Rho directs widespread termination of intragenic and stable RNA transcription
Rho directs widespread termination of intragenic and stable RNA transcription
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DOI：
10.1073/pnas.0903846106
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发表时间：
2009-09-08
影响因子：
11.1
通讯作者：
Landick, Robert
中科院分区：
文献类型：
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作者：
Peters, Jason M.;Mooney, Rachel A.;Landick, Robert
转录终止因子Rho是RNA聚合酶（RNAP）的全局调节因子。虽然已对单个Rho依赖性终止子进行了广泛研究，但对Rho在全基因组范围内对RNAP调控的位点知之甚少。使用染色质免疫沉淀和微阵列（ChIP芯片），我们研究了响应于Rho特异性抑制剂双环霉素（Bicyclomycin，简称Bicyclomycin）的大肠杆菌RNAP分布的变化。我们发现了大约200个Rho终止的位点，平均分为2类：基因间（在基因的末端）和基因内（在基因内）。基因间类包含非编码RNA，如小RNA（sRNA）和转移RNA（tRNA），建立了以前未被重视的作用Rho在终止稳定的RNA合成。终止子的基因内类包括一组以前未表征的短反义转录本，如通过与相应基因的方向相反的在BCM处理的细胞中RNAP分布的转变所判断的。这些Rho终止的反义转录物指出了非编码转录在大肠杆菌中的作用。大肠杆菌的基因调控，可能类似于无处不在的非编码转录最近发现，在真核基因调控中发挥无数的作用。
The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found approximate to 200 Rho-terminated loci that were divided evenly into 2 classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a previously uncharacterized set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation.