as enhancers, are marked with H3K4me1/2 but not H3K4me3 (Heintzman et al. 2007). Other histone marks distinguish repressed, poised, and active enhancers, with H3K27 methylation and acetylation marking repressed and active enhancers, respectively. Third, two major forms of repressive chromatin are associated with specific histone modifications. Classical heterochromatin (including telomeres and many repetitive sequences) is marked with H3K9 methylation, while genes repressed by Polycomb-group factors are marked with H3K27me3. H3K27-methylated nucleosomes can be either in a repressed state and lack other marks, or in a poised “bivalent” state in combination with the active mark H3K4me3 (Bernstein et al. 2006). Finally, nucleosomes associated with centromeres often contain the H3-like CENP-A protein, and during M phase, a broad pericentric domain of nucleosomes are marked with H3S10ph. Overall, there is a striking correspondence of histone state with the function of genomic regions, and because of this, mapping of histone modifications is an effective method to discover genes and regulatory elements (Guttman et al. 2009, 2010; Hon et al. 2009; Ernst and Kellis 2010).
