Previously, we found that chromatin remodeling was required for Th2 cytokine gene expression. We found that transcription factors recruited the SWI/SNF remodeling enzyme BRG1 to specific sites in Th2 cells. BRG1 was required before and after Th2 differentiation. We found that the BAF-specific subunit BAF250a/Arid1a was required for cytokine gene activation. We found the ISWI remodeling enzyme SNF2H could activate and repress gene expression in T cells. Using a genomic approach, we found that BRG1 interprets both differentiation and activation signals and plays a causal role in gene regulation, chromatin structure, and cell fate. Our findings suggest that BRG1 binding is a useful marker for identifying active cis-regulatory regions in protein-coding and miRNA genes. We also found that distal enhancers were functional in a chromatin template assay, but not in standard enhancer assays. Progress: While different versions of SWI/SNF complexes, including BAF and PBAF, have been described based on unique subunit composition, the specific function of PBAF in Th cell function and cytokine expression has not been reported. Using mice conditionally deficient for a PBAF-specific component, BAF180/Pbrm1, we examined the role of the PBAF SWI/SNF complex in Th cell development and gene expression using. We found that T cell development in the thymus and lymphoid periphery is largely normal when the BAF180 gene was deleted late in thymic development. Gene expression analysis suggested that BAF180 was more important in gene repression than in gene activation, both in Nave (Thp) and differentiated (Th2) cells. BAF180-deficient Th2 cells expressed elevated amounts of the immunoregulatory cytokine IL-10. BAF180 bound directly to regulatory elements in the Il-10 locus. Binding was correlated with IL-10 expression, even at very distal elements in the vicinity of the neighboring IL24 and IL20 genes., In the absence of BAF180 (a PBAF component), BAF250 (BAF) complexes were bound instead. In the absence of BAF180, increased histone acetylation and CBP recruitment to the IL-10 locus were found;thus, the SWI/SNF ATP-dependent chromatin remodeling system could regulate histone modifications. These results demonstrate that BAF180 is a repressor of IL-10 transcription in Th2 cells and suggest that the differential recruitment of different SWI/SNF subtypes can have direct consequences on chromatin structure and gene transcription. Interestingly, a 100 kb human transgene encompassing the IL10 gene and the DNA between the IL19 and MAPKAPK2 genes provided only weak expression in T cells, suggesting distal regulatory elements were yet to be discovered (Proc Natl Acad Sci U S A. 2009, 106:17123, PMID: 19805095). It is possible the BRG1 binding we find in the vicinity of the IL24 and IL20 genes marks additional regulatory regions;these sites were also bound by Stat6 and Stat5b. Importantly, the BRG1 binding we found was correlated with IL-10 expression. Genome-wide BRG1 binding data in 6 murine T cell subsets (Raw sequence reads, aligned tags BRG1 binding regions and ChIP-seq stats for all T helper subsests) were deposited in GEO, and are publicly available at accession number GSE23719. Comprehensive gene expression data in 4 murine T helper subsets, WT and BAF180 deficient cells, were deposited in GEO and are publicly available at accession number GSE31676). Our results provide new information on the regulation of T cell fate and function by chromatin remodeling enzymes. This work could be important in understanding the biological basis of, and identifying therapeutic targets for, autoimmune disorders, allergy and atopy, and vaccine response. Future: No further work is planned on this project.
