Epigenetic Mechanisms in Development and Disease

 

Summary: Epigenetics

Each individual is born with the same unique set of genes in almost every cell in their body that act as an instruction manual for how the cell should work. Genes influence factors such as hair colour, gender and of course, whether one can role their tongue or not. However, as every cell in the body has the same set of genes or ‘instructions’, how do cells become for example either brain cells or muscle cells? The answer partly lies in a process called epigenetic regulation.

 

 

 

General Background: DNA Methylation

It is well established that modification of DNA at CpGs by the addition of a methyl group at the 5 position of cytosine affects gene expression by suppressing the function of gene regulatory elements including promoters, enhancers, insulators and enhancer blockers 1. Dynamic changes in DNA methylation patterns during development or in cancer cells contributes directly to altered transcription expression profiles 2;3. Over 70% of CpGs are methylated in vertebrate DNA, but distinct patterns can be observed between different somatic and germline tissues 4. These inherited patterns of methylation were hypothesised early on to have functional consequences and initial studies indicated that there was a correlation between the methylation status of a gene and its expression state5;6.

 

DNA Methylation in Vertebrates

A number of DNA methyltransferase enzymes (Dnmt1, Dnmt2, Dnmt3a and Dnmt3b) have been identified by biochemical and sequence analysis, all of which contain a highly conserved C-terminal catalytic domain and, with the exception (so far) of Dnmt2, a variable N-terminal extension 7. This domain contains a number of protein interaction motifs that allows the different Dnmts (1, 3a &3 b) to interact with each other and numerous other nuclear proteins 4. Database screening also identified Dnmt3L, which lacks the conserved PC and ENV residues in motifs IV and VI of the catalytic domain. Recombinant Dnmt3L protein is unable to methylate DNA, but it interacts with Dnmt3a and Dnmt3b and co-localizes with these enzymes in the nuclei of transfected cells. Genetic evidence suggests that Dnmt3L cooperates with the Dnmt3 methyltransferases to carry out de novo methylation of maternally imprinted genes during oogenesis and early mouse embryogenesis 8;9.

 

General Background: The Maintenance Methyltransferase, DNMT1

DNMT1 co-localises with late replicating DNA in tissue culture cells and it is thought to be required for the remethylation of hemi–methylated DNA substrates that occur after DNA replication 10;11.

 

As such it is regarded as a maintenance methylase that propagates pre-existing patterns of methylation, however recent evidence suggests that Dnmt3a and 3b are also necessary to maintain DNA methylation patterns in somatic cells due to the low fidelity of the Dnmt1 enzyme 12;13. However, DNMT1 probably has additional cellular roles that have yet to be fully explored, e.g. in DNA repair and cell cycle checkpoint signalling.

 

 

Collaborators outwith the Unit

• Dr Egor Prokhortchouk; Analysis of Kaiso function in development.  
• Dr Sari Pennings & Professor Sir Ian Wilmut: Epigenetic reprogramming and pronuclear asymmetry in early mouse development (BBSRC funded).
• Edinburgh Breakthrough Breast Cancer Consortium: The elucidation of epigenetic mechanisms in tumour biology and evolution (Breakthrough Breast Cancer funded).

 

Lab Members

Current lab members involved in this work are:

• Dr Richard Meehan
• Dr Donncha Dunican
  
• Dr Colm Nestor
• D Sproul
• J Thomson
• J Reddington
• Ms Katharine Appleby (Technician)
  

 

1. Epigenetics (this page)

2. Expression of xDnmt1 mRNA during Xenopus Development
   

3. Transcriptional Repression by DNA Methylation?

4. Our Work

 

Epigenetic regulation puts a chemical signpost on genes that are relevant to the cell type, so that in the muscle cell example, a gene for myosin is modified so that it is continually used by the cell, as myosin is an important component of muscles. Likewise pluripotent genes (Oct4 and Nanog) that are necessary for stem cell identity have a particular epigenetic signature in cells in which they are expressed that is different to the profile that is observed in non-expressing cells.

 

The original concept of epigenetics by Conrad Waddinton referred to the causal analysis of the biological transitions leading from zygote to adult, 1;2. This combined developmental and genetic approaches to study animal and plant biology.

 

Purpose

• Define epigenetic pathways in development and disease.
  
• We primarily focus on DNA methyltransferases (which methylate cytosines at CpG dinucleotides) and methyl-CpG binding proteins (MeCPs), which bind methylated DNA.
  
• Define the epigenetic and nuclear metabolism pathways through which DNA methyltransferases and MeCPs interact and function.
  
• Study model systems and disease states to understand how these key components fulfils their roles and discover additional genetic and environmental factors that modify their activity and function.
• To understand the role of epigenetics in setting up gene expression states during development (embryonic stem (ES) cells) and how these distinct expression states are maintained in differentiated tissues and organs, e.g germ cells.
• To determine how abnormal epigenetic states occur and are maintained in disease states, especially during the carcinogenic process.

 

Introduction: Epigenetics and Chromatin

Until recently, the developmental process in animals cannot normally be reversed, as the developmental potential of somatic cells becomes more restricted as cellular specification proceeds, in spite of their unchanged genetic makeup. The setting up and stable maintenance of heritable patterns of gene expression relies on chromatin architecture within the cell nucleus, which is established by multiple remodelling and modifying mechanisms1. With the discovery of new information, the general definition of epigenetics becomes more refined and specific. Current epigenetic research has become essential for understanding how gene expression programs are set up during development and subsequently altered in disease states, especially cancer and induced embryonic stem cells (iES)2;3.

 

It is now recognised that there are potential epigenetic inheritance systems through which non-DNA variations can be transmitted in cell lineages and across generations4. See The Epigenome for a primer on epigenetics.