple dilution of the parental RNA in future generations could not be the answer because the inherited phenotypes lasted much longer than would be possible if this were the case. This led Dr. Rechavi to the discovery that small RNAs were amplified in each generation, and the effect of a stimulus could affect multiple generations. More recently, Dr. Rechavi and his team studied the interplay of neurons and the germ line and how information can be passed on from the brain to the germ line.

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 epigenetic factors play in this process.

References

• Oded Rechavi, Gregory Minevich, Oliver Hobert (2011) Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans (Cell) DOI: 10.1016/j.cell.2011.10.042

Contact

• Active Motif on Twitter