The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.
The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.
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DOI：
10.1101/gr.153668.112
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发表时间：
2013-08
期刊：
影响因子：
7
通讯作者：
Ahringer J
中科院分区：
文献类型：
--
作者：
Chen RA;Down TA;Stempor P;Chen QB;Egelhofer TA;Hillier LW;Jeffers TE;Ahringer J
RNA聚合酶转录起始位点在秀丽隐杆线虫中很大程度上是未知的。大多数蛋白质编码转录本的起始5′端被反式剪接去除，非编码起始位点尚未研究。我们表征了RNA Pol II转录起始的景观，鉴定了73，500个不同的起始簇。双向转录频繁，在120 bp处具有转录配对的峰值。我们分配转录起始位点7691蛋白质编码基因，并发现它们显示典型的真核启动子的功能。引人注目的是，大多数起始事件发生在具有增强子样染色质特征的区域。基于转录起始簇与转录因子结合位点的重叠，我们定义了2361个转录的基因间增强子。值得注意的是，跨越这些增强子的生产性转录延伸主要与最近的下游基因的方向相同。从上游增强子向下游基因的定向延伸可能潜在地将RNA聚合酶II递送到近端启动子，或者可替代地可能直接作为远端启动子起作用。我们的研究结果为研究后生动物的转录调控提供了新的资源。
RNA polymerase transcription initiation sites are largely unknown in Caenorhabditis elegans. The initial 5′ end of most protein-coding transcripts is removed by trans-splicing, and noncoding initiation sites have not been investigated. We characterized the landscape of RNA Pol II transcription initiation, identifying 73,500 distinct clusters of initiation. Bidirectional transcription is frequent, with a peak of transcriptional pairing at 120 bp. We assign transcription initiation sites to 7691 protein-coding genes and find that they display features typical of eukaryotic promoters. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. Based on the overlap of transcription initiation clusters with mapped transcription factor binding sites, we define 2361 transcribed intergenic enhancers. Remarkably, productive transcription elongation across these enhancers is predominantly in the same orientation as that of the nearest downstream gene. Directed elongation from an upstream enhancer toward a downstream gene could potentially deliver RNA polymerase II to a proximal promoter, or alternatively might function directly as a distal promoter. Our results provide a new resource to investigate transcription regulation in metazoans.
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DOI：
10.1895/wormbook.1.5.2
发表时间：
2012-11-20
期刊：
WormBook : the online review of C. elegans biology
影响因子：
--
作者：
Blumenthal, Thomas
通讯作者：
Blumenthal, Thomas
影响因子：
64.5
作者：
Guenther, Matthew G.;Levine, Stuart S.;Young, Richard A.
通讯作者：
Young, Richard A.
影响因子：
7.5
作者：
Juven-Gershon, Tamar;Hsu, Jer-Yuan;Kadonaga, James T.
通讯作者：
Kadonaga, James T.
影响因子：
7.5
作者：
Barrera, Leah O.;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
7
作者：
Allen, Mary Ann;Hillier, LaDeana W.;Blumenthal, Thomas
通讯作者：
Blumenthal, Thomas