Schema for REST - Repressor Element 1-Silencing Transcription Factor (REST) binding sites
  Database: mm9    Primary Table: rest    Row Count: 2,423   Data last updated: 2009-09-20
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 612smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3660936int(10) unsigned range Start position in chromosome
chromEnd 3661185int(10) unsigned range End position in chromosome
name ESC_NSC_chr1_3660937_3661185varchar(255) values Name of item

Sample Rows
 
binchromchromStartchromEndname
612chr136609363661185ESC_NSC_chr1_3660937_3661185
621chr147981844798246ESC_NSC_chr1_4798185_4798246
623chr150130265013042ESC_NSC_chr1_5013027_5013042
636chr167219456722019ESC_only_chr1_6721946_6722019
652chr188503028850330ESC_only_chr1_8850303_8850330
655chr192887069288711ESC_NSC_chr1_9288707_9288711
671chr11132021711320316ESC_only_chr1_11320218_11320316
671chr11139141711391434ESC_only_chr1_11391418_11391434
684chr11298053512980723ESC_only_chr1_12980536_12980723
715chr11713571717135731ESC_NSC_chr1_17135718_17135731

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

REST (rest) Track Description
 

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