c During mouse preimplantation development, the generation of the inner cell mass (ICM) and trophoblast lineages comprises upregulation of Nanog expression in the ICM and its silencing in the trophoblast. However, the underlying epigenetic mechanisms that differentially regulate Nanog in the first cell lineages are poorly understood. Here, we report that BRG1 (Brahmarelated gene 1) cooperates with histone deacetylase 1 (HDAC1) to regulate Nanog expression. BRG1 depletion in preimplantation embryos and Cdx2-inducible embryonic stem cells (ESCs) revealed that BRG1 is necessary for Nanog silencing in the trophoblast lineage. Conversely, in undifferentiated ESCs, loss of BRG1 augmented Nanog expression. Analysis of histone H3 within the Nanog proximal enhancer revealed that H3 lysine 9/14 (H3K9/14) acetylation increased in BRG1-depleted embryos and ESCs. Biochemical studies demonstrated that HDAC1 was present in BRG1-BAF155 complexes and BRG1-HDAC1 interactions were enriched in the trophoblast lineage. HDAC1 inhibition triggered an increase in H3K9/14 acetylation and a corresponding rise in Nanog mRNA and protein, phenocopying BRG1 knockdown embryos and ESCs. Lastly, nucleosome-mapping experiments revealed that BRG1 is indispensable for nucleosome remodeling at the Nanog enhancer during trophoblast development. In summary, our data suggest that BRG1 governs Nanog expression via a dual mechanism involving histone deacetylation and nucleosome remodeling. C ell fate decisions are crucial for the development of multicellular organisms. In higher animals, such as placental mammals, the first cell fate decision occurs during preimplantation development, when the totipotent blastomeres differentiate into the blastocyst inner cell mass (ICM) and trophoblast lineages (1). The proper development of the blastocyst ICM and trophoblast lineages is critical for embryo implantation, placentation, gastrulation, and full-term development. Abnormal development of the ICM and trophoblast lineages may contribute to pregnancy loss, reproductive disorders, and birth defects.Early lineage formation in preimplantation embryos is mediated by a combination of transcriptional and epigenetic mechanisms (2, 3). During blastocyst formation, the expression of key transcription factors, such as octamer-binding transcription factor 4 (OCT4), Nanog homeobox (NANOG), and sex-determining region Y box 2 (SOX2), becomes restricted to the pluripotent ICM, while transcription factor AP-2 gamma (TFAP2C), GATA binding protein 3 (GATA3), and caudal type homeobox 2 (CDX2) are expressed exclusively in the trophoblast lineage (4-10). The spatial and temporal expression of these lineage-specific factors is controlled by position-dependent HIPPO signaling, transcription factor regulatory loops, and chromatin modifications (2,3,(10)(11)(12). For example, the HIPPO signaling pathway differentially regulates lineage formation via the downregulation of CDX2 expression in the ICM and SOX2 expression in the trophoblast (10, 12). In conjunction with the HIPPO pathway, O...