Histone Modification Patterns in Human Genome

Source: Wang et al. (2008). Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics 40:897-903.

Histone modification is one of the strategies employed by the eukaryotic systems to regulate their gene expression. For example, histone acetylation acts as an activator; whereas, methylation (depending on the site) can both be a repressor and activator. The "histone code hypothesis" states that a combination of histome modifications acts as an indicator of the chromatin state. Using ChIp-Seq technique, the authors make genome-wide maps for 18 different acetylations and 19 different methylations. Their results adds fascinating knowledge to our understanding of histone modifications. For example, they find a positive correlation between acetylation sites and expression, as previously known, but they show spacial arrangements for different types of acetylation. Some of these modifications are focused on TSS (transcription start site); whereas, others are in promoters or even in the gene itself.

Of the 4339 combinatorial patterns observed by the authors, most occur only once. 13 of these patterns, being the most frequent ones, are located in more than 62 genes each. Comparing the presence of these patterens with gene-expression data, the authors have classified the patterns into three distinct groups:
1. Low expression: High occurrence of H3K27me3 modification and other methylations but not acetylation.
2. Average expression: Generally including backbone modifications.
3. High expression: H2BK5me1, H4K16ac, H4K20me1 and H3K79me1/2/3 in addition to the modification
backbone.

I won't detail all the observations but they also report distinct histon modification patterns at enhancer sites.