## Description

These tracks display evidence of open, accessible chromatin in ENCODE cell types. 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 data: 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 data: 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 data: 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). For each view, there are multiple subtracks that display individually on the browser. Each view within each track has separate display controls, as described here. Specific aspects of the views vary by track. The views include:
Peaks
Regions of significant DNaseI hypersensitivity.
Signal
The density of tags mapping within a sliding window.
Raw Signal
Density graph (wiggle) of signal enrichment based on aligned read density.

## 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 over a specific set of cell types. Consequently, data related to these tracks be available under ENCODE 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.