Specific epigenetic modifications

DNA methylation
Methylation of 5 group of cytosines within CpG dinucleotides

Post-translational histone modifications

Methylation, ubiquitination, phosphorylation, sumoylation, acetylation of residues in the N-terminal tails of histones

Chromatin remodelling
ATP dependent chromatin remodelling complexes shift nucleosomes

Histone variants
Histones with varying stabilities or specialist domains that alter the function of the nucleosome

Noncoding RNAs
piRNAs and other siRNAs that can direct epigenetic machinery Long noncoding RNAs may direct epigenetic enzymes to sites in the genome

Histone variants
Different variants exist for histones H2A, H3 and H1 Each variant has specific properties that differ from the canonical histones, useful for different functions e.g.
- Increased stability vs decreased stability - Amino acids that can be modified such as Serine (can be phosphorylated), not found in canonical histones - Others we dont yet understand

Histone variant deposition

- How are histone variants deposited? - Using ATP-dependent chromatin remodelling proteins - Can be replication dependent or independent i.e. does or doesnt rely on cell division

Histone variants variant H3

Centromeric histone variants e.g. CENP-A (different names in other species) - Centromere specific (centromere is the primary constriction of a metaphase chromosome)

centromere

Histone variants variant H2A.X

H2A.X involved in DNA repair - Universal histone variant, highly conserved - C terminal motif differs from canonical H3 - Has Serine at position 139, which can be phosphorylated - H2A.X-ph, called -H2A.X, localised in double strand breaks (DSB), and is involved in DNA repair

Histone variants variant H2A.X

- S139 phosphorylated by kinases at DSB - -H2A.X recruits DNA repair proteins, including epigenetic factors that alter chromatin state at DSB - Phosphatase cleaves phosphate group after repair is complete DNA stained blue -H2A.X green, marks DSB post irradiation

Histone variants variant macroH2A

MacroH2A inactive X chromosome - Found only in vertebrates - Contains large 200 amino acid C terminal macro domain - Enriched on the inactive X chromosome, chromosome made up of facultative heterochromatin

Histone variants summary

Many different variants, 3 we discussed Variants possess particular domains or amino acids that enable specific features Histone variants are known that are involved in structural aspects of the chromosome, DNA repair and transcriptional silencing or activation

Acknowledgements
Chromosome (http://commons.wikimedia.org/wiki/File:Chromosome-upright.png) By Magnus Manske, modifications 'upright chromosome' by User:Dietzel65 (Nupedia, then en.wikipedia) [CC-BY-SA-3.0 (http://creativecommons.org/ licenses/by-sa/3.0/)], via Wikimedia Commons YH2AX Foci in a nucleus of a mouse cell(http://commons.wikimedia.org/wiki/File %3AYH2AX_Foci_in_a_nucleus_of_a_mouse_cell.tif) by By Newheavyions (Own work) [CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons