Abstract
BackgroundTranscription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells. This process typically requires pioneer transcription factors (TFs) to induce de novo formation of enhancers at previously closed chromatin. Mechanistic information on this process is currently sparse.ResultsHere we explore the mechanistic basis by which GATA3 functions as a pioneer TF in a cellular reprogramming event relevant to breast cancer, the mesenchymal to epithelial transition (MET). In some instances, GATA3 binds previously inaccessible chromatin, characterized by stable, positioned nucleosomes where it induces nucleosome eviction, alters local histone modifications, and remodels local chromatin architecture. At other loci, GATA3 binding induces nucleosome sliding without concomitant generation of accessible chromatin. Deletion of the transactivation domain retains the chromatin binding ability of GATA3 but cripples chromatin reprogramming ability, resulting in failure to induce MET.ConclusionsThese data provide mechanistic insights into GATA3-mediated chromatin reprogramming during MET, and suggest unexpected complexity to TF pioneering. Successful reprogramming requires stable binding to a nucleosomal site; activation domain-dependent recruitment of co-factors including BRG1, the ATPase subunit of the SWI/SNF chromatin remodeling complex; and appropriate genomic context. The resulting model provides a new conceptual framework for de novo enhancer establishment by a pioneer TF.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0897-0) contains supplementary material, which is available to authorized users.
Highlights
Transcription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells
Our studies provide experimental evidence that GATA3 can direct alterations in local chromatin during the mesenchymal to epithelial transition (MET) reprogramming process, including pioneer factor activity, that differ depending on local context and that these alterations proceed through an intermediate consisting of nucleosomal DNA bound by a pioneer factor
GATA3 binding sites acquire open chromatin structure and enhancer-like histone modifications To investigate chromatin reprogramming during the MET process, we utilized MDA-MB-231 breast cancer cells, in which GATA3, and its known partners, FOXA1 and estrogen receptor-α, are below limits of detection at the protein level
Summary
Transcription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells This process typically requires pioneer transcription factors (TFs) to induce de novo formation of enhancers at previously closed chromatin. Pioneer factors have at least three fundamental properties as recently described by Iwafuchi-Doi and Zaret [10]: (1) they can interact with their cognate recognition sequences in Takaku et al Genome Biology (2016) 17:36 nuclease-resistant chromatin prior to activation of transcription; (2) they increase local chromatin accessibility as a prelude to productive binding of other factors; and (3) they have integral roles in the establishment of cell lineage. Other TFs involved in reprogramming of somatic cells to pluripotency such as Oct, Sox, and Klf, function as pioneer factors utilizing unique adaptations of their DNA recognition surfaces to accommodate nucleosome structure, which likely represents a common genome interrogation mechanism of the pioneer class [18, 19]. Validated pioneer factors exhibit large structural diversity in sequence-recognition domains, mechanism(s) underlying chromatin opening may vary
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