Epigenetics Podcast

Epigenomics (Henk Stunnenberg)

In the fifth Episode of the Epigenetics Podcast of Active Motif our host Dr. Stefan Dillinger sits down with Prof. Henk Stunnenberg, full professor and head of the Department of Molecular Biology at the Radboud University in Nijmegen, to talk about his research in Epigenetics and his contributions to the BLUEPRINT and Human Cell Atlas consortia.
References
Stunnenberg Lab - http://molbio.science.ru.nl/about/molecular-biology/henk-stunnenberg/
The Blueprint Consortium - http://www.blueprint-epigenome.eu
Human Cell Atlas - https://www.humancellatlas.org/
Hendrik G. Stunnenberg, Sergio Abrignani, … Martin Hirst (2016) The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery (Cell) DOI: 10.1016/j.cell.2016.11.007
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Aging and Epigenetics (Peter Tessarz)

The aging population and challenges that arise from aging are one of the great scientific challenges of this time. In the fourth episode of the Epigenetics Podcast from Active Motif, our host Dr. Stefan Dillinger talks with Dr. Peter Tessarz from the Max Planck Institute for Biology of Ageing about his contributions to the field of aging and also, which epigenetic factors play a role in this process.
References for this episode:
Tessarz Lab: https://www.age.mpg.de/science/research-labs/tessarz/
Hayflick, Moorhead. 1961. The serial cultivation of human diploid cell strains. Exp Cell Res. Dec;25:585-621.
Donna Lowe, Steve Horvath and Kenneth Raj. 2016. Epigenetic clock analyses of cellular senescence and ageing. Oncotarget. 2016; 7:8524-8531. https://doi.org/10.18632/oncotarget.7383
Peter Tessarz, Helena Santos-Rosa, … Tony Kouzarides. 2014. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature. 2014 Jan 23; 505, 564–568. doi:10.1038/nature12819
Peter Tessarz, Tony Kouzarides. 2014. Histone core modifications regulating nucleosome structure and dynamics. Nature Reviews Molecular Cell Biology. 2014 Oct 15: 15, 703–708. doi:10.1038/nrm3890
Payel Sen, Parisha P. Shah, Rafaella Nativio, & Shelley L. Berger. 2016. Epigenetic Mechanisms of Longevity and Aging. Cell. 2016 Aug 11: 166,4,822-839. DOI: http://dx.doi.org/10.1016/j.cell.2016.07.050
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Cancer and Epigenetics (David Jones)

Cancer has become one of the most dangerous diseases of the aging population of industrialized countries. Finding tools to fight cancer is hard, because Cancer presents itself as highly heterogeneous, with over 100 types of cancers described. Not only does Cancer affect aged humans, it has been observed in children in the form of e.g. Medulloblastoma. In the third episode of Active Motif's Epigenetics Podcast, our host Dr. Stefan Dillinger sits down with Dr. David Jones, group leader at the German Cancer Research Center in Heidelberg, to talk about his research on Medulloblastoma and also the emerging role of epigenetic factors in Cancer.
References for this episode
Alioto, Ivo Buchhalter, … Ivo G. Gut. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications. 2015 Dec 9; 6, Article number: 10001 doi:10.1038/ncomms10001
David TW Jones, Natalie Jäger, … Peter Lichter. ICGC PedBrain: Dissecting the genomic complexity underlying medulloblastoma. Nature. 2012 Aug 2; 488(7409): 100–105. doi:10.1038/nature11284
Jeremy Schwartzentruber, Andrey Korshunov, … Nada Jabado. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012 Feb 9; 482, 226–231 doi:10.1038/nature10833
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The Nucleosome (Ada and Don Olins)

The Nucleosome is the basic building unit of chromatin. It consists out of 147 base pairs of double stranded DNA wrapped around the Histone core octamer that consists out of 2 copies of each dimer of H2A/H2B, and H3/H4. Nucleosomes are organized like "beads on a string" to form a modifiable regulatory basis for higher order structures of chromatin. The first images of the nucleosome as a particle was published by our guests Ada and Don Olins from the University of New England in 1974 (Olins, A. L. & Olins, D. E. Spheroid Chromatin Units (ν Bodies). Science 183, 330–332 (1974).). This observation lead the way to numerous discoveries around chromatin which ultimately culminated in the discovery of the 2.8 Angstrom high-resolution crystal structure 20 years ago in the year 1997 (Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260 (1997).)
References for this episode
Ada L. Olins, Donald E. Olins. Spheroid Chromatin Units (ν Bodies). Science. 25 Jan 1974: Vol. 183, Issue 4122, pp. 330-332. DOI: 10.1126/science.183.4122.330
Ada L. Olins, Donald E. Olins, et al. An epichromatin epitope. Nucleus. 2011 Jan-Feb; 2(1): 47–60. DOI: 10.4161/nucl.2.1.13271
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Multiple Challenges in ChIP (Adam Blattler)

Chromatin Immunoprecipitation (ChIP) was first developed in Drosophila, where interactions of RNA Pol II with genes were investigated (Mol. Cell. Biol. August 1985 vol. 5 no. 8 2009-2018). Then, in a 1993 publication, (Genes & Dev. 1993 7:592-604), the group of James Broach described the association of histone acetylation state with transcriptional gene silencing in yeast. The technique was first used successfully in mammalian cells by Richard Treisman's group, published in 1998 (Cell (1998) 92:475-87).Chromatin Immunoprecipitation is used to link specific states of chromatin to individual loci in a cell, to understand how genes are regulated, and to decipher the Histone Code. In this Episode, we discuss the multiple challenges of ChIP experiments and the difficulties that can arise during different steps of the process.
References for this episode
Epigenetics News:
Chung-Chau Hon, Jordan A. Ramilowski, … Alistair R. R. Forrest. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature. March 2017. doi:10.1038/nature21374
Jennifer L. Guerriero, Alaba Sotayo, … Anthony Letai. Class IIa HDAC inhibition reduces breast tumours and metastases through anti-tumour macrophages. Nature. March 2017. doi:10.1038/nature21409
Nitika Taneja, Martin Zofall, … Shiv I. S. Grewal. SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication. Molecular Cell. April 2017. DOI:10.1016/j.molcel.2017.02.006
Multiple Challenges in ChIP
D. S. Gilmour, J. T. Lis. In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Molecular and Cellular Biology. August 1985. doi:10.1128/MCB.5.8.2009
M. Braunstein, A. B. Rose, … J. R. Broach. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes & Development. 1993. doi:10.1101/gad.7.4.592
Arthur S. Alberts, Olivier Geneste, Richard Treisman. Activation of SRF-Regulated Chromosomal Templates by Rho-Family GTPases Requires a Signal that Also Induces H4 Hyperacetylation. Cell. February 1986. doi:10.1016/S0092-8674(00)80941-1
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