Despite exhaustiveiy 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 stronglygoverns the patterns of expressed genes. Here, we used nuc-iear run-on assays and microarrays to systematically interrogate changes in nascent transcription in cells treated with the topoisomerase inhibitor camptothecin (CRT). Analysis of the promotersof 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 immunopreci-pitation assays. Importantly, after RNAi-rnediated 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.
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