We examined the role of ATP-dependent chromatin remodeling in T cell function. Our previous work identified an activating role for BAF complexes, SWI/SNF complexes containing BAF250, in cytokine gene expression in T helper cells [24, 35, 47]. In the current study we examined the contribution of PBAF, a different SWI/SNF complex containing BAF180, in T cell function and cytokine expression using T cell specific BAF180-deficient mice. We identified numerous BAF180-dependent changes in gene expression in our microarray analysis; however, overall Th cell development and cytokine expression were intact. BAF180 was a negative regulator of IL-10 transcription and, in the absence of BAF180, histone modifications were reprogrammed and BAF250-containing BAF complexes were recruited to the IL-10 locus.
We find the binding patterns of BAF180 and BAF250 are overlapping, yet readily distinguishable. Our data are consistent with the model that SWI/SNF exists in distinct BAF and PBAF complexes, determined by several independent research groups examining different species. Our data are also consistent with a stepwise assembly model, as proposed based upon time-resolved cell imaging studies . These data are more difficult to reconcile with the proposal that BAF180 and BAF250 are, or can be, in the same complex [70, 71]. We note that genetic studies have found different targets and functions for the BAF-specific subunits BAF250a/Arid1a and BAF250b/Arid1b in ES cells [36, 37]. Differences have also been found for the PBAF-specific subunits BAF180, BAF200 and BRD7 [25, 31]. There may be different BAF and PBAF complexes; alternatively, it may be that only some SWI/SNF subunits within a complex contribute to function at a particular locus. Direct, comprehensive comparison of these subunits would extend our understanding of the SWI/SNF system.
The targeting of remodeling complexes to specific DNA elements is mediated by association with transcription factors, histone modifications, non-coding RNA and interactions with the general transcription machinery [4, 42, 72–76]. Our previous studies identified important roles for transcription factors, particularly STATs, in the recruitment of BRG1 to specific regulatory elements in T cells [4, 24, 47]. Interestingly, Stat6 has been shown to be a critical transcription factor in the Th2-specific expression of IL-10 and IL-24 [67, 77], and analysis of BRG1 and Stat6 ChIP-Seq data reveal Stat6 binding at many of the distal regulatory elements in the IL-10 locus occupied by BAF and PBAF complexes [47, 57]. Whether or not Stat6 is mediating the recruitment of SWI/SNF to the IL-10 locus or if Stat6 preferentially interacts with BAF or PBAF complexes remains to be determined. Ets-1 is reported to be a repressor of IL-10 expression [78, 79], and Ets sequence motifs are enriched at BRG1 binding sites in resting Th cells .
Our recent examination of BRG1 did not reveal repression as a prominent function for SWI/SNF, by comparison of Th2S gene expression and BRG1 binding . We note that most BAF180-mediated repression was in uTh2 cells, and we did not examine resting cell gene expression in our previous work. Alternatively, there may be more SWI/SNF activation targets than repression targets; this assessment awaits analysis of BAF250a KO and BRG1 KO Th2 cells for direct comparison under identical conditions. A previous report suggested Brm more important for repression, BRG1 more important for activation . It is unclear how BAF180 complexes are mediating repression; they may be working as repressor complexes, or preventing the binding and function of activator complexes containing BAF250.
It is perhaps surprising that we found that deletion of BAF180 (late in T cell development) does not strongly perturb early T cell development. We have used a CRE expression cassette that induces deletion at a late DN stage, potentially bypassing an earlier requirement for BAF180 expression. Several other factors, such as GATA3, BRG1, TCF7, β-catenin and BPTF, appear to be required for early T cell development [22, 81–85]. Given that BRG1 has obvious effects on T cell development, we could have found that BAF180 deletion would also have strong effects on T cell development. BAF180-deficient mice have defects in cardiac development  and BAF180 is a cell cycle regulator in some settings [43, 44]; it is not clear what determines the relative importance of PBAF complexes in different cell states.
Genetic variants within IL-10 have been associated with human disease. The human SNP rs3024505, associated with Type 1 Diabetes, Crohn's disease and ulcerative colitis [15–17], maps to BRG1, STAT6, and STAT4 binding at +6.3 k in the mouse. Ulcerative colitis is also linked to rs3024493 , within intron 3; this is 1 k upstream of BRG1, STAT4 and CBP binding at +3.2 k, and slightly downstream of BRG1 binding and H3K9 acetylation at +1.8 k. Behcet's disease is associated with a variant (rs1800871) that lies near the IL-10 promoter , adjacent to BRG1, STAT6 and CBP binding. The proximity of these genetic variants to these remodeling enzyme and transcription factor binding regions suggests these binding regions may regulate IL-10 gene expression in a physiologically relevant manner.
Previous studies on breast cancer cells suggested BAF180 is a tumor suppressor gene that positively regulates the expression of the cell cycle inhibitor p21 through direct interaction and activation of the p21 promoter . A positive role for BAF250a in the regulation of p21 transcription has been suggested in studies in a pre-osteoblast line . However BAF250a can also serve as a repressor of c-myc in these same cells while another BAF-specific protein, BAF250b, is an activator of c-myc . We observed a slight decrease in the ability of BAF180-deficient Th cells to proliferate in response to T cell activation and enhanced expression of cell cycle inhibitors, including p21 (CDKN1), suggesting that in T cells BAF180 is a repressor of these genes. We also observed binding of PBAF complexes to the p21 locus in T cells (data not shown). At this time, there is no simple relationship between BAF/PBAF complexes and cell cycle progression.