Epigenetic Mechanisms RCPA Lecture Jeff Craig Early Life
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RCPA Lecture Epigenetic Mechanisms Jeff Craig Early Life Epigenetics Group, MCRI Dept. of Paediatrics Overview • What is epigenetics? • Chromatin • The epigenetic code What is epigenetics? “the interactions of genes with their environment, which bring the phenotype into being” (Conrad Waddington, 1942, Endeavour, 1: 18) “the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence” (Art Riggs, 1996, in Epigenetic Mechanisms of Gene Regulation, CSHLP) “the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states” (Adrian Bird, 2007, Nature, 447: 396) What is epigenetics? • Intrinsic to development • Reversible • Involved in cancer & other complex diseases • Encoded in ‘chromatin’ Chromatin Epigenetics is mediated by chromatin P P C P G P G P C P Methylated Functional DNA RNA Modified & variant Histones Chromatin remodellers Feinberg, R (2008) Nature 454: 711-715 DNA methylation me me CpG density • Occurs mainly at CpG in mammalian DNA • Most CpGs are methylated • Those that are not are clustered in “CpG islands” • Most CpG islands within gene promoters • Methylation of CpG islands associated with gene silencing me me me Gene The Nucleosome Acetylated (H3K9Ac) Histone tail modifications: = active how they can influence function Histone H3 Lysine 9 =H3K9 Covalent histone tail modifications Adapted from Felsenfeld & Groudine, 2003 Methylated (H3K9me3) Histone tail modifications: = inactive how they can influence function Histone H3 Lysine 9 =H3K9 Covalent histone tail modifications Adapted from Felsenfeld & Groudine, 2003 H3K4Me3 Histone tail modifications: how they can influence function H3K27me3 Covalent histone tail modifications Adapted from Felsenfeld & Groudine, 2003 The epigenetic code: sequence-specific signals, writers, marks, readers & erasers How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Sequence-specific factors (signals) e.g. ncRNA, transcription factors, bind to DNA. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. methyltransferases) recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic modifiers (writers) e .g. acetyl- & methyltransferases recruited. • Epigenetic marks written. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Sequence-specific factors (signals) can be lost without affecting the “memory” of the epigenetic marks Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks bound by “readers” (complexes of chromatin proteins, which determine structure & function). Readers Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks bound by “readers” (complexes of chromatin proteins, which determine structure & function). Readers Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by lysine demethylases (LSDs), histone deacetylases (HDACs) Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me How does it all fit together? The Epigenetic code: signals, writers, marks, readers & erasers • Epigenetic marks erased e.g by demethylases & deacetylases. Me (redundancy in the system) http://en.wikipedia.org/wiki/Histone-modifying_enzymes Summary of the epigenetic code • Sequence-specific signals bind to DNA. • Writers recognise these signals and add epigenetic marks. • Epigenetic “memory” can be retained despite loss of the original signals. • Readers bind to epigenetic marks and recruit macromolecular complexes. • Erasers can remove these marks and associated macromolecular complexes. Lysine 9 of Histone H3: marks, writers & readers Readers: bromodomain proteins e.g. BRM | H3K9Ac H3K9 Gene activation Writer: histone acetyltransferase (HAT) Writer: histone methyltransferase (HMT) H3K9me3 | Readers: chromodomain proteins e.g. HP1, Polycomb Gene silencing Lysine 9 of Histone H3: erasers H3K9Ac H3K9 Eraser: histone deacetylase (HDAC) Eraser: lysine demethylase (LSD) H3K9me3 Well-studied epigenetic codes involving ncRNA Slc22a3/EMT X inactivation silencing Sequencespecific factors writers marks readers XIST RNA AIR ncRNA within IGF2R EZH2 HMTase G9a HMTase H3K27me3 H3K27me3 Polycomb repressive complex 2 DNA methylation via DNA methyltranferase Repressive complex Chromatin: a gradient between 2 extremes Loose & active euchromatin • Early replicating • Nuclear interior Tight & inactive heterochromatin • late replicating • Nuclear periphery The Histone Code governs other aspects of chromatin structure and function • • • • Expression potential Elongation Pre-mRNA splicing DNA damage Study coordinators Jeff Craig Richard Saffery Ruth Morley Obstetricians Euan Wallace Michael Permezel Mark Umstad Research Nurses Anne Krastev Sarah Healy Tina Vaiano Nicole Brooks Sheila Holland Jenny Foord Bernie McCudden St Vincent’s Hospital Kerin O’Dea Acknowledgements Admin Assistants Hien Ng Gerri McIlroy The Lab Miina Ollikainen Boris Novakovic Mandy Parkinson-Bates HK Ng Anna Czajko Eric Joo Bobbie Andronikos Nisa Abdul Aziz Nicole Carson Jane Loke Boistats/bioinformatics John Carlin Lavinia Gordon Katherine Smith John Galati Gordon Smyth Alicia Oshlak MCRI Stefan White Stanley Ho Resources • • • Recent reviews aimed at science undergraduates: • Jones PA et al (2008) Moving AHEAD with an international human epigenome project. Nature 454, 711-715. • Mathers, M (2008) Proc. Nutr. Soc. 67: 390 • Qiu, J (2006) Nature 441: 143 • Pray, L.A. (2004) The Scientist 18 Great articles on epigenetics aimed at a lay audience: • http://www.time.com/time/health/article/0,8599,1951968,00 .html • www.scienceinschool.org/repository/docs/issue2epigenetics.pdf • www.muktomona.com/Special_Event_/Darwin_day/evolution_asim120206.htm Web resources • Genetic Science Learning Center, University of Utah: http://learn.genetics.utah.edu • The Epigenome Network of excellence: http://epigenome.eu/
