RCPA Lecture Epigenetic chanisms 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 chanisms 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 G P P G C P P thylated Functional DNA RNA Modified & variant Histones Chromatin remodellers Feinberg, R (2008) Nature 454: 711-715
DNA methylation Occurs mainly at CpG in mammalian DNA me me me Most CpGs are methylated Those that are not are clustered in CpG islands Most CpG islands within gene promoters thylation of CpG islands associated with gene silencing CpG density me me Gene
The Nucleosome
Histone tail modifications: Acetylated (H3K9Ac) = active how they can influence function Histone H3 Lysine 9 =H3K9 Covalent histone tail modifications Adapted from Felsenfeld & Groudine, 2003
Histone tail modifications: thylated (H3K9me3) = inactive how they can influence function Histone H3 Lysine 9 =H3K9 Covalent histone tail modifications Adapted from Felsenfeld & Groudine, 2003
H3K43 Histone tail modifications: how they can influence function Covalent histone tail modifications H3K27me3 Adapted from Felsenfeld & Groudine, 2003
The epigenetic code: sequence-specific signals, writers, marks, readers & erasers
Sequence-specific factors (signals) e.g. ncrna, transcription factors, bind to DNA.
Epigenetic modifiers (writers) e.g. methyltransferases) recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Epigenetic modifiers (writers) e.g. acetyl- & methyltransferases recruited. Epigenetic marks written.
Sequence-specific factors (signals) can be lost without affecting the memory of the epigenetic marks
Epigenetic marks bound by readers (complexes of chromatin proteins, which determine structure & function). Readers
Epigenetic marks bound by readers (complexes of chromatin proteins, which determine structure & function). Readers
Epigenetic marks erased e.g by lysine demethylases (LSDs), histone deacetylases (HDACs)
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
Epigenetic marks erased e.g by demethylases & deacetylases.
(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 H3K9me3 Readers: chromodomain proteins e.g. HP1, Polycomb Gene activation Writer: histone acetyltransferase (HAT) Writer: histone methyltransferase (HMT) Gene silencing
Lysine 9 of Histone H3: erasers H3K9Ac H3K9 H3K9me3 Eraser: histone deacetylase (HDAC) Eraser: lysine demethylase (LSD)
Well-studied epigenetic codes involving ncrna Sequencespecific factors writers X inactivation XIST RNA EZH2 HMTase Slc22a3/EMT silencing AIR ncrna within IGF2R G9a HMTase marks readers H3K27me3 Polycomb repressive complex 2 DNA methylation via DNA methyltranferase H3K27me3 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 Acknowledgements Admin Assistants Boistats/bioinformatics Hien Ng John Carlin Gerri McIlroy Lavinia Gordon The Lab Katherine Smith Miina Ollikainen John Galati Boris Novakovic Gordon Smyth Mandy Parkinson-Bates Alicia Oshlak HK Ng Anna Czajko MCRI Eric Joo Stefan White Bobbie Andronikos Stanley Ho Nisa Abdul Aziz Nicole Carson Jane Loke St Vincent s Hospital Kerin O Dea
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/