These tracks display maps of chromatin state of ENCODE cell types. Histones are a group of closely-related proteins that together form the nucleosome. There are six histone families: H1, H2A, H2B, H3, H4, and H5. Each nucleosome core is formed by two H2A-H2B dimers and a H3-H4 tetramer, while H1 and H5 bind the nucleosome and DNA. When histone proteins undergo post-transcriptional modifications at specific amino acids (methylation, acyetylation), these modifications (referred to as marks) perform a role in regulating the winding of the DNA around the nucleosome. This in turn regulates gene expression by controlling the accessibility of the chromatin. Histone marks vary in their effect. Promoters, enhancers, transcribed regions, and silenced regions are each associated with specific histone marks.

The ChIP-seq method enables identifying regions of DNA that interact with specific histone marks. This method involves cross-linking histones and other DNA associated proteins to genomic DNA within cells using formaldehyde. The cross-linked chromatin is subsequently extracted, mechanically sheared, and immunoprecipitated using specific antibodies. This has the effect of capturing segments of DNA that are bound to the protein selected by the antibody. After reversal of cross-links, the immunoprecipitated DNA is sequenced and mapped to the human reference genome. The relative enrichment of each antibody-target (epitope) across the genome is inferred from the density of mapped fragments. If the antibody is specific to a given histone mark, then this procedure identifies segments of the genome associated with that mark.

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