Deciphering the epigenetic code

Lead Research Organisation: Imperial College London
Department Name: Unlisted

Abstract

As every cell of our bodies contains every gene it follows that for cells to perform different functions some genes much be switched off and others switched on in a given cell type. These studies will examine how cells remember to keep some genes on and others off. We will do this by examining the way genes are packaged and labelled as on or off by directly looking at the packaging surrounding active and inactive genes. When these mechanisms go wrong this can lead to diseases, by understanding this process we hope to work out better ways to treat such diseases in the future.

Technical Summary

Histone tails protruding from the nucleosome are modified at selected amino acids, by e.g. lysine acetylation, lysine and arginine methylation, serine phosphorylation and attachment of ubiquitin, generating an epigenetic code thought to be essential for cells to establish and ?remember? specific programmes of gene expression during cellular differentiation.

Recently new insights have been gained into how single histone modifications affect chromatin function. However, to fully decipher the information capacity of histone tails, a better understanding is essential of how specific combinations of tail modifications are generated and how the modification of one residue can affect that of another.

The main tools presently used to study the epigenetic code are antibodies against specific histone modifications. Unfortunately, such approaches miss the potential effect of various combinations of histone modifications. Furthermore, it has been proven to be extremely difficult to generate antisera even to single histone modifications with a high enough selectivity, to distinguish between similar modifications on different residues or different modifications on the same residue, for example di-versus trimethylated histones.

It is now apparent that the application of high-resolution mass spectometry approaches should allow the unambiguous identification of histone modifications associated with particular chromatin fractions. Such techniques require specialist expertise which we will obtain by collaboration with Axel Imhof (University of Munich) allowing the establishment of this methodology for our use (and the use of others). Such methodology will negate the use of specific antisera or at least make their use less critical. Moreover, we also use mass spectrometry to better define the specificity of antibodies directed against histone modifications.

Genetic studies of the archetypal epigenetic phenomenon of position-effect variegation (PEV) have proved invaluable for identifying key components and modifiers of chromatin structure. In PEV, a gene located abnormally close to heterochromatin is stochastically silenced in a proportion of cells in which it is normally expressed. The extent of silencing in PEV is dependent on histone-modifying enzymes and proteins that bind to the specific sites created by these enzymes. In three model organisms (yeast, Drosophila and mice), we will determine the modifications associated with silent chromatin. Subsequently, the histone-tail residues carrying these modifications will then be altered by targeted mutagenesis (in yeast) to directly test the role of particular histone tail (H3 and H4) amino acids in the establishment of gene silencing/activation and centromere function.
 
Description Royal Society Post Doctoral Fellowship
Amount £120,000 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2006 
End 01/2009
 
Title HP1beta-bio 
Description Established a murine model to enable chromatin immunoprecipitation and purification of protein complexes using a biotin-tagged version of heterochromatin-protein 1 expressed in vivo. 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Provided To Others? No  
Impact Will enable epigenomic maps to be established for this protein using ex vivo tissue circumventing technical problems the field has faced related to use of antibodies for this purpose. 
 
Title HP1gamma transgenics 
Description Murine model to explore function of key chromatin component. 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Provided To Others? No  
Impact Established that this modifier is a potential modifier of heterochromatin-mediated silencing and triplet-repeat diseases. 
 
Title Identification of histone H3 K4acetylation as a novel post-translational modification using a novel antibody 
Description Polyclonal antibody specific to histone H3 lysine 4 acetylation 
Type Of Material Technology assay or reagent 
Year Produced 2011 
Provided To Others? Yes  
Impact Identification that histone H3 is modified on a key residue, lysine 4, in yeast and mammals. This changes our understanding of how gene's are regulated in eukaryotes as indicated by our genome-wide epigenomic and functional studies. 
 
Title TROY 
Description Epigenome bioinformatics tool to visualise gene expression profiles simulataneously with genome-wide data provided by chromatin immunoprecipitation. 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Provided To Others? No  
Impact Has allowed rapid identification an interrogation of regions of the genome responding to epigenetic modifiers 
 
Description AI 
Organisation Ludwig Maximilian University of Munich (LMU Munich)
Department Adolf Butenandt Institute
Country Germany 
Sector Academic/University 
PI Contribution Mass spectometry
Collaborator Contribution Identification of a novel histone modification
Impact Identification of a novel histone modification
 
Description KE 
Organisation Karolinska Institute
Country Sweden 
Sector Academic/University 
PI Contribution We discovered a novel histone modification, investigated its function and provided the antibody to enable chromatin immunoprecipitation
Collaborator Contribution Epigenomic mapping by microarray using chromatin immunorprecipitation
Impact Fundamental key information on the function of a novel histone modification in euakryotes
Start Year 2009
 
Description LA 
Organisation Medical Research Council (MRC)
Department MRC Clinical Sciences Centre (CSC)
Country United Kingdom 
Sector Public 
PI Contribution Initiated and established group working on histone modifications from yeast to mammals
Collaborator Contribution Expertise in yeast genetics
Impact Discovery and characterisation genome-wide of a novel histone modification central to transcriptional regulation.
 
Description RA 
Organisation Wellcome Trust
Department Wellcome Trust Centre for Cell Biology
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution PI on cross-disciplinary project to identify and characterise the role of histone modifications in gene regulation in eukaryotes.
Collaborator Contribution They have provided in-depth knowledge, training and reagents as well as directly contributing to the research project as co-investigator
Impact Identification of a function for histone H3 K4 in regulating gene silencing.
 
Description TV documentary 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Interviewed for EU funded TV documentarty on Epigenetics

Communicated key ideas to a large lay audience
Year(s) Of Engagement Activity 2009
 
Description TV-interview Dublin 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Type Of Presentation Keynote/Invited Speaker
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interviewed at International conference for Friedreich's Ataxia

Raised the profile of the need for research in triplet-repeat diseases
Year(s) Of Engagement Activity 2008