These tracks display evidence of open chromatin in
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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