E-GEOD-48678 - Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin

Status
Released on 29 October 2013, last updated on 4 May 2014
Organism
Homo sapiens
Samples (9)
Protocols (4)
Description
The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a “cleavable complex”. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment affected transcription initiation, elongation, termination, splicing and enhancer activity. Following removal of camptothecin, transcription spread as a wave from the 5’-end of genes with no recovery of transcription apparent from RNA polymerases stalled in the body of genes. As a result, camptothecin preferentially inhibited the expression of large genes such as proto-oncogenes, and anti-apoptotic genes while smaller ribosomal protein genes, pro-apoptotic genes and p53 target genes showed relative higher expression. In addition, a set of mitotic regulator genes and histone genes were inhibited in a size-independent manner. Cockayne syndrome group B fibroblasts showed a very similar RNA synthesis recovery profile to normal fibroblasts suggesting that transcription-coupled repair is not involved in the repair of transcription-blocking TOP1 lesions. These findings of the effects of camptothecin on transcription have important implications for its anti-cancer activities and may aid in the design of improved combinatorial treatments involving Top1 poisons. Analysis of the effect of Camptothecin (CPT) on transcription. Normal fibroblasts and Cockayne syndrome group B fibroblasts were exposed to CPT for 60 minutes, after which a washout was performed. Nascent RNA was labeled using bromouridine for 15 minutes starting at time points: 1) 15 minutes before the washout; 2) Immediately after the washout; 3) 15 minutes after the washout. Test samples are compared to control cells that were not exposed to CPT.
Experiment type
RNA-seq of coding RNA 
Contacts
Mats Ljungman <tenbroek@med.umich.edu>, Artur Veloso, Benjamin Biewen, Jayendra Prasad, Karan Bedi, Leonardo Carmo de Andrade Lima, Michelle T Paulsen, Thomas E Wilson
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-48678.idf.txt
Sample and data relationshipE-GEOD-48678.sdrf.txt
Processed data (1)E-GEOD-48678.processed.1.zip
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