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.

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