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

• The TF rPeak Clusters track shows genomic regions bound by DNA-associated proteins involved in transcriptional regulation from ENCODE 4.
• 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.