Figure 5. BCL11B maintains mSWI/SNF occupancy at T_EFF loci via indirect cooperativity.

a, Reciprocal co-immunoprecipitations of IgG, SMARCA4, BCL11B and PBRM1 (columns) from nuclear extracts (1mg/mL) of total thymocytes from wild-type mice and immunoblots of co-immunoprecipitating SMARCA4, PBRM1 and BCL11B (rows). (Input sample, immunoprecipitant (IP), flow-through fraction of non-interacting proteins (FT), molecular weight markers (M)). b, Density sedimentation (glycerol gradient; horizontal axis) and immunoblot of SMARCA4, PBRM1 and BCL11B (rows) from nuclear extracts of total thymocytes from wild-type mice. 1mg total extract loaded onto gradient. c, Representative heatmaps of BAF155 CUT&RUN in sorted BCL11B WT vs. BCL11B cKO DN2-DN3 primary thymocytes (1 of n=3), ATAC-seq in in vitro differentiated SMARCA4 WT vs. SMARCA4 cKO ETPs (1 of n=3), sorted BCL11B WT vs. BCL11B cKO DN2-DN3 primary thymocytes (1 of n=2) and BCL11B occupancy (ChIP-seq²⁷) in DN2-DN3 thymocytes (1 of n=2) intersecting jointly SMARCA4-induced, BCL11B-induced (top) and jointly SMARCA4-induced, BCL11b-repressed (bottom) T_EFF loci. d, Representative genome browser of BAF155 CUT&RUN in sorted BCL11B WT vs. BCL11B cKO DN2-DN3 primary thymocytes (1 of n=3), BCL11B occupancy (ChIP-seq²⁷) in DN2-DN3 thymocytes (1 of n=2), ATAC-seq in sorted BCL11B WT vs. BCL11B cKO primary DN2-DN3 thymocytes (1 of n=2), in vitro differentiated SMARCA4 WT vs. SMARCA4 cKO DN2-DN3 thymocytes (1 of n=2), in vitro differentiated SMARCA4 WT vs. SMARCA4 cKO DN2-DN3 thymocytes (1 of n=2), T_EFF cells (1 of n=2) and B_EFF cells (1 of n=2) at Il27 (T_EFF=T_H2) , Ctla4 (T_EFF= CD8⁺ T_RM), Plekhg6 (T_EFF=CD8⁺ T_{EFF in vitro}) (SMARCA4-induced, BCL11B-induced; left), Il17a (T_EFF=T_H17) and Tox2 (T_EFF=T_FH) (SMARCA4-induced, BCL11B-repressed; right) loci.