Figure 5.

ZFP91 functions as a transcription factor in TCLs and targets keynote genes from histone modification, WNT, NF-kB, and MAP kinase signaling. (A) Western blot of phosphorylated (p-ERK) and total ERK in SU-DHL-1 parental and len-regrown cells treated with 1 μM len for indicated timepoints compared with DMSO. (B) SU-DHL-1 parental and len-regrown cells were single-cell sorted and plated. Wells with proliferating cells were counted 3 weeks after plating. Data are from 3 independent experiments and assessed by 2-tailed Student t test (means plus or minus SD). (C) Venn diagram shows the numbers of genes with significantly altered expression upon ZFP91 knockout (KO) in SU-DHL-1 parental and len-regrown (RG) cells compared with their wild-type counterparts. (D) Heatmaps of ZFP91 ChIP-seq signals centered on ZFP91 peaks in SU-DHL-1 parental and len-regrown cells (N = 1419). Peaks were defined as common (n = 529), enriched in parental (n = 122), or enriched in len-RG (n = 768) cells as indicated at right. (E) Analysis of PRO-seq signal near distal ZFP91 peaks enriched in len-regrown cells. To focus on sites of enhancer RNA (eRNA) synthesis within ZFP91-bound enhancers, metagene plots were centers at sites of maximum PRO-seq signal within 2kb of ZFP91 peaks. Graphed are PRO-seq reads in 25nt bins, smoothed over 3 neighbors. (F) Violin plots show the fold change in RNA-seq or PRO-seq signal in len-regrown vs parental cells within genes nearest to distal ZFP91 peaks. Genes were divided based on whether the ZFP91 peak was common or enriched in parental or len-RG cells. P values are from Kruskal Wallis tests. (G) Analysis of the overlapping of ZFP91 ChIP-seq peaks from SU-DHL-1 len-regrown cells and 3 primary IMiD-resistant TCL lines by Bedtools. (H) IGV tracks show ZFP91 binding at MAP3K12, FZD2, HDAC5, GHDC, and IKBKE with H3K4me3, H3K27ac, PRO-seq, and RNA-seq signals in SUP-M2 cells. IGV, Integrative Genomics Viewer.