Fig. 4

TOP1cc (TOP1 and its bound DNA fragment) are processed by lysosomes (A) LysoIP performed after 5 h of 50 nM CPT, and quantification graph (n = 3). Error bar, SD. (B) LysoIP performed after 5 h of 50 nM CPT (n = 3). (C) Quantification of DNA by Picogreen assay to detect DNA purified by LysoIP after 6 h of treatment (n = 3). Two-way ANOVA. Error bar, SD. Around 450 ng of DNA fragments of less than 1 kb were purified from 20 million cells by LysoIP after treatment with 50 nM CPT and 50 nM BAF. (D) Distribution of the LysoIP-purified DNA, mapped reads sequenced by NGS. (E) Genomic distribution of the LysoIP-purified mapped reads sequenced by NGS. (F) Proportional Eulerr representation of the overlap among the different ChIP-seq of TOP1cc, TOP1cc-seq 1 (MCF7—GEO: GSE135808),87 TOP1cc-seq 2 (LNCAP—GEO: GSE135808),87 and TOP1-seq (HCT116—GEO: GSE57628).88 All conditions were treated with CPT. (G) Genomic browser alignment on genome hg38 of the different TOP1cc ChIP-seq and LysoIP-seq at RAD23A gene loci as sequence tags per million (TPM). (H) Immunofluorescence after 4 h of 50 nM CPT (nM) or 1 μM CPT (μM) and quantification (n = 3). Scale bar, 10 μm. Two-way ANOVA. ∗p < 0.05; ns, not significant. See also Figure S4.