RNA splicing is required to remove introns from
pre-mRNA, and alternative splicing generates
protein diversity.
Topoisomerase I (Top1) has been shown to be coupled with splicing by regulating
serine/arginine-rich splicing proteins. Prior studies on isolated genes also showed that Top1
poisoning by
camptothecin (
CPT), which traps Top1 cleavage complexes (Top1cc), can alter RNA splicing. Here, we tested the effect of Top1 inhibition on splicing at the genome-wide level in human colon
carcinoma HCT116 and
breast carcinoma MCF7 cells. The
RNA of HCT116 cells treated with
CPT for various times was analyzed with ExonHit Human Splice Array. Unlike other exon array platforms, the ExonHit arrays include junction probes that allow the detection of splice variants with high sensitivity and specificity. We report that
CPT treatment preferentially affects the splicing of splicing-related factors, such as RBM8A, and generates transcripts coding for inactive
proteins lacking key functional domains. The splicing alterations induced by
CPT are not observed with
cisplatin or
vinblastine and are not simply due to reduced Top1 activity, as Top1 downregulation by
short interfering RNA did not alter splicing like
CPT treatment. Inhibition of
RNA polymerase II (Pol II) hyperphosphorylation by 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (
DRB) blocked the splicing alteration induced by
CPT, which suggests that the rapid Pol II hyperphosphorylation induced by
CPT interferes with normal splicing. The preferential effect of
CPT on genes encoding
splicing factors may explain the abnormal splicing of a large number of genes in response to Top1cc.