<style> #title { height: 100% !important; display: flex !important; flex-direction: column !important; justify-content: center !important; } </style> <section id="title" data-background="/images/presentations/bg.svg.png" data-transition-speed="slow"> # What is epigenetics? Nathan Sheffield <div class="bullet"> <img src="/images/external/uva_dgs_logo.svg" height="85"> <img src="/images/logo/logo_databio_long.svg" height="65"> </div> <span style="font-size:0.6em"><a href="http://www.databio.org/slides">www.databio.org/slides</a></span> </section> --- ## What is epigenetics? --- <div class="well"> There has always been a place in biology for words that have different meanings for different people. Epigenetics is an extreme case, because it has several meanings with independent roots. (Bird 2007) </div> <div class="well"> The meaning of the term "epigenetics" has itself undergone an evolution. (Felsenfeld 2014) </div> --- <div class="well"> the causal study of embryological development (Waddington 1957, The strategy of the genes) </div> <img src="/_modules/epigenetics/waddington-epigenetics-hilight.png" width="1000"> --- <img src="/_modules/epigenetics/epigenetic_landscape.jpg" width="800"> --- <div class="well"> The study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence (Riggs et al. 1996) </div> <img src="/_modules/epigenetics/division.svg" width="400"> --- <div class="well"> a change in the state of expression of a gene that does not involve a mutation, but that is nevertheless inherited in the absence of the signal (or event) that initiated the change. (Ptashne and Gant 2002) </div> <img src="/_modules/epigenetics/epigenetics-demo.svg" width="1000"> --- <div class="well"> the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. (Bird 2007) </div> <img src="/_modules/epigenetics/bird-epigenetics.svg" width="500"> --- ## What is epigenetics? <div class="well"> the causal study of embryological development (Waddington 1957, The strategy of the genes) </div> <div class="well"> The study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence (Riggs et al. 1996) </div> <div class="well"> a change in the state of expression of a gene that does not involve a mutation, but that is nevertheless inherited in the absence of the signal (or event) that initiated the change. (Ptashne and Gant 2002) </div> <div class="well"> the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. (Bird 2007) </div> --- ## What is epigenetics? <div class="well"> Epigenetics refers to changes in gene regulation brought about through modifications to the DNA's packaging proteins or the DNA molecules themselves without changing the underlying sequence. (Lord and Cruchaga 2014, Nature Neuroscience) </div> <div class="well"> the study of the mechanisms that allow cells to translate the nearly constant genome content of a multicellular organism into multiple functional and stable cellular conditions (Schwartzman and Tanay 2015) </div> <div class="well"> Epigenetic processes are a means by which endogenous and exogenous cues exert long-term control over gene expression (Nugent et al. 2015) </div> --- ## What is epigenetics? The pop definition: <div class="well"> The word literally means "on top of genetics," and it's the study of how individual genes can be activated or deactivated by life experiences. (<i>The Week</i>, 2013) </div> --- <img src="/_modules/epigenetics/week_epigenetics.png" width="750"> --- <img src="/_modules/epigenetics/discover_epigenetics.png" width="750"> --- <img src="/_modules/epigenetics/division.svg" width="350"> <img src="/_modules/epigenetics/division_human.svg" width="350" class="fragment"> --- ## What is epigenomics? <div class="well"> epigenomics is the study of the physical modifications, associations and conformations of genomic DNA sequences (Schwartzman and Tanay 2015) </div> <div class="well"> epigenomics is the study of the chemical modification and physical conformation of cellular DNA and bound proteins (Sheffield 2017) </div> <i>The word "epigenome" lacks the baggage of heritability.</i> --- <img src="/_modules/epigenetics/rosa2013_chromatin.png" width="550"> Rosa et al. 2013 --- ## Histone variants <img src="/_modules/epigenetics/Nucleosome_structure.png" width="650" style="background:white"> https://en.wikipedia.org/wiki/Histone_octamer --- ## Histone modification (PTM) <img src="/_modules/epigenetics/Histone_modifications.png" width="1000" style="background:white"> https://en.wikipedia.org/wiki/Histone --- ## DNA Methylation <img src="/_modules/epigenetics/dnameth_intro.svg" width="750"> --- ## Chromatin conformation <img src="/_modules/epigenetics/chromatin-conformation.png" width="900">