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 Overlayed
H3K4Me1 and Overlayed 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 Overlay H3K4Me3
track shows a histone mark associated with promoters. The DNase Clusters track shows regions
where the 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 hypersensitive 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 Super-track just shows a selection of the most informative data of
To view the full description, click here.