Project name: Mus musculus

Description: Murine embryonic stem cells (ESCs) are defined by continuous self-renewal and pluripotency. A diverse repertoire of protein isoforms arising from alternative splicing are expressed in ES cells without defined biological roles. Sall4, a transcription factor essential for pluripotency, exists as two isoforms (Sall4a and Sall4b). By genome-wide location analysis, we have determined that Sall4b, and 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 ESCs 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.Overall design: ES cells expressing the BirA ligase, which attaches biotin to a specific target sequence, were transfected with either Sall4a or Sall4b that had been engineered to have the biotinylation sequence at the N-terminus. ChIP-on-Chip was then performed to identify loci bound by Sall4a or Sall4b.

Data type: Epigenomics

Sample scope: Multiisolate

Relevance: ModelOrganism

Release date: 2010-09-13

Last updated: 2010-03-24