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GENETICS
Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome

David C. Grainger ^*, , Douglas Hurd , Marcus Harrison , Jolyon Holdstock , and Stephen J. W. Busby ^*

^*School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; and Oxford Gene Technology, Begbroke Science Park, Sandy Lane, Yarnton, Oxford OX5 1PF, United Kingdom

Edited by Sankar Adhya, National Institutes of Health, Bethesda, MD, and approved October 14, 2005 (received for review August 4, 2005)

Chromatin immunoprecipitation and high-density microarrays have been used to monitor the distribution of the global transcription regulator Escherichia coli cAMP-receptor protein (CRP) and RNA polymerase along the E. coli chromosome. Our results identify targets occupied by CRP and genes transcribed by RNA polymerase in vivo. Many of the loci of CRP binding are at known CRP regulated promoters. However, our results show that CRP also interacts with thousands of weaker sites across the whole chromosome and that this "background" binding can be used as a probe for organization within the E. coli folded chromosome. In rapidly growing cells, we show that the major sites of RNA polymerase binding are 90 transcription units that include genes needed for protein synthesis. Upon the addition of rifampicin, RNA polymerase is distributed among >500 functional promoters. We show that the chromatin immunoprecipitation and high-density-microarrays methodology can be used to study the redistribution of RNA polymerase induced by environmental stress, revealing previously uncharacterized aspects of RNA polymerase behavior and providing an alternative to the "transcriptomics" approach for studying global transcription patterns.

chromatin immunoprecipitation | genomics | stringent response | transcription

Conflict of interest statement: No conflicts declared.

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: ChIP, chromatin immunoprecipitation; CRP, E. coli cAMP-receptor protein; IPTG, isopropyl -D-thiogalactoside.

To whom correspondence should be addressed. E-mail: d.grainger{at}bham.ac.uk.

© 2005 by The National Academy of Sciences of the USA

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