The role of individual subunits in the targeting and function of the mammalian BRG1-associated factors (BAF) complex in embryonic stem cell (ESC) pluripotency maintenance has not yet been elucidated. Here we find that the Bromodomain containing protein 9 (BRD9) and Glioma tumor suppressor candidate region gene 1 (GLTSCR1) or its paralog GLTSCR1-like (GLTSCR1L) define a smaller, non-canonical BAF complex (GBAF complex) in mouse ESCs that is distinct from the canonical ESC BAF complex (esBAF). GBAF and esBAF complexes are targeted to different genomic features, with GBAF co-localizing with key regulators of naive pluripotency, which is consistent with its specific function in maintaining naive pluripotency gene expression. BRD9 interacts with BRD4 in a bromodomain-dependent fashion, which leads to the recruitment of GBAF complexes to chromatin, explaining the functional similarity between these epigenetic regulators. Together, our results highlight the biological importance of BAF complex heterogeneity in maintaining the transcriptional network of pluripotency.

ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here, we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation. Changes in accessibility are predictive of changes in expression and correlate with loss of H3K4me and H3K27ac marks, nucleosome spacing, and transcription factor binding, particularly at growth pathway genes including MET. We find that ARID1B knockdown in ARID1A mutant ovarian cancer cells causes similar loss of enhancer architecture, suggesting that this is a conserved function underlying the synthetic lethality between ARID1A and ARID1B.

b Cyclin-dependent kinase 7 (CDK7) activates cell cycle CDKs and is a member of the general transcription factor TFIIH. Although there is substantial evidence for an active role of CDK7 in mRNA synthesis and associated processes, the degree of its influence on global and gene-specific transcription in mammalian species is unclear. In the current study, we utilize two novel inhibitors with high specificity for CDK7 to demonstrate a restricted but robust impact of CDK7 on gene transcription in vivo and in in vitro-reconstituted reactions. We distinguish between relative low-and high-dose responses and relate them to distinct molecular mechanisms and altered physiological responses. Low inhibitor doses cause rapid clearance of paused RNA polymerase II (RNAPII) molecules and sufficed to cause genome-wide alterations in gene expression, delays in cell cycle progression at both the G 1 /S and G 2 /M checkpoints, and diminished survival of human tumor cells. Higher doses and prolonged inhibition led to strong reductions in RNAPII carboxyl-terminal domain (CTD) phosphorylation, eventual activation of the p53 program, and increased cell death. Together, our data reason for a quantitative contribution of CDK7 to mRNA synthesis, which is critical for cellular homeostasis. C yclin-dependent kinases (CDKs) form the enzymatic components of a group of heterodimeric serine/threonine kinases that have important roles in multiple cellular processes (1). CDK7/KIN28 was originally identified as a critical regulator of mRNA transcription in Saccharomyces cerevisiae (2-5). In vertebrates CDK7 has a dual function, influencing cell cycle progression and RNA polymerase II (RNAPII) transcription (6). Specifically, CDK7 forms the CDK-activating kinase (CAK) with two other TFIIH subunits, cyclin H and MAT1. The CAK activates downstream cell cycle CDKs, including cdc-2/CDK1, CDK2, CDK4, and CDK6, by phosphorylating key threonine residues in a process known as T-loop activation (7,8). In transcription, as RNAPII begins to lose contact with many of the general transcription factors (GTFs) during promoter escape, CDK7, functioning as part of the TFIIH complex, phosphorylates RNAPII and allows the elongation complex to move downstream away from the transcription start site (TSS) (reviewed in reference 9). Specifically, CDK7 directly targets the carboxyl-terminal domain (CTD) of the Rpb1 subunit of RNAPII, which is comprised of 52 heptad repeats (Y 1 S 2 P 3 T 4 S 5 P 6 S 7 ) in humans. While the serine 2 (Ser2), serine 5 (Ser5), and serine 7 (Ser7) residues are all subject to phosphorylation, CDK7 preferentially targets Ser5 and Ser7 (10-17). Phosphorylation patterning of the CTD is important as it influences the association of numerous nuclear factors with RNAPII (18,19), as was recently demonstrated in yeast, where KIN28-driven phosphorylation of Ser5 residues was shown to trigger dissociation of the coactivator Mediator (20). In mammals, the exact mechanisms linking CTD phosphorylation (CTD-P) with transcription are yet to be fully elucidate...

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