An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

Abstract

Mammalian SWI/SNF [also called BAF (Brg/Brahma-associated factors)] ATP-dependent chromatin remodeling complexes are essential for formation of the totipotent and pluripotent cells of the early embryo. In addition, subunits of this complex have been recovered in screens for genes required for nuclear reprogramming in Xenopus and mouse embryonic stem cell (ES) morphology. However, the mechanism underlying the roles of these complexes is unclear. Here, we show that BAF complexes are required for the self-renewal and pluripotency of mouse ES cells but not for the proliferation of fibroblasts or other cells. Proteomic studies reveal that ES cells express distinctive complexes (esBAF) defined by the presence of Brg (Brahma-related gene), BAF155, and BAF60A, and the absence of Brm (Brahma), BAF170, and BAF60C. We show that this specialized subunit composition is required for ES cell maintenance and pluripotency. Our proteomic analysis also reveals that esBAF complexes interact directly with key regulators of pluripotency, suggesting that esBAF complexes are specialized to interact with ES cell-specific regulators, providing a potential explanation for the requirement of BAF complexes in pluripotency.BAF complexes ͉ BAF155 ͉ Brg E S cells are pluripotent cells capable of both limitless selfrenewal and differentiation into all embryonic lineages. These abilities are conferred by various mechanisms, including transcription factors (1-3), possibly Polycomb complexes (4, 5), microRNAs (6), and histone modification enzymes (7) that work in coordination to maintain the expression of pluripotency genes while repressing lineage-determinant genes. The involvement of such mechanisms in pluripotency has been investigated extensively in recent years (reviewed in ref. 8), but the role of chromatin remodeling enzymes remains unclear.The mammalian genome encodes about 30 SWI2/SNF2-like ATPases, which are assembled into SWI/SNF-like complexes with ATP-dependent chromatin remodeling activity. Of these, Brg and Brm are alternative ATPases of a family of 2-MDa multisubunit SWI/SNF or BAF complexes and make up the prototypic mammalian SWI/SNF-like chromatin remodeling complexes (9, 10). BAF complexes have been shown to be essential for many aspects of mammalian development (11-13). A role of BAF complexes in pluripotency is suggested by observations that deletion of Brg, BAF155 (or Srg3), and BAF47 (or hSNF5) all lead to peri-implantation lethality and failure of the totipotent cells that give rise to both the inner cell mass and trophoblast to survive and grow (14-16). The catalytic ATPase subunit, Brg, also was recovered in screens for factors essential for nuclear reprogramming (17) and to ES cell morphology (18). In addition, ES cells lacking BAF250 have defects in ES cell maintenance and differentiation (19,20). However, the mechanism by which BAF complexes help to establish and maintain pluripotency is not understood.In vitro, BAF complexes use energy generated from ATP hydrolysis to alter DNA-nucleosome contacts (21) and can also e...

Epigenetic regulation of aging stem cells

“…However, we also note that regulators of DNA methylation are required for the function of a variety of adult stem cells (Zhao et al, 2003;Ma et al, 2009;Trowbridge et al, 2009;Sen et al, 2010;Trowbridge and Orkin, 2010;Wu et al, 2010), and that they complex with chromatin modifiers to elicit changes in chromatin state (Jones et al, 1998;Nan et al, 1998;Fuks et al, 2003). In addition, chromatin remodeling factors are also important for stem and progenitor cell function (Lessard et al, 2007;Ho et al, 2009;Ho and Crabtree, 2010), suggesting that several epigenetic mechanisms could coordinately control adult stem cell gene expression programs during organismal aging.…”

Brg1 is required for stem cell maintenance in the murine intestinal epithelium in a tissue-specific manner

“…In line with the vast network of protein interactions involving Brg1, the latter has been reported to be involved in regulation of various physiological processes. Consistent with early developmental failure of Brg1 deficient mice [4], Brg1 has been implicated in a number of early developmental events such as zygotic genome activation [5], the segregation of the inner cell mass and trophectoderm [6], and transcriptional control of the key regulators of embryonic stem cell pluripotency and self-renewal [7,8]. In addition to its role in early development, Brg1 has also has been implicated in various processes at later stages of embryonic development, mainly in aiding differentiation along various cell lineages (reviewed in [9]) as well as in maintenance and differentiation of certain somatic stem cells including neural [10] and mesenchymal stem cells [11,12].…”

The Short Isoform of NF‐YA Belongs to the Embryonic Stem Cell Transcription Factor Circuitry

“…4C): essentially all showed a decrease in expression under conditions of LIF withdrawal and recovered normal expression in cells grown with TAT-NF-YAs. We checked the levels of expression of components of the esBAF complex, shown to be important to maintain the pluripotent state by conditioning the genome for LIF/STAT3 signaling [27]: the CCAAT Smarca4 and Smarcc1 indeed increased upon transduction of cells with TAT-NF-YAs. The effects were relatively modest only on Sall4 and Check1 and negligible on the CCAAT-less Nes and Mll1 genes.…”

“…We analyzed the sites of several TFs-E2F1, NANOG, KLF4, SOX2, ESRRB, STAT3, OCT4, and CTCF-for which ChIP-Seq data in mESCs are available [6,27,28], including NF-Y [23]. We retrieved the promoters of genes bound by these TFs and scanned them with Pscan; using the latest NF-Y positional sequence frequency matrix, we have gathered from genomic studies [11], at a score of 0.8, which recovers most bona fide NF-Y sites.…”