Epigenetics Podcast

DNA Methylation and Mammalian Development (Déborah Bourc'his)

In this episode of the Epigenetics Podcast, we caught up with Déborah Bourc'his from L'Institut Curie in Paris to talk about her work on the role of DNA methylation in mammalian development.
During her postdoc years Déborah Bourc'his was able to characterize DNMT3L, a protein with unknown function at that time. It turned out that this protein is the cofactor responsible for stimulating DNA methylation activity in both the male and the female germline. Later on she discovered a novel DNA methylation enzyme called DNMT3C, which was unknown because it was not properly annotated, there was no sign of expression, and it was only expressed in male fetal germ cells. Furthermore, this enzyme only evolved in rodents, as a defense against young transposons.
In this episode we discuss the story behind how Déborah Bourc'his was able to discover and characterize the DNA methylation enzymes DNMT3L and DNMT3C and their role in mammalian development.
 
References
R. Duffie, S. Ajjan, … D. Bourc’his (2014) The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals (Genes & Development) DOI: 10.1101/gad.232058.113
Natasha Zamudio, Joan Barau, … Déborah Bourc’his (2015) DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination (Genes & Development) DOI: 10.1101/gad.257840.114](https://doi.org/10.1101/gad.257840.114)
Marius Walter, Aurélie Teissandier, … Déborah Bourc’his (2016) An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells (eLife) DOI: 10.7554/eLife.11418](https://doi.org/10.7554/eLife.11418)
Joan Barau, Aurélie Teissandier, … Déborah Bourc’his (2016) The DNA methyltransferase DNMT3C protects male germ cells from transposon activity (Science (New York, N.Y.)) DOI: 10.1126/science.aah5143
Maxim V. C. Greenberg, Juliane Glaser, … Déborah Bourc’his (2017) Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth (Nature Genetics) DOI: 10.1038/ng.3718
Roberta Ragazzini, Raquel Pérez-Palacios, … Raphaël Margueron (2019) EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells (Nature Communications) DOI: 10.1038/s41467-019-11800-x
Dura, M., Teissandier, A., Armand, M., Barau, J., Bonneville, L., Weber, M., Baudrin, L. G., Lameiras, S., & Bourc’his, D. (2021). DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis [Preprint]. Developmental Biology. https://doi.org/10.1101/2021.04.19.440465
 
Related Episodes
Effects of DNA Methylation on Diabetes (Charlotte Ling)
Epigenetic Reprogramming During Mammalian Development (Wolf Reik)
Effects of DNA Methylation on Chromatin Structure and Transcription (Dirk Schübeler)
CpG Islands, DNA Methylation, and Disease (Sir Adrian Bird)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

Chromatin Analysis using Mass Spectrometry (Axel Imhof)

In this episode of the Epigenetics Podcast, we caught up with Axel Imhof from the Ludwig Maximilian University of Munich in Germany to talk about his work on the identification of chromatin associated proteins using mass spectrometry.
As the head of the Proteomics Core Facility Axel Imhof collaborates with research groups around the world. In addition, in his own lab, he focuses on the assembly and composition of chromatin, how environmental metabolites influence epigenetic marks, and how chromatin factors can be used as markers for pathological states.
In this episode we discuss what has changed in the field of mass spectrometry over the years, how Axel Imhof takes advantage of collaborations, how metabolites influence chromatin, and how he is helping to bring epigenetic profiling via mass spectrometry to the clinic.
 
References
Bonaldi, T., Regula, J. T., & Imhof, A. (2003). The Use of Mass Spectrometry for the Analysis of Histone Modifications. In Methods in Enzymology (Vol. 377, pp. 111–130). Elsevier. https://doi.org/10.1016/S0076-6879(03)77006-2
Völker-Albert, M. C., Pusch, M. C., Fedisch, A., Schilcher, P., Schmidt, A., & Imhof, A. (2016). A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin. Molecular & Cellular Proteomics, 15(3), 945–959. https://doi.org/10.1074/mcp.M115.053553
Scharf, A. N. D., Meier, K., Seitz, V., Kremmer, E., Brehm, A., & Imhof, A. (2009). Monomethylation of Lysine 20 on Histone H4 Facilitates Chromatin Maturation. Molecular and Cellular Biology, 29(1), 57–67. https://doi.org/10.1128/MCB.00989-08
Van den Ackerveken, P., Lobbens, A., Turatsinze, J.-V., Solis-Mezarino, V., Völker-Albert, M., Imhof, A., & Herzog, M. (2021). A novel proteomics approach to epigenetic profiling of circulating nucleosomes. Scientific Reports, 11(1), 7256. https://doi.org/10.1038/s41598-021-86630-3
 
Related Episodes
Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni)
Transcription and Polycomb in Inheritance and Disease (Danny Reinberg)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC (Steven Henikoff)

In this episode of the Epigenetics Podcast, we caught up with Steven Henikoff from the Fred Hutchinson Cancer Research Center in Seattle to talk about his work on Chromatin Profiling: From ChIP to CUT&RUN, CUT&Tag and CUTAC.
In the last few years Steven Henikoff has been developing methods which profile the chromatin landscape by using enzyme tethering. The quest first started with ChEC-Seq, which improved on Uli Laemmli's method of Chromatin endogenous cleavage (ChEC) but used sequencing as a read-out rather than southern blotting. Next, Cleavage Under Targets & Release Using Nuclease (CUT&RUN) was developed by making a fusion protein of Protein A and micrococcal nuclease (MNase), making it possible to achieve antibody-targeted cleavage of chromatin fragments. And finally, Cleavage Under Targets & Tagmenation (CUT&Tag) was developed by using Transposase Tn5 instead of MNase, which adds sequencing adapters and fragments chromatin at the same time, streamlining the protocol even further.
In this episode we discuss how working on centromeres set the stage for Steven Henikoff’s subsequent work, how he developed CUT&RUN and CUT&Tag, what the advantages and disadvantages of those methods are and how he developed all those experiments at home in his garage.
 
References
Takehito Furuyama, Steven Henikoff (2009) Centromeric nucleosomes induce positive DNA supercoils (Cell) DOI: 10.1016/j.cell.2009.04.049
Kristina Krassovsky, Jorja G. Henikoff, Steven Henikoff (2012) Tripartite organization of centromeric chromatin in budding yeast (Proceedings of the National Academy of Sciences of the United States of America) DOI: 10.1073/pnas.1118898109
Jorja G. Henikoff, Jitendra Thakur, … Steven Henikoff (2015) A unique chromatin complex occupies young α-satellite arrays of human centromeres (Science Advances) DOI: 10.1126/sciadv.1400234
Epigenomics Methods: ChEC-Seq, CUT&RUN, AutoCUT&RUN, Improved CUT&RUN, CUT&Tag, Automated CUT&Tag, CUTAC, scCUT&Tag.
 
Related Episodes
The Role of Non-Histone Proteins in Chromosome Structure and Function During Mitosis (Bill Earnshaw)
Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden)
In Vivo Nucleosome Structure and Dynamics (Srinivas Ramachandran)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

Effects of DNA Methylation on Diabetes (Charlotte Ling)

In this episode of the Epigenetics Podcast, we caught up with Charlotte Ling from Lund University in Sweden, to talk about her work on the role of DNA methylation in diabetes.
Dr. Charlotte Ling investigates how epigenetics influences diabetes, a major age-related disease that affects millions of people around the world. She and her team identified CpG-SNPs and differentially methylated DNA in human pancreatic islets, associated with Type 2 Diabetes. In addition, she explored the impact of a six-month exercise intervention plan on DNA methylation and health in middle-aged diabetic men.
Later-on, looking for useful applications for this knowledge, she determined blood-based biomarkers for diabetes and for successful treatment with Metformin, a common drug used for diabetes patients.
In this episode we discuss how Charlotte Ling ended up in the field of diabetes, how the success of her work impacted her ability to go on vacations, and how the results of her work are now used to develop blood-based biomarkers.
 
References
Karl Bacos, Linn Gillberg, … Charlotte Ling (2016) Blood-based biomarkers of age-associated epigenetic changes in human islets associate with insulin secretion and diabetes (Nature Communications) DOI: 10.1038/ncomms11089
Sonia García-Calzón, Alexander Perfilyev, … Charlotte Ling (2020) Epigenetic markers associated with metformin response and intolerance in drug-naïve patients with type 2 diabetes (Science Translational Medicine) DOI: 10.1126/scitranslmed.aaz1803
Madhusudhan Bysani, Rasmus Agren, … Charlotte Ling (2019) ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes (Scientific Reports) DOI: 10.1038/s41598-019-44076-8
 
Related Episodes
Epigenetic Reprogramming During Mammalian Development (Wolf Reik)
Diabetes and Epigenetics (Jean-Sébastien Annicotte)
Nutriepigenetics: The Effects of Diet on Behavior (Monica Dus)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

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

In this episode of the Epigenetics Podcast, we caught up with Monica Dus from the University of Michigan to talk about her work on nutriepigenetics and the effects of diet on behavior.
The focus of Monica Dus and her team is to study the effect of sugar on the brain and how diet has an effect on behavior. The Dus lab takes a multidisciplinary approach to answer questions like "What causes animals to overeat if they consume foods rich in sugar, salt, and fat?" and "How does such a diet alter the basic physiology and biochemistry of the brain to promote food intake and weight gain?" By doing this, they showed recently that the Polycomb Repressive Complex 2 (PRC2) plays a role in reprogramming the sensory neurons of Drosophila Melanogaster, reducing sweet sensation and hence promoting obesity when flies are fed a high sugar diet. In response to that diet the binding of PRC2 to chromatin in sweet gustatory neurons is altered and reshapes the developmental transcriptional network.
In this episode we discuss how flies taste food and sugar, how sugar modulates taste, and how a high sugar diet influences the taste and amount of food flies eat.
 
References
Monica Dus, SooHong Min, … Greg S. B. Suh (2011) Taste-independent detection of the caloric content of sugar in Drosophila (Proceedings of the National Academy of Sciences of the United States of America) DOI: 10.1073/pnas.1017096108
Christina E. May, Anoumid Vaziri, … Monica Dus (2019) High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster (Cell Reports) DOI: 10.1016/j.celrep.2019.04.027
Daniel Wilinski, Jasmine Winzeler, … Monica Dus (2019) Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster (Nature Communications) DOI: 10.1038/s41467-019-11933-z
Anoumid Vaziri, Morteza Khabiri, … Monica Dus (2020) Persistent epigenetic reprogramming of sweet taste by diet (Science Advances) DOI: 10.1126/sciadv.abc8492
How to Science Podcast
NeuroEpic Podcast
 
Related Episodes
Transcription and Polycomb in Inheritance and Disease (Danny Reinberg)
The Role of Small RNAs in Transgenerational Inheritance in C. elegans (Oded Rechavi)
Epigenetic Origins Of Heterogeneity And Disease (Andrew Pospisilik)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

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

In this episode of the Epigenetics Podcast, we caught up with 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.
During her Post-Doc years Céline Vallot worked on the inactive X chromosome. Using RNA-Seq she discovered a novel long noncoding RNA (lncRNA) called XACT. This lncRNA is expressed from and coats the active X chromosome in human pluripotent cells. Céline Vallot also showed that XACT is specific to humans and cannot be found in mice.
After starting her own lab, Céline Vallot began to focus on Single Cell Epigenomics in Cancer. She and her team developed a high-throughput single-cell ChIP-seq approach which relies on a droplet microfluidics platform to profile the chromatin landscape of thousands of cells. By doing so they could show that a subset of cells within untreated drug-sensitive tumors share a common chromatin signature. This would have been impossible with common bulk approaches. These cells are characterized by the loss of H3K27me3, which leads to stable transcriptional repression, influencing genes that are known to promote resistance to treatment.
In this episode we discuss how Céline Vallot 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.
 
References
Céline Vallot, Christophe Huret, … Claire Rougeulle (2013) XACT , a long noncoding transcript coating the active X chromosome in human pluripotent cells (Nature Genetics) DOI: 10.1038/ng.2530
Kevin Grosselin, Adeline Durand, … Annabelle Gérard (2019) High-throughput single-cell ChIP-seq     identifies heterogeneity of chromatin states in breast cancer (Nature Genetics) DOI: 10.1038/s41588-019-0424-9
Pacôme Prompsy, Pia Kirchmeier, … Céline Vallot (2020) Interactive analysis of single-cell epigenomic landscapes with ChromSCape (Nature Communications) DOI: 10.1038/s41467-020-19542-x
Justine Marsolier, Pacôme Prompsy, … Céline Vallot (2021) H3K27me3 is a determinant of chemotolerance in triple-negative breast cancer (bioRxiv) DOI: 10.1101/2021.01.04.423386
 
Related Episodes
Dosage Compensation in Drosophila (Asifa Akhtar)
Epigenetics and X-Inactivation (Edith Heard)
Cancer and Epigenetics (David Jones)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

Epigenetic Regulation of Stem Cell Self-Renewal and Differentiation (Margaret “Peggy” Goodell)

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
Shannon McKinney-Freeman, Margaret A. Goodell (2004) Circulating hematopoietic stem cells do not efficiently home to bone marrow during homeostasis (Experimental Hematology) DOI: 10.1016/j.exphem.2004.06.010
Stuart M. Chambers, Chad A. Shaw, … Margaret A. Goodell (2007) Aging hematopoietic stem cells decline in function and exhibit epigenetic dysregulation (PLoS biology) DOI: 10.1371/journal.pbio.0050201
Grant A. Challen, Deqiang Sun, … Margaret A. Goodell (2011) Dnmt3a is essential for hematopoietic stem cell differentiation (Nature Genetics) DOI: 10.1038/ng.1009
 
Related Episodes
Epigenetic Reprogramming During Mammalian Development (Wolf Reik)
Effects of DNA Methylation on Chromatin Structure and Transcription (Dirk Schübeler)
CpG Islands, DNA Methylation, and Disease (Sir Adrian Bird)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com

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

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
Dustin E. Schones, Kairong Cui, … Keji Zhao (2008) Dynamic regulation of nucleosome positioning in the human genome (Cell) DOI: 10.1016/j.cell.2008.02.022
Zhibin Wang, Chongzhi Zang, … Keji Zhao (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes (Cell) DOI: 10.1016/j.cell.2009.06.049
Wenfei Jin, Qingsong Tang, … Keji Zhao (2015) Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples (Nature) DOI: 10.1038/nature15740
Binbin Lai, Weiwu Gao, … Keji Zhao (2018) Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing (Nature) DOI: 10.1038/s41586-018-0567-3
Related Episodes
In Vivo Nucleosome Structure and Dynamics (Srinivas Ramachandran)
Development of Site-Specific ChIP Technologies (Hodaka Fujii)
Multiple Challenges in ChIP (Adam Blattler)
 
Contact
Active Motif on Twitter
Epigenetics Podcast on Twitter
Active Motif on LinkedIn
Active Motif on Facebook
Email: podcast@activemotif.com