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

被引:229
作者
Grainger, DC [1 ]
Hurd, D
Harrison, M
Holdstock, J
Busby, SJW
机构
[1] Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England
[2] Oxford Gene Technol, Oxford OX5 1PF, England
基金
英国惠康基金;
关键词
chromatin immunoprecipitation; genomics; stringent response; transcription;
D O I
10.1073/pnas.0506687102
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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 CRIP binding are at known CRIP 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 approximate to 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.
引用
收藏
页码:17693 / 17698
页数:6
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