Large-scale efforts in histone state mapping in multiple model systems (Liu et al. 2005; Sinha et al. 2006; Filion et al. 2010; Ernst et al. 2011; Weiner et al. 2015) reveal a number of conserved aspects of chromatin structure. First, the process of transcription leaves a massive footprint on chromatin, with different histone modifications deposited by the initiation (5′ end of genes) and elongation (middle and 3′ ends) forms of RNA polymerase. Marks at the 5′ ends of genes include H3K4 di/trimethylation (H3K4me3), H3 and H4 tail hyperacetylation (H3K4/9/14/18/27ac and H4K5/8/12ac), H3.3 and H2A.Z variants, and H3K56 acetylation. The 5′ ends of poised genes have lower levels of histone tail acetylation but are marked with H3K4me3. Gene body nucleosomes are typically marked with H3K36me3 and H3K79me3 and are generally somewhat depleted of histone tail acetylations. Second, distal regulatory elements, such 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
