Genome-wide patterns of histone modifications in yeast

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Abstract
The availability of antibodies that are directed against specific histone-modification sites has allowed the mapping of these sites at the whole-genome level using microarrays. Recent data in Saccharomyces cerevisiae are analysed to ask whether unique histone-modification patterns have specific functions. The preferences of enzymes for particular histone sites and chromosomal locations are described. Different enzymes can affect the same genomic regions to generate unique patterns of modifications. In particular, there are differences between the histone-modification patterns of heterochromatin, subtelomeric heterochromatin-adjacent regions, centromeric chromatin, promoters and coding regions. The roles of histone-modification patterns at these domains are discussed. The fully deacetylated, demethylated state is necessary for repression of gene activity in heterochromatin. Domains that are partially deacetylated might be activated more easily. Both acetylation and deacetylation are important for gene activity. Certain sites, including H4K16, are hypoacetylated at active genes, and histone deacetylases that deacetylate H4K16 (for example, Hos2) have also been described as activators of transcription. Hypoacetylation and methylation of certain lysine residues have been shown to affect the binding of chromosomal proteins to target genes. These studies also provide a link between the methylation of a lysine residue (H3K36) and the recruitment of the histone deacetylase Rpd3 to a gene. Finally, the availability of similar studies in Schizosaccharomyces pombe, which is widely divergent in evolution from S. cerevisiae, suggests that the findings above might be extrapolated to other eukaryotes.