Gene Set: RAO_BOUND_BY_SALL4_ISOFORM_A

Standard name RAO_BOUND_BY_SALL4_ISOFORM_A
Systematic name M2517
Brief description Loci bound exclusively by SALL4 [GeneID=57167] isoform a in ES cells (embryonic stem).
Full description or abstract Murine embryonic stem (ES) cells are defined by continuous self-renewal and pluripotency. A diverse repertoire of protein isoforms arising from alternative splicing is expressed in ES cells without defined biological roles. Sall4, a transcription factor essential for pluripotency, exists as two isoforms (Sall4a and Sall4b). Both isoforms can form homodimers and a heterodimer with each other, and each can interact with Nanog. By genomewide location analysis, we determined that Sall4a and Sall4b have overlapping, but not identical binding sites within the ES cell genome. In addition, Sall4b, but not Sall4a, binds preferentially to highly expressed loci in ES cells. Sall4a and Sall4b binding sites are distinguished by both epigenetic marks at target loci and their clustering with binding sites of other pluripotency factors. When ES cells expressing a single isoform of Sall4 are generated, Sall4b alone could maintain the pluripotent state, although it could not completely suppress all differentiation markers. Sall4a and Sall4b collaborate in maintenance of the pluripotent state but play distinct roles. Our work is novel in establishing such isoform-specific differences in ES cells.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 20837710   Authors: Rao S,Zhen S,Roumiantsev S,McDonald LT,Yuan GC,Orkin SH
Exact source Table 1S, 2S: bound by Sal4a but not by Sal4b
Related gene sets (show 2 additional gene sets from the source publication)

(show 10 gene sets from the same authors)
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Organism Mus musculus
Contributed by Arthur Liberzon (Broad Institute)
Source platform SEQ_ACCESSION
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.1: First introduced

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