ENC DNase/FAIRE Tracks
 
ENCODE Open Chromatin by DNaseI HS and FAIRE tracks   (All Regulation tracks)

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Master DNaseI HS  DNaseI Hypersensitive Site Master List (125 cell types) from ENCODE/Analysis  Data version: ENCODE Jan 2011 Freeze
Uniform DNaseI HS  DNaseI Hypersensitivity Uniform Peaks from ENCODE/Analysis  Data version: ENCODE Jan 2011 Freeze (Sept 2012 Analysis Pubs)
Open Chrom Synth  DNaseI/FAIRE/ChIP Synthesis from ENCODE/OpenChrom(Duke/UNC/UTA)  Data version: ENCODE Mar 2012 Freeze
Duke DNaseI HS  Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University)  Data version: ENCODE July 2012 Freeze
UNC FAIRE  Open Chromatin by FAIRE from ENCODE/OpenChrom(UNC Chapel Hill)  Data version: ENCODE July 2012 Freeze
UW DNaseI DGF  DNaseI Digital Genomic Footprinting from ENCODE/University of Washington  Data version: ENCODE July 2012 Freeze
UW DNaseI HS  DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington  Data version: ENCODE July 2012 Freeze

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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.