Richard Meehan: Epigenetic Mechanisms in Development and Disease

Research Programme

Epigenetics

Epigenetics is the study of heritable changes in gene expression that are not encoded in the DNA of the genome. In molecular terms it is associated with chemical modification of DNA and the proteins that make up the basic building block of chromatin, the nucleosome. In order to organise the approximately 2 metres of human DNA into cell nucleus, it needs to be selectively packaged. It is estimated that the human body contains about 50 trillion cells—which corresponds to 100 trillion meters of DNA per human, which needs to be organized in such a way that it facilitates distinct gene expression in multiple tissue types. Compaction of DNA is achieved by arranging DNA around a set of basic histone proteins into chromatin which is further organised into higher order structures that can be visualised as chromosomes. Regions of chromosomes associated with active genes have a particular chemical signature of DNA and chromatin, while regions that are silent have a complementary distinct pattern of chemical modification. One view is that the active and inactive chemical modifications (Epigenetic changes) contribute to the formation of a chromatin architecture that facilitates differential gene expression networks in diverse tissues.

Model for how loss of methylcytosine deoxygenase activity (demethylase: TET1/2/3) may lead to the accumulation of abnormal methylation patterns in culture, in development and in cancer cells (See Nestor et al, 2015).

Mounting evidence suggest that diagnostic alterations in the epigenetic patterns occur during cancer initiation, progression and treatment of cancer. This may, as some propose, directly contribute to cancer causation or alternatively reflect transformative conversions directed by instructive genetic changes (mutation) in cancer. Programmed epigenetic changes are also observed during the regulation of development, during cellular reprogramming, as a result of cellular stress, under different nutrient conditions, as part of physiological aging and when DNA is repaired following a mutational event. There are huge efforts directed towards identifying the dynamic functions and patterns of various modifications to DNA and chromatin (see ENCODE project) in multiple tissue types and disease states.

In molecular terms, epigenetic regulation puts a chemical signpost on genes that are relevant to their expression state in a specific cell type. Specific chemical tags can be deposited on the DNA and/or histones that make up chromatin by a set of enzymes in response to signals in early embryos and developmental cues later in life. In a muscle cell example, a gene for myosin is chemically modified in a way that is associated with its continual use by this cell, as myosin is an important component of muscles. Likewise pluripotent genes (Oct4 and Nanog) that are necessary for embryonic stem cell identity have a particular epigenetic (chemical) signature in cells in which they are expressed that is different to the profile that is observed in non-expressing cells. These differing ‘tag’ patterns and combinations can be used to evaluate cell identity, as different cell types with distinct gene expression patterns will have unique epigenetic signatures.

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

Our work

An intensive area of research is the ‘DNA methylation toolbox’. This consists of the enzymes (DNA methyltransferases) that deposit the chemical tags (methyl groups) on DNA (cytosine is modified to 5-methyl cytosine (5mC); DNA methylation) and their decoders, which may be proteins that are attracted to methylated DNA.

Methylated DNA can signal gene silencing and is considered a protective mechanism that prevents inappropriate expression of genes and other DNA elements in our genome. For example genes that may be important for liver function would be out of place if they were expressed in the reproductive organs and vice versa. So we study what, when and where genes are methylated and what happens if this process is perturbed either experimentally or in disease states? Recently, a mammalian DNA de-methylation pathway has been described that is dependent on-Ten-Eleven Translocation (TET) proteins, TET1/2/3, which catalyse the hydroxylation of 5mC to 5-hydroxymethylcytosine (5hmC) and further derivatives. This potentially makes the DNA methylation pathway very dynamic in normal development and in disease states. The biological properties of 5hmC and its unique tissue profiles suggest it has specific functions with respect to the regulation of gene expression.

We want to know the mechanisms of gene repression by DNA methylation, how does the process work and is it primary regulation mechanism? How does DNA methylation contribute to gene silencing, does it do it by-self or in combination with other factors, is DNA methylation the only ‘barcode’ that contributes to gene silencing or does it work in combination with another ‘barcode’ found on the nuclear DNA storage proteins; the histones? We try to challenge what we think we know about the role of epigenetics in gene regulation; to find out if our theories are consistent or require reconsideration.

This research can be described as ‘basic’ but it also leads into applied area’s including cancer research and a new research program termed environmental epigenetics. In the latter case we focus on the detection of compounds in our environment that may upset the epigenetic profile of organisms, perhaps by interfering with the enzymes (components) that are required to maintain the epigenetic barcode that is characteristic of different organs. Signal induced epigenetic alterations have been suggested to be associated with exposure to particular chemicals leading to a predisposition to certain conditions including asthma and as already mentioned, cancer.

Objectives

We wish to understand the role of epigenetics in setting up gene expression states during early development and how these distinct expression states are maintained in differentiated tissues and organs, for example germ cells.
We primarily focus on trying to understand the roles of DNA methyltransferases (which methylate cytosines at CpG dinucleotides) and methyl-cytosine deoxygenases (TET enzymes), which further modify 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). 5hmC and its derivatives may participate in a DNA demethylation pathway.
We investigate model systems and disease states to understand how these key components accomplishes their roles and to discover additional genetic and environmental factors that modify their activity and function.
We want to determine how and why abnormal epigenetic states occur and are maintained in disease states, especially during the carcinogenic process.
We are exploring the utility of 5hmC profiling as an identifier of cell state.
We wish to determine the interplay between DNA and histone modifications in determining overall chromatin organization and its relevance to gene the regulation of gene expression and cell identity.

Research Path

Now you see it, now you don't: the epigenetic mark, 5-hydroxymethylcytosine (5hmC), does a disappearing act in culture. Mouse skin cells before and after cell culture show major loss of 5hmC, one of the many rapid molecular changes observed in cell cultures, reported by Nestor and colleagues in Genome Biology (2015;16:11. doi: 10.1186/s13059-014-0576-y). Images depict the loss of red immunostaining for 5hmC in nuclei from cells grown in culture, but not green immunofluorescence (5-methylcytosine) and blue DAPI staining (DNA). Scale bar 5 microns. Image courtesy of the S. Pennings lab.

We persue many of the above goals in collaboration with members of the HGU and Institute of Genetics and Cancer (formerly IGMM). We rely on the excellent technical services of the HGU/IGC to support our program. Much of what we do now depends on the analysis of big data sets, so we also depend on bioinformatics tools to sieve through our big data sets and gain further insight.

We discuss and plan experiments (wet work and bioinformatics) that test our ideas about epigenetics and control of gene expression. Once we have found something interesting, we ask does this help in our understanding of the molecular basis of epigenetic function? Once we have obtained a set of interesting results, what are their implications in the context of our research field, in biology and in human health?

We work on a topic that has applications in many fields (e.g. control of gene expression, genome stability, stem cells, early development, reproduction, disease (cancer), behaviour and response to the environment). As part of our commitment to public engagement of science we think how best to submit our work for publication and dissemination.

This article was published on 1 Apr, 2021