En masse nascent transcription analysis to elucidate regulatory transcription factors

Jinshui Fan, Ming Zhan, Jikui Shen, Jennifer L. Matindale, Xiaoling Yang, Tomoko Kawai, Myriam Gorospe

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Despite exhaustively informing about steady-state mRNA abundance, DNA microarrays have been used with limited success to identify regulatory transcription factors (TFs). The main limitation of this approach is that altered mRNA stability also strongly governs the patterns of expressed genes. Here, we used nuclear run-on assays and microarrays to systematically interrogate changes in nascent transcription in cells treated with the topoisomerase inhibitor camptothecin (CPT). Analysis of the promoters of coordinately transcribed genes after CPT treatment suggested the involvement of TFs c-Myb and Rfx1. The predicted CPT-dependent associations were subsequently confirmed by chromatin immunoprecipitation assays. Importantly, after RNAi-mediated knockdown of each TF, the CPT-elicited induction of c-Myb- and/or Rfx1-regulated mRNAs was diminished and the overall cellular response was impaired. The strategies described here permit the successful identification of the TFs responsible for implementing adaptive gene expression programs in response to cellular stimulation.

Original languageEnglish (US)
Pages (from-to)1492-1500
Number of pages9
JournalNucleic Acids Research
Issue number5
StatePublished - 2006

ASJC Scopus subject areas

  • Genetics


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