Fig. 3: CFAP20 suppresses CD R-loops at promoters.
From: CFAP20 salvages arrested RNAPII from the path of co-directional replisomes
a, Distribution of DRIP–seq reads across indicated regions of the ITGA11 gene in the specified cell lines and conditions. b, Metaprofiles of DRIP–seq aligned around 508 promoters (TSSs) of genes >50 kb (top) or 135 TSSs with ≥1.5-fold higher DRIP signal from –2 kb to +3 kb around TSSs (bottom) in CFAP20-KO relative to WT. c, Metaprofiles of DRIP–seq in the indicated cell lines and conditions aligned around 508 terminators (TTSs) of genes >50 kb (top) or 135 TTSs with ≥1.5-fold higher DRIP signal from −2 kb to +3 kb around TSSs (bottom) in CFAP20-KO relative to WT. d, Metaprofiles of DRIP–seq in WT and CFAP20-KO cells aligned around HO (n = 408) TSSs relative to origins mapped by OK–seq5. Data are averages after trimming the top and bottom 5% of data (a trim-mean of 0.1) to remove extreme values. e, Metaprofiles of DRIP–seq in WT and CFAP20-KO cells aligned around CD (n = 1,395) TSSs relative to origins mapped by OK–seq5. Data as in d. f, Schematic of episomal system for transcription–replication conflicts. The unidirectional EBV replication origin (oriP; red) is placed either behind (HO) or in front (CD) of the EBNA1 gene containing the R-loop-forming mAIRN segment (blue) under TetON control. g, DRIP–quantitative PCR (qPCR) in HEK293T cells with mAIRN HO or CD plasmids, transfected with control or CFAP20 siRNAs ± DOX for 48 h. DRIP signals around the mAIRN TSS are shown as % input; data represent n = 3 biological independent experiments. Significance by one-way ANOVA with Šidák’s correction. P values from left to right: 0.4616 and <0.0001. h, Heat maps of CFAP20 ChIP–seq in TY-CFAP20 cells aligned around origins mapped by OK–seq5. i, Metaprofiles of DRIP–seq (red), CFAP20 ChIP–seq (green) and BrU–seq (blue) in the indicated cell lines within a 25-kb window adjacent to origins extending up to 75 kb. Data are Trimmean 0.1 to remove extreme values.
