Description
This track, produced as part of the ENCODE Project, contains deep sequencing DNase data
that will be used to identify sites where regulatory factors bind to the genome
(footprints).
Footprinting is a technique used to define the DNA sequences that interact
with and bind DNA-binding proteins, such as transcription factors,
zinc-finger proteins, hormone-receptor complexes, and other
chromatin-modulating factors like CTCF. The technique depends upon the
strength and tight nature of protein-DNA interactions. In their native chromatin
state, DNA sequences that interact directly with DNA-binding proteins are
relatively protected from DNA-degrading endonucleases, while the exposed/unbound
portions are readily degraded by such endonucleases. A massively parallel
next-generation sequencing technique to define the DNase hypersensitive sites
in the genome was adopted. The DNase samples were sequenced using next-generation
sequencing machines to significantly higher depths of 300-fold or greater. This produces
a base-pair level resolution of the DNase susceptibility maps of the native
chromatin state. These base-pair resolution maps represent and are dependent
upon the nature and the specificity of interaction of the DNA with the
regulatory/modulatory proteins binding at specific loci in the genome; thus
they represent the native chromatin state of the genome under investigation.
The deep sequencing approach has been used to define the footprint landscape of
the genome by identifying DNA motifs that interact with known or novel DNA-binding proteins.
Display Conventions and Configuration
This track is a multi-view composite track that contains multiple data types
(views). For each view, there are multiple subtracks that display
individually on the browser. Instructions for configuring multi-view tracks
are here.
For each cell type, this track contains the following views:
- HotSpots
- DNaseI hypersensitive zones identified using the HotSpot algorithm.
- Peaks
- DNaseI hypersensitive sites (DHSs) identified as signal peaks within
FDR 1.0% hypersensitive zones.
- Signal
- Per-base count of sequence reads whose 5' end (corresponding to a
DNaseI-induced DNA cut) coincides with the given position.
- Raw Signal
- The density of tags mapping within a 150 bp sliding window
(at a 20 bp step across the genome).
NOTE: The names of the signal views in this track are reversed from conventions used in
other ENCODE tracks, where the less processed signal is termed 'Raw'.
DNaseI sensitivity is shown as the absolute density of in vivo
cleavage sites across the genome mapped using the Digital DNaseI methodology
(see below).
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.
Methods
Cells were grown according to the approved
ENCODE cell culture
protocols. Digital DNaseI was performed by DNaseI digestion of
intact nuclei, followed by isolation of DNaseI 'double-hit' fragments as
described in Sabo
et al. (2006), and direct sequencing of
fragment ends (which correspond to
in vivo DNaseI cleavage
sites) using the Solexa platform (27 bp reads). High-quality reads were
mapped to the GRCh37/hg19 human genome using
Bowtie 0.12.5
(Eland was used to map to NCBI36/hg18);
only unique mappings were kept. DNaseI sensitivity is directly reflected
in raw tag density (
Signal), which is shown
in the track as density of tags mapping within a 150 bp sliding window
(at a 20 bp step across the genome). DNaseI hypersensitive zones
(
HotSpots) were identified using the HotSpot algorithm
described in Sabo
et al. (2004). False discovery rate thresholds
of 1.0% (FDR 1.0%) were computed for each cell type by applying
the HotSpot algorithm to an equivalent number of random uniquely
mapping 36-mers. DNaseI hypersensitive sites (DHSs or
Peaks)
were identified as signal peaks within 1.0% (FDR 1.0%) hypersensitive zones
using a peak-finding algorithm. Only DNase Solexa libraries from unique
cell types producing the highest quality data, as defined by Percent
Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth
of over 200 million tags.
Verification
Results were validated by
conventional DNaseI hypersensitivity assays using end-labeling/Southern
blotting methods.
Images and their associated mappings can be found in the supplemental data.
Release Notes
This is Release 4 (August 2012) of this track, which includes 10 new experiments across 8 cell lines.
A number of previously released Peaks have been replaced by updated versions.
The affected database tables and files include 'V2' in the name, and metadata is marked with "submittedDataVersion=V2",
followed by the reason for replacement, "Fixed bug in peak calls that artificially reduced the number of peaks".
Previous versions of files are available for download from the
FTP site.
Credits
These data were generated by the UW ENCODE group.
Contact:
Richard Sandstrom
References
Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al.
Discovery of functional noncoding elements by digital analysis of chromatin structure.
Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42.
Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al.
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.
Nat Methods. 2006 Jul;3(7):511-8.
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, above.
The full data release policy for ENCODE is available
here.