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 specific 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. Sequencing these next-generation-sequencing
DNase samples to significantly higher depths of 300-fold or greater 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 0.5% hypersensitive zones.
- Signal
- The density of tags mapping within a 150 bp sliding window
(at a 20 bp step across the genome).
- Raw Signal
- Density graph (wiggle) of signal enrichment based on aligned read density.
DNaseI sensitivity is shown as the absolute density of in vivo
cleavage sites across the genome mapped using the Digital DNaseI methodology
(see below). Data have been normalized to 25 million reads per cell type.
Methods
Cells were grown according to the approved ENCODE cell culture
protocols. Digital DNaseI was performed by DNaseI digestion of
intact nuclei, followed by isolating 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 genome; 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 0.5% (FDR 0.005) 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 0.5% (FDR 0.005) 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.
Release Notes
This is the initial release of this track.
Credits
These data were generated by the UW ENCODE group.
Contact:
Richard Sandstrom
References
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.
Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J,
Hall R, Mack J, Dorschner M 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.
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.
|
Top⇑ |