ENCODE Regulation Layered H3K4Me3 Track Settings

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H3K4Me3 Mark (Often Found Near Promoters) on 7 cell lines from ENCODE

Track collection: Integrated Regulation from ENCODE

Description

These tracks contain information relevant to the regulation of transcription from the ENCODE Project.

The Transcription track shows transcription levels assayed by sequencing of polyadenylated RNA from a variety of cell types.
The Layered H3K4Me1 and Layered H3K27Ac tracks show where modification of histone proteins is suggestive of enhancer and, to a lesser extent, other regulatory activity. These histone modifications, particularly H3K4Me1, are quite broad. The actual enhancers are typically just a small portion of the area marked by these histone modifications.
The Layered H3K4Me3 track shows a histone mark associated with promoters.
The DNase I Hypersensitivity tracks indicate where chromatin is hypersensitive to cutting by the DNase enzyme, which has been assayed in a large number of cell types. Regulatory regions, in general, tend to be DNase-sensitive, and promoters are particularly DNase-sensitive.
The Txn Factor ChIP tracks show DNA regions where transcription factors, proteins responsible for modulating gene transcription, bind as assayed by chromatin immunoprecipitation with antibodies specific to the transcription factor followed by sequencing of the precipitated DNA (ChIP-seq).

These tracks complement each other and together can shed much light on regulatory DNA. The histone marks are informative at a high level, but they have a resolution of just ~200 bases and do not provide much in the way of functional detail. The DNase hypersensitivity assay is higher in resolution at the DNA level and can be done on a large number of cell types since it's just a single assay. At the functional level, DNase hypersensitivity suggests that a region is very likely to be regulatory in nature, but provides little information beyond that. The transcription factor ChIP assay has a high resolution at the DNA level and, due to the very specific nature of the transcription factors, is often informative with respect to functional detail. However, since each transcription factor must be assayed separately, the information is only available for a limited number of transcription factors on a limited number of cell lines. Though each assay has its strengths and weaknesses, the fact that all of these assays are relatively independent of each other gives increased confidence when multiple tracks are suggesting a regulatory function for a region.

For additional information, please click on the hyperlinks for the individual tracks above. Also note that additional histone marks and transcription information is available in other ENCODE tracks. This integrative supertrack just shows a selection of the most informative data of most general interest.

To view the full description, click here.

All tracks in this collection (9)

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Graph configuration help

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	GM12878	H3K4Me3 Mark (Often Found Near Regulatory Elements) on GM12878 Cells from ENCODE	Data format
	H1-hESC	H3K4Me3 Mark (Often Found Near Promoters) on H1-hESC Cells from ENCODE	Data format
	HSMM	H3K4Me3 Mark (Often Found Near Promoters) on HSMM Cells from ENCODE	Data format
	HUVEC	H3K4Me3 Mark (Often Found Near Promoters) on HUVEC Cells from ENCODE	Data format
	K562	H3K4Me3 Mark (Often Found Near Promoters) on K562 Cells from ENCODE	Data format
	NHEK	H3K4Me3 Mark (Often Found Near Promoters) on NHEK Cells from ENCODE	Data format
	NHLF	H3K4Me3 Mark (Often Found Near Promoters) on NHLF Cells from ENCODE	Data format

Assembly: Human Dec. 2013 (GRCh38/hg38)
Data coordinates converted via liftOver from: Feb. 2009 (GRCh37/hg19)

Note: lifted from hg19

Description

Chemical modifications (e.g., methylation and acetylation) to the histone proteins present in chromatin influence gene expression by changing how accessible the chromatin is to transcription. A specific modification of a specific histone protein is called a histone mark. This track shows the levels of enrichment of the H3K4Me3 histone mark across the genome as determined by a ChIP-seq assay. The H3K4Me3 histone mark is the tri-methylation of lysine 4 of the H3 histone protein, and it is associated with promoters that are active or poised to be activated. Additional histone marks and other chromatin associated ChIP-seq data is available at the Broad Histone page.

Display Conventions and Configuration

By default, this track uses a transparent overlay method of displaying data from a number of cell lines in the same vertical space. Each of the cell lines in this track is associated with a particular color, and these colors are relatively light and saturated so as to work best with the transparent overlay. The color of these tracks match their versions from their lifted source on the hg19 assembly. The colors are consistent with the other hg19 lifted tracks located in the ENCODE Regulation supertrack, with the exception being the DNase tracks, as they were not lifted from hg19 and are colored to reflect similarity of cell types.

Credits

This track shows data from the Bernstein Lab at the Broad Institute, as part of the ENCODE Consortium.

Data Release Policy

Primary ENCODE data produced during the 2007-2012 production phase were subject to a restriction period. However, the data here are past those restrictions and are freely available. The full data release policy for ENCODE is available here.