Description
These tracks display evidence of open chromatin in
ENCODE
cell types.
Open chromatin describes segments of DNA that are unpacked and accessible
to the regulatory factors, enzymes, and smaller molecules in the cell.
This is in contrast to closed chromatin, which is packed and
inaccessible. Transcriptionally-active chromatin tends to be more open,
while condensed, densely-packed chromatin tends to be silent.
Open chromatin was identified using complementary methods including:
DNaseI hypersensitivity (HS), Formaldehyde-Assisted Isolation of
Regulatory Elements (FAIRE), and chromatin immunoprecipitation (ChIP)
for select regulatory factors.
DNaseI HS: DNaseI is an enzyme
that has long been used to map
general chromatin accessibility, and DNaseI "hyperaccessibility" or
"hypersensitivity" is a feature of active cis-regulatory sequences. The
use of this method has led to the discovery of functional regulatory
elements that include enhancers, silencers, insulators, promotors,
locus control regions and novel elements. DNaseI hypersensitivity
signifies chromatin accessibility following binding of trans-acting
factors in place of a canonical nucleosome.
FAIRE: FAIRE (Formaldehyde
Assisted Isolation of Regulatory
Elements) is a method to isolate and identify nucleosome-depleted
regions of the genome. FAIRE was initially discovered in yeast and
subsequently shown to identify active regulatory elements in human
cells (Giresi et al., 2007). Although less well-characterized than
DNase, FAIRE also appears to identify functional regulatory elements
that include enhancers, silencers, insulators, promotors, locus control
regions and novel elements.
ChIP: ChIP (Chromatin
Immunoprecipitation) is a method to identify
the specific location of proteins that are directly or indirectly bound
to genomic DNA. By identifying the binding location of
sequence-specific transcription factors, general transcription
machinery components, and chromatin factors, ChIP can help in the
functional annotation of the open chromatin regions identified by
DNaseI HS mapping and FAIRE.
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
Ho L, Crabtree GR. Chromatin remodelling during development.
Nature. 2010 Jan 28;463(7280):474-84.
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.
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.
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