Description
This track contains genome-wide maps of Repressor Element 1-Silencing
Transcription Factor (REST) binding sites in mouse stem cells, generated
by the Stem Cell and Developmental Biology Group at the
Genome Institute of Singapore.
REST is a zinc finger transcriptional repressor that regulates a large
cohort of neural genes throughout development. Aberrant REST activity
has been implicated in various disease states, including cancer, epilepsy,
Huntington's disease and cardiovascular disease.
Display Conventions and Configuration
- The Embryonic Stem Cells only PET clusters (marked: ESC_only)
are colored red.
- The Embryonic and Neural Stem Cells PET clusters (marked: ESC_NSC)
are colored blue.
Methods
The ChIP-PET (chromatin immunoprecipitation coupled to paired-end di-tagging)
method was used to identify genomic loci occupied by REST. 36 bp PETs
generated from ChIP DNA fragments enriched for REST binding regions were
sequenced using the high-throughput 454 sequencing technology.
REST binding sites were defined as those having at least five overlapping
PETs (PET5+). Mapping was carried out in two isogenic cell lines:
the mouse embyronic stem cell E14, and the neural stem cell line NS5.
The REST binding sites are divided into two categories:
- ESC and NSC shared sites, "ESC_NSC" (PET5+ in ESC, PET2+ in NSC)
- ESC-specific sites, "ESC_only" (PET5+ in ESC, PET<2 in NSC)
Negligible numbers of NS-only sites were identified. The coordinates
displayed represent the PET minimal overlap region, defined as the region
that is overlapped in common by all PETs constituting a cluster.
Credits
These data were generated by the
Stanton Group at the
Genome Institute of Singapore.
References
Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L,
Pollard SM et al.
REST regulates distinct transcriptional networks in embryonic and neural stem
cells. PLoS Biol. 2008 Oct 28;6(10):e256.
PMID: 18959480; PMC: PMC2573930
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