Epigenetics: what is it and why does it happen?

1. Epigenetics: what is it and why does it happen? Louise Williams 18/10/2007

2. Outline • What is Epigenetics? • Mechanisms of epigenetic control • Histone modification • Polycomb-trithorax gene expression • Methylation • Methylation – How, when and why it occurs. • Some examples from ‘real life’!

3. Epigenetics • Epigenetics describes heritable changes in genome function that occur without a change in the nucleotide sequence.

4. Epigenetics can explain how tissue specific gene expression is initiated and maintained. • All nucleated cells in an organism contain the same DNA but do not all express the same genes. • In early embryos, asymetry and axes are set up by cell to cell communication, but this cellular identity must be maintained throughout the organisms’ life. • The maintenance of cellular identity is ensured by epigenetic mechanisms which provide a kind of ‘cell memory’.

5. Mechanisms of epigenetic programming • Histone Modification • Polycomb-trithorax gene regulation • DNA Methylation

6. Histones • Transcriptionally inactive DNA is organised into a condensed structure around histones. • The dense structure prohibits proteins involved in gene expression, DNA replication, DNA repair etc from interacting with the DNA. • This structure can be reversibly modified to a more accessible conformation by histone modification and chromatin remodelling. • The pattern of histone modifications is known as the histone code.

7. Histone modification (1) • The two main mechanisms of histone modification are acetylation and methylation. • Acetylation: • Histone acetyltransferases catalyse the addition of acetyl groups to the N-terminal tail of a histone octamer. • This reduces the affinity of histones for DNA and allows RNA polymerase and transcription factors to access the promoter region. • Histone deacetylases have the oposite effect – they remove acetyl groups and promote transcriptional repression

8. Histone modification (2) • Methylation: • This is carried out by methyltransferases which target certain arginine and lysine residues in the histone • Histone arginine methylation is involved in transcriptional activation, but histone lysine methylation can also be involved in transcriptional repression. • Histone methylation interactes with DNA methylation to permit the stable transmission of an epigenetic state to daughter cells.

9. Chromatin remodelling • Chromatin remodelling complexes use ATP hydrolysis to temporarily alter the structure of nucleosomes. • This allows access to the DNA by interacting molecules. • This remodelled state can be retained even after the complex has disassociated. • Some remodelling complexes can restore an inactive state.

10. Polycomb-trithorax gene • This group of genes has been extensively studied in the fruitfly. • The polycomb gene repressors and trithorax gene activators maintain the correct expression of several key developmental regulators including the homeotic (Hox) genes by changing the structure of chromatin either into closed or open conformations. • this 'freezes' the expression status of a target gene - this active or inactive state remains mitotically stable and is clonally inherited.

11. DNA Methylation (1) • Cytosine methyl transferases recognise CpG target sequences. • Methylation at the 5’ carbon gives 5-methylcytosine. • There are moderately high levels of methylation within the genome, which are concentrated in large domains of methylated DNA which is separated by equally large domains of unmethylated DNA. This is called mosaic methylation.

12. DNA Methylation (2) • Methyltransferases preferentially recognise hemi-methylated CpGs and will therefore perpetuate the methylation pattern of a strand of DNA after replication. This is known as maintenance methylation. • The methylation pattern of differentiated cells will vary according to cell type, but methylation patterns within a cell lineage are stable.

13. ‘epigenetic reprogramming’ (1) • During early development, there are dramatic changes in DNA methylation. • Primordial germ cells are highly methylated, but will loose this during development. • After gonadal differentiation, re-methylation occurs. • The sperm genome is more methylated than the egg genome, and sex specific differences can be seen, especially at imprinted loci.

14. ‘epigenetic reprogramming’ (2) • After fertilisation, both egg and sperm DNA is highly methylated. • At the pre-implantation stage, genome-wide demethylation occurs. • At the pre-gastrulation stage, de novo methylation is carried out. • The extent of methylation occuring will depend on the cell type – somatic cell lineages are highly methylated whereas trophoblast lineages are undermethylated.

15. Role of DNA methylation (1) • The precise or primary function of DNA methylation is unknown. There are two contrasting theories: • The Host Defence Model • The Gene Regulation Model

16. The Host Defence Model • This model equates the function of DNA methylation in mammals to that of bacteria. • About 45% of the human genome can be classified as belonging to transposon families. • These sequences are highly methylated (about 90% of methylated CpGs are within these sequences). • This has led to the view that DNA methylation is repressing transposition of these elements which would be extremely damaging.

17. The Gene Regulation Model • DNA methylation is viewed as a mechanism for silencing transcription. • Promoter regions that are transcriptionally active tend to be unmethylated • Thought to have acquired a special function in vertebrates to regulate expression of endogenous genes and reduce “transcriptional noise” in the cell. • Also possible that methylation has a role in promoting specialised gene expression patterns, i.e. allele-specific gene expression in imprinting regions and X inactivation

18. Examples of Epigenetic disease • ATRX (α-thalassaemia/mental retardation syndrome, X-linked) • Consistent changes in methylation patterns of ribosomal DNA, Y-specific repeats and subtelomeric regions • Fragile X • (CGG)n in 5’ UTR of FMR1 gene expands and becomes methylated de novo • ICF (immuno-deficiency, centromeric region instability & facial anomalies) • Caused by mutation in DNMT3B involved in establishing DNA methylation patterns • RETT syndrome • Due to germline mutations in MeCP2 • MeCP2 protein is involved in chromatin remodelling • Cancer • Changes in DNA mathylation (hyper- or hypo-methylation) are thought to occur early in cancer development and may contribute to tumorigenesis.

19. Reference • Human Molecular Genetics (2004) • Most ‘information’ was taken from here - a full list of other journals / websites consulted can be provided on request.