ENC Histone Super-track Settings
 
ENCODE Histone Modification Tracks   (All Regulation tracks)

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Broad ChromHMM  Chromatin State Segmentation by HMM from ENCODE/Broad  
Broad Histone  Histone Modifications by ChIP-seq from ENCODE/Broad Institute  
SYDH Histone  Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/USC/Harvard  
UW Histone  Histone Modifications by ChIP-seq from ENCODE/University of Washington  
wgEncodeHistoneSuper.html

Description

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.

Display Conventions

These tracks are multi-view composite tracks that contains multiple data types (views). Each view within each track has separate display controls, as described here. Most ENCODE tracks contain multiple subtracks, corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages.

Credits

These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions, to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks.

References

Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J Cell Biochem. 2002;87(2):117-25.

Segal E, Widom J. What controls nucleosome positions? Trends Genet. 2009 Aug;25(8):335-43.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.