Analyses of genome-wide histone modifications in the mammalian genome

Epigenetic mechanisms regulate the transcriptional programs in response to developmental and environmental cues through DNA and histone modifications, histone variants, chromatin regulators, as well as other epigenetic layers and their interactions. There are at least 18 types of histone modifications discovered so far, mainly methylation, acetylation, ubiquitination, and phosphorylation, that occur predominantly on the histone tails. Chromatin immunoprecipitation and sequencing has enabled the genome-wide mapping of histone modifications, histone variants, and chromatin regulators from over 100 human cell types, even at the level of single cells. In this chapter, we summarize the functions and global distributions of major histone modifications, histone variants, and chromatin regulators, depicting those that are mainly located in cis-regulatory regions and gene bodies. We illustrate how histone marks can be used to identify epigenetic abnormalities in human disease. Finally, we describe major challenges in this field and highlight key areas for future studies.