Fig. 3

SF3B2 modulates RNA polymerase II activity. A, B Line plot of nascent transcript density around TSS, 5'ss, and 3'ss in siSF3B2 and siControl-treated FaDu cells A or GFP- and GFP-SF3B2-FaDu cells B. The nascent transcript was analyzed using PRO-seq. C, D Pausing index of Pol2 in siSF3B2 and siControl-treated FaDu cells C or GFP- and GFP-SF3B2-FaDu cells D. Only PAR-CLIP, genes with SF3B2 peaks on RNA but not chromatin, n = 901. Only CT, genes with SF3B2 peaks on chromatin but not RNA, n = 2202. Without binding, genes without SF3B2 peaks, n = 7780. P value was calculated using the pairwise Wilcox rank sum test adjusted with Bonferroni correction. E Line plot of nascent transcript density centering SF3B2 PAR-CLIP peaks. F Dot plot of percent spliced in the index (Psi/Ψ). The red dot indicates the significantly changed local splicing variation (LSV). Pie chart of LSV with significant and non-significant change. A 100% stacked bar plot of the significantly changed LSV. A3SS, alternative 3′ splice site; A5SS, alternative 5′ splice site; ES, exon skipping; IR, intron retention. G A 100% stacked bar plot of genes stratified by SF3B2 PAR-CLIP and CUT&Tag peaks with or without the significantly changed LSV. Genes were stratified into four categories: genes with SF3B2 PAR-CLIP and CUT&Tag peaks (PAR/CUT); genes with CUT&Tag peaks (−/CUT); genes with SF3B2 PAR-CLIP peaks (PAR/−); genes without SF3B2 peaks (−/−). SF3B2 KD, knockdown of SF3B2. SF3B2 OE, GFP-SF3B2 overexpression. P value was calculated using the Fisher’s Exact test with Monte Carlo simulation