An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network

Abstract

To understand the mechanism underlying the roles of these complexes in ES cells, we performed high-resolution genome-wide mapping of the core ATPase subunit, Brg, using ChIP-Seq technology. We find that esBAF, as represented by Brg, binds to genes encoding components of the core ES transcriptional circuitry, including Polycomb group proteins. esBAF colocalizes extensively with transcription factors Oct4, Sox2 and Nanog genome-wide, and shows distinct functional interactions with Oct4 and Sox2 at its target genes. Surprisingly, no significant colocalization of esBAF with PRC2 complexes, represented by Suz12, is observed. Lastly, esBAF colocalizes with Stat3 and Smad1 genome-wide, consistent with a direct and critical role in LIF and BMP signaling for maintaining self-renewal. Taken together, our studies indicate that esBAF is an essential component of the core pluripotency transcriptional network, and might also be a critical component of the LIF and BMP signaling pathways essential for maintenance of self-renewal and pluripotency.BAF complexes ͉ Brg ͉ SWI/SNF ATP-dependent chromatin remodeling E mbryonic stem cells (ES) maintain an epigenetic state that enables both self-renewal and differentiation into all embryonic lineages (1). Recent studies reveal that in ES cells Oct4, Sox2, Nanog, and Klf4 elaborate a core transcriptional circuitry (2-4), working in coordination with Polycomb complexes (5, 6), microRNAs (7), and histone modification enzymes (8) to stably maintain the expression of pluripotency genes, and to repress lineage determinant genes. This transcriptional circuitry is kept in exquisite balance, because it can be perturbed both by reducing or increasing the levels of core regulators such as Oct4, Sox2, and Nanog, causing ES cells to lose self-renewal ability and/or pluripotency (9-14). At the same time, ATP-dependent chromatin remodeling enzymes in the Tip60/p400 and SWI/SNF families have been recently shown to be crucial for the maintenance and function of ES cells (15). Recent findings by us and others have shown that components of mammalian SWI/SNF (or BAF, Brg/Brahma Associated Factors) complex, Brg, BAF155, and BAF250A are crucial for the proliferation, self-renewal and pluripotency of ES cells (16,17,18). ES cells deficient in Brg maintain the expression of Oct4, Sox2, and Nanog for several cell divisions but rapidly lose colony morphology and proliferative capacity characteristic of ES cells (16). Upon prolonged absence of Brg, remaining ES cells down-regulate pluripotency markers such as Oct4 and Sox2 (16,17), reflecting the complete loss of ES cell identity secondary to the effects of Brg depletion or suggesting that Brg is required to maintain stable expression of these markers over many cell divisions. In addition, the composition of BAF complexes in ES cells (esBAF) is biochemically and functionally specialized. esBAF complexes are defined by the incorporation of Brg but not Brm, BAF155 but not BAF170, and BAF60A but not BAF60C (16). When esBAF complexes are altered by enforced incorpora...

Absolute requirement for STAT3 function in small-intestine crypt stem cell survival

“…Others have suggested that elevated Bmi1 expression (at least in murine ES cells) is rather a marker of differentiation and associated with exit from the selfrenewing/pluripotent state. 20 …”

“…20 Interestingly, the Eed gene is transcriptionally controlled by STAT3 (and Oct4) in murine ES cells, with STAT3/Oct4 (via Eed) reversibly silencing differentiationassociated genes such as Tbx5, GATA6 and Cdx2. 21 Further, Eed and Bmi1 can function antagonistically -in haematopoietic cell proliferation, Eed demonstrated an anti-proliferative function, negatively regulating lymphoid and myeloid progenitor cell numbers in the bone marrow, 22 whereas Bmi1 positively regulated primitive bone marrow progenitor cell proliferation.…”

“…20 Chromatin immunoprecipitation-sequencing demonstrated a highly statistically significant 70% co-occupation of murine ES cell target genes by both STAT3 and the esBAF ATPase component Brg. 20 Figure 10 Further, knocking-down Brg expression upregulated the expression of several polycomb group (PcG) genesincluding Bmi1, Cbx7 and Ring1a -which normally contribute to the polycomb repressive complex 1. These genes also contained a statistically significant region bound by Brg, with the suggestion that esBAF/Brg normally antagonises PcG function in murine ES cells by binding to and repressing PcG gene transcription.…”

The evolving biology of cell reprogramming

“…These observations are interesting given the role of an ES cell form of BAF in maintaining pluripotency [99][100][101] and the detection of Brg1 and Baf155 in Oct4 protein complexes [76]. This may suggest that BAF acts by facilitating chromatin binding of Oct4 to promoters during factor-directed reprogramming.…”

Histone Regulation in the CNS: Basic Principles of Epigenetic Plasticity

“…Therefore, it can be inferred that BAF complexes function during early neurodevelopment to promote maintenance and differentiation of neural progenitors, thereby allowing for proper neural tube formation. To date, genome-wide mapping studies of BAF complex subunits in neurons have not been reported, so it remains unclear as to the exact role that BAF complexes might have in guiding chromatinregulated transcriptional programs necessary for early neurodevelopmental processes; however, studies performed in embryonic stem (ES) cells indicate that thousands (B10 000) of BAF-binding sites exist throughout the mammalian genome, and that nearly half of these sites localize to transcriptional start sites (Ho et al, 2009). Such patterns of BAF complex enrichment in ES cells indicate that chromatin-remodeling complexes may indeed be critical for aspects of developmental transcriptional plasticity, yet the exact roles of these genome-wide chromatin associations remain unclear.…”