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.