Extended Data Fig. 3: Identification and characterization of KCTD10 binding genome wide.
From: KCTD10 is a sensor for co-directional transcription–replication conflicts
a, genomic features associated with KCTD10 peaks from cells transfected with empty vector (EV) or FLAG-tagged KCTD10 (FL-KCTD10) and treated with control (DMSO) or ICRF193 (100 nM) for 4 h. b, mean coverage of FL-KCTD10 in control or ICRF193-treated cells along the gene body (± 3 kb). c, representative window showing FL-KCTD10 binding in control and ICRF193-treated cells and the association with gene bodies and replication fork direction (RFD). d, venn diagram showing genome-wide co-occurrence of KCTD10-bound genes with co-directional conflicts in control and ICRF193-treated cells. e, circos plot showing overlap between KCTD10-bound genes in control and ICRF193-treated cells. Magenta curves link exact gene matches. Teal curves link genes that belong to the same enriched ontology term. f, enrichment analysis of transcription factor targets from KCTD10-bound genes in control and ICRF193 treated cells. p-values reported from a hypergeometric test with a Benjamini-Hochberg correction. g, quantification of relative pCHK2 and pCHK1 levels to total protein controls (CHK2 and CHK1, respectively. Data are presented as mean values ± SD (n = 3 biologically independent experiments). h-i, colony formation assays with KCTD10-deficient or control U2OS cells in the presence of ATRi (VX970, h) and DNA-PKi (NU7441, i). Data are presented as mean values ± SD (n = 3 biologically independent experiments). j, IC50 values derived from experiments shown in panels b-c and Fig. 2d. k-l, PLA for POLR2A-PCNA in KCT10-deficient U2OS cells treated with CHK2i (BML277, 1 μM) or DMSO for 24 h. k, quantification of PLA foci. Data are presented as mean values ± SD (n = 200 cells examined over 3 independent experiments). l, representative images. Scalebars = 10 μm. p-values were calculated with a one-way ANOVA with Bonferroni’s multiple comparisons test unless otherwise stated.
