PDF file - 2059K, Importance of Exon numbers for transcript downregulation by CPT (SF1); CPT up-regulates the p53 signaling pathway genes (SF2); Down-regulation of RNA degradation-related genes after CPT treatment (SF3); Down-regulation of ubiquitin-related genes after CPT treatment (SF4); Top1 down-regulation does not impacts gene expression for CUL5 and UBE2W (SF5); miR-142-3p decreases cell survival, and down-regulation of its target genes BCL2L1 and MAP3K7IP2 sensitize to CPT (SF6). *** List of Primers (ST1); List of the 3808 down-regulated genes in CPT-treated HCT116 cells, by 2-fold or more (ST2); List of the 835 up-regulated genes in CPT-treated HCT116 cells, by 2-fold or more (ST3).
ARTICLE ABSTRACTTopoisomerase I (Top1) relaxes DNA supercoiling by forming transient cleavage complexes (Top1cc) up- and downstream of transcription complexes. Top1cc can be trapped by carcinogenic and endogenous DNA lesions and by camptothecin, resulting in transcription blocks. Here, we undertook genome-wide analysis of camptothecin-treated cells at exon resolution. RNA samples from HCT116 and MCF7 cells were analyzed with the Affy Exon Array platform, allowing high-resolution mapping along 18,537 genes. Long genes that are highly expressed were the most susceptible to downregulation, whereas short genes were preferentially upregulated. Along the body of genes, downregulation was most important toward the 3′-end and increased with the number of exon–intron junctions. Ubiquitin and RNA degradation-related pathway genes were selectively downregulated. Parallel analysis of microRNA with the Agilent miRNA microarray platform revealed that miR-142-3p was highly induced by camptothecin. More than 10% of the downregulated genes were targets of this p53-dependent microRNA. Our study shows the profound impact of Top1cc on transcription elongation, especially at intron–exon junctions and on transcript stability by microRNA miR-142-3p upregulation. Cancer Res; 73(15); 4830–9. ©2013 AACR.