Description

This track, produced as part of the ENCODE Project, displays maps of histone modifications genome-wide using ChIP-seq in different cell lines. The ChIP-seq method involves first using formaldehyde to cross-link histones and other DNA-associated proteins to genomic DNA within cells. The cross-linked chromatin is subsequently extracted, sheared, and immunoprecipitated using specific antibodies. 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.

Chemical modifications (e.g. methylation or acetylation) of the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription factors. Shown for each experiment (defined as a particular antibody and a particular cell type) is a track of enrichment for the specifically modified histone (Signal), along with sites that have the greatest enrichment (Peaks). Also, included for each cell type is the input signal, which represents the control condition where no antibody targeting was performed. In general, the following chemical modifications have associated genetic phenotypes:

• H3K4me3 and H3K9ac are considered to be marks of active or potentially active promoter regions
• H3K4me1 and H3K27ac are considered to be marks of active or potentially active enhancer regions\
• H3K36me3 and H3K79me2 are considered to be marks of transcriptional elongation
• H3K27me3 and H3K9me3 are considered to be marks of inactive regions.

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here.

For each cell type, this track contains the following views:

Peaks

Regions of signal enrichment based on processed data (usually normalized data from pooled replicates).

Signal

Density graph (wiggle) of signal enrichment based on aligned read density.

Peaks and signals displayed in this track are the results of pooled replicate sequence. Alignment files for each replicate are available for download.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. Briefly, cells were cross-linked, chromatin was extracted and sonicated using a Bioruptor sonicator (Diagenode) to an average size of 300-500 bp, and individual ChIP assays were performed using antibodies to modified histones. For the K562, MCF-7, HCT-116, NTera-2 (NT2-D1), PANC-1 and PBMC histone ChIP-seq samples, immunoprecipitates were collected using protein G-coupled magnetic beads; a detailed ChIP and library protocol can be found at the Roadmap Epigenome Project. For the U2OS histone ChIP-seq samples, immunoprecipitates were collected using StaphA cells. Library DNA was quantitated using either a Nanodrop or a BioAnalyzer and sequenced on an Illumina GA2.

The sequencing reads were mapped to the genome using the Eland alignment program. ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags, a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.

For each 1 Mb segment of each chromosome, a peak height threshold was determined by requiring a false discovery rate <= 0.05 when comparing the number of peaks above threshold as compared to the number obtained from multiple simulations of a random null background with the same number of mapped reads (also accounting for the fraction of mapable bases for sequence tags in that 1 Mb segment). The number of mapped tags in a putative binding region is compared to the normalized (normalized by correlating tag counts in genomic 10 kb windows) number of mapped tags in the same region from an input DNA control. Using a binomial test, only regions that have a p-value <= 0.05 are considered to be significantly enriched compared to the input DNA control.

Release Notes

This is Release 3 (June 2012) of this track, which adds 9 new experiments for the MCF-7, HCT-116 and PANC-1 cell lines.

Credits

These data were generated and analyzed by the labs of Peggy Farnham (USC/Norris Cancer Center; previously at UC Davis) and Michael Snyder at Stanford University.

Contact: Peggy Farnham for questions concerning data collection and usage and Philip Cayting for data scoring and submission inquiries.

References

Blahnik KR, Dou L, Echupare L, Iyengar S, O'Geen H, et al. Characterization of the Contradictory Chromatin Signatures at the 3' Exons of Zinc Finger Genes. PLoS One. 2011;6(2):e17121.

O'Geen H, Echipare L, Farnham PJ Using ChIP-seq technology to generate high-resolution profiles of histone modifications. Methods Mol Biol. 2011;791;265-286.

O'Geen H, Frietze S, Farnham PJ Using ChIP-seq Technology to Identify Targets of Zinc Finger Transcription Factors. Methods Mol Biol. 2010;649:437-455.

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, above. The full data release policy for ENCODE is available here.