Identification of FOXP1 target genes by ChIP sequencing combined with RNA sequencing. (A-J) Either all (siFOXP1.1) or preferentially the high-molecular-weight isoforms (siFOXP1.2) of FOXP1 (isoforms designated FOXP1_8 and 1_6) were depleted in the 3 DLBCL cell lines (U-2932, SU-DHL6, and RIVA) for 72 hours prior to the assessment of FOXP1 levels, cell viability, and cell death. An unspecific control siRNA was used for comparison. (A) FOXP1 levels as assessed by western blotting with α-TUBULIN as loading control. (B-D) Cell viability as determined by CellTiter Blue assay. (E-G) Apoptosis as determined by Annexin V staining followed by flow cytometry. (H-J) Apoptosis as determined by cleaved/active caspase-3 staining followed by flow cytometry. Data represent means + SEM of at least 3 independent experiments per cell line (B-J). (K) Western blot showing FOXP1 expression in the 4 cell lines used for ChIP-sequencing with α-TUBULIN as loading control. (L) Top enriched motif as identified by DREME in U-2932 (E = 4.1e-295) and SU-DHL6 (E = 2.1e-486) cells. (M) Venn diagram showing the overlap of identified ChIP peaks in the 3 FOXP1-positive cell lines. (N) 27 FOXP1 targets as identified by RNA sequencing and ChIP sequencing. Log₂-transformed gene expression (counts per million; blue/red color code) of U-2932 and SU-DHL6 cell lines transfected with the indicated siRNAs is shown alongside the fold enrichment of ChIP peaks in the same cell lines (gray/green color code). *P < .05, **P < .01, and ***P < .001 (2-tailed Student t test). n.s., not significant.