T-bet regulates gene transcription mainly via distal chromatin coaccessibility in CLL cells. (A) T-bet–mediated regulation of T-bet-dependent genes. Promoter with an ATAC peak containing a T-bet binding motif, blue; coaccessible link of the promoter to the distal T-bet peak within 1 Mb, yellow; no link to the T-bet motif peak, gray. (B) Number of coaccessible links from T-bet–dependent gene promoters without (left) or with (right) ATAC peak with T-bet binding motif within a 1 Mb window in Tbx21^–/– and Tbx21^+/+ TCL1 cells. Whiskers represent the standard error of biological replicates (n = 2). (C) Overlap of coaccessible links from T-bet–dependent genes with distal T-bet peaks within 100 kb in Tbx21^–/– and Tbx21^+/+ TCL1 cells. The coaccessible links from the biological replicates were merged. (D) Gene expression of Nos1 in Tbx21^–/– (n = 6) and Tbx21^+/+ TCL1 cells (n = 5) from bulk RNA-seq data. (E) Coaccessibility in Tbx21^–/– and Tbx21^+/+ TCL1 cells at the T-bet-dependent gene Nos1 region. Browser tracks and coaccessible links from the biological replicates were merged. Top: browser tracks of pseudobulk chromatin accessibility from single cells. Middle: 2 kb regions around peaks from pseudobulk chromatin accessibility with no accessibility change (gray), significantly higher accessibility in Tbx21^+/+ TCL1 cells (black), and significantly higher accessibility in Tbx21^–/– TCL1 cells (blue); T-bet binding motif positions and gene annotation in black. Bottom: coaccessible links between peaks at Nos1 promoters and distal peaks in Tbx21^–/– and Tbx21^+/+ TCL1 cells. Promoters of Nos1 (1 kb around the TSS1-3) are marked in red.