title: Transcription poisoning by Topoisomerase I is controlled by gene length, splice sites, and miR-142-3p.
abstract: Topoisomerase 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.
authors.affiliation: Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute; NIH Center for Advancing Translational Sciences, Bethesda, MD 20892-4255, USA.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Solier
authors.forename: Michael C
authors.initials: MC
authors.lastname: Ryan
authors.forename: Scott E
authors.initials: SE
authors.lastname: Martin
authors.forename: Sudhir
authors.initials: S
authors.lastname: Varma
authors.forename: Kurt W
authors.initials: KW
authors.lastname: Kohn
authors.forename: Hongfang
authors.initials: H
authors.lastname: Liu
authors.forename: Barry R
authors.initials: BR
authors.lastname: Zeeberg
authors.forename: Yves
authors.initials: Y
authors.lastname: Pommier
mesh_terms: D002166:Camptothecin / Q000494:pharmacology; D045744:Cell Line, Tumor; D004264:DNA Topoisomerases, Type I / Q000235:genetics*; D005786:Gene Expression Regulation / Q000235:genetics*; D045325:HCT116 Cells; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012326:RNA Splicing / Q000187:drug effects / Q000235:genetics; D034741:RNA, Small Interfering; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059004:Topoisomerase I Inhibitors / Q000494:pharmacology; D014158:Transcription, Genetic / Q000187:drug effects / Q000235:genetics*; D014162:Transfection
chemical_list: C555159:MIRN142 microRNA, human; D035683:MicroRNAs; D034741:RNA, Small Interfering; D059004:Topoisomerase I Inhibitors; D004264:DNA Topoisomerases, Type I; D002166:Camptothecin