title: Master transcription factors and mediator establish super-enhancers at key cell identity genes.
abstract: Master transcription factors Oct4, Sox2, and Nanog bind enhancer elements and recruit Mediator to activate much of the gene expression program of pluripotent embryonic stem cells (ESCs). We report here that the ESC master transcription factors form unusual enhancer domains at most genes that control the pluripotent state. These domains, which we call super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Reduced levels of Oct4 or Mediator cause preferential loss of expression of super-enhancer-associated genes relative to other genes, suggesting how changes in gene expression programs might be accomplished during development. In other more differentiated cells, super-enhancers containing cell-type-specific master transcription factors are also found at genes that define cell identity. Super-enhancers thus play key roles in the control of mammalian cell identity.
authors.affiliation: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Warren A
authors.initials: WA
authors.lastname: Whyte
authors.forename: David A
authors.initials: DA
authors.lastname: Orlando
authors.forename: Denes
authors.initials: D
authors.lastname: Hnisz
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Abraham
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Lin
authors.forename: Michael H
authors.initials: MH
authors.lastname: Kagey
authors.forename: Peter B
authors.initials: PB
authors.lastname: Rahl
authors.forename: Tong Ihn
authors.initials: TI
authors.lastname: Lee
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism; D002460:Cell Line; D019070:Cell Lineage; D053595:Embryonic Stem Cells / Q000378:metabolism*; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D006801:Humans; D056892:Mediator Complex / Q000378:metabolism*; D051379:Mice; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D056892:Mediator Complex; D014157:Transcription Factors