En masse nascent transcription analysis to elucidate regulatory transcription factors

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, w...

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Main Authors:	Fan, Jinshui, Zhan, Ming, Shen, Jikui, Martindale, Jennifer L., Yang, Xiaoling, Kawai, Tomoko, Gorospe, Myriam
Format:	Online
Language:	English
Published:	Oxford University Press 2006
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1408309/

id	pubmed-1408309
recordtype	oai_dc
spelling	pubmed-14083092006-03-23 En masse nascent transcription analysis to elucidate regulatory transcription factors Fan, Jinshui Zhan, Ming Shen, Jikui Martindale, Jennifer L. Yang, Xiaoling Kawai, Tomoko Gorospe, Myriam Article 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. Oxford University Press 2006 2006-03-15 /pmc/articles/PMC1408309/ /pubmed/16540593 http://dx.doi.org/10.1093/nar/gkj510 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Fan, Jinshui Zhan, Ming Shen, Jikui Martindale, Jennifer L. Yang, Xiaoling Kawai, Tomoko Gorospe, Myriam
spellingShingle	Fan, Jinshui Zhan, Ming Shen, Jikui Martindale, Jennifer L. Yang, Xiaoling Kawai, Tomoko Gorospe, Myriam En masse nascent transcription analysis to elucidate regulatory transcription factors
author_facet	Fan, Jinshui Zhan, Ming Shen, Jikui Martindale, Jennifer L. Yang, Xiaoling Kawai, Tomoko Gorospe, Myriam
author_sort	Fan, Jinshui
title	En masse nascent transcription analysis to elucidate regulatory transcription factors
title_short	En masse nascent transcription analysis to elucidate regulatory transcription factors
title_full	En masse nascent transcription analysis to elucidate regulatory transcription factors
title_fullStr	En masse nascent transcription analysis to elucidate regulatory transcription factors
title_full_unstemmed	En masse nascent transcription analysis to elucidate regulatory transcription factors
title_sort	en masse nascent transcription analysis to elucidate regulatory transcription factors
description	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.
publisher	Oxford University Press
publishDate	2006
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1408309/
_version_	1611381335534862336

En masse nascent transcription analysis to elucidate regulatory transcription factors

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