Our group is interested in defining the mechanisms by which chromatin modifications function to regulate cellular processes. Our attention is focused on a set of enzymes (acetylases, deacetylases, methylases and kinases), which regulate transcription by covalently modifying histones. We would like to understand what biological processes these enzymes control and the precise role of each modification on chromatin dynamics. In addition, a number of chromatin modifying enzymes have been implicated in the genesis of cancer so we are dissecting as far as possible, in the pathways misregulated in cancer cells.

We are taking a number of complimentary approaches in both yeast and human cells to characterise chromatin modifications. We use yeast as a model system whenever possible, to investigate their mechanism of action. The recently developed Chromatin Immunoprecipiation-sequencing technology is used to map the global position of histone modifications in both yeast and human cells. Recombinant nucleosome arrays carrying specific modifications are being constructed, in order to understand how they affect compaction of chromatin.

Chromatin-modifying enzymes are deregulated in cancer.

Histones are very highly modified. Despite their abundance, we believe that more modifications are likely to exist on histones. This complexity is probably necessary because histones integrate many signalling pathways with biological processes involving DNA metabolism and function. A major drive at the moment is to identify new histone modifications, as the pathways that control them may well be deregulated in cancer. In recent years, we have identified two novel pathways that modify chromatin, arginine deimination and proline isomerisation. Both of these modifications appear to have a negative effect on transcription. Most recently we have defined a new arginine methylation pathway that modifies histone H3R2. Di-methylation acts to inhibit the enzyme which tri-methylates H3K4 and therefore is a gatekeeper for transcriptional activation. In contrast, mono-methylation of H3R2 tracks with active transcription and does not prevent H3K4 methylation.

Selected publications:

• Nelson CJ, Santos-Rosa H and Kouzarides T (2006) Proline isomerisation of histone H3 regulates lysine methylation and gene expression. Cell 126, 905-916.

• Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M, Bahler J, Green RD and Kouzarides T (2007) Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449, 928-932

Isomerisation of proline 38 in the histone H3 tail has the potential to bend the tail and affect chromatin structure.

Genome-wide pattern of methylation for mono-and-di-methyl H3R2 on genes in yeast (light blue = least active and dark blue = most active genes).

Methylation of H3R2 prevents the binding of the SPP1 component of the Set1 methylase complex and in doing so controls the deposition of H3K4 tri-methylation and subsequent gene activity.