Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.
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DOI：
10.1093/nar/gkq775
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发表时间：
2011-01
影响因子：
14.9
通讯作者：
Davuluri RV
中科院分区：
文献类型：
--
作者：
Sun H;Wu J;Wickramasinghe P;Pal S;Gupta R;Bhattacharyya A;Agosto-Perez FJ;Showe LC;Huang TH;Davuluri RV
在不同的细胞环境和组织类型中使用不同的启动子增加了哺乳动物基因组转录的复杂性。确定替代启动子及其在不同组织中的活性是理解哺乳动物基因及其同工型转录调控的主要挑战之一。为了确定不同组织中替代启动子的使用，我们在5个成年小鼠组织（脑、肝、肺、脾和肾）中使用针对RNA Pol-II的抗体进行了ChIP-seq实验。我们的分析确定了38 639个Pol-II启动子，其中包括12 270个新的启动子，用于蛋白质编码和非编码小鼠基因。其中，6384个启动子是组织特异性的，是CpG缺乏的，我们发现只有34%的新启动子位于富含CpG的区域，这表明新启动子大多是组织特异性的。通过鉴定给定组织中每个注释基因的Pol-II结合启动子，我们发现37%的蛋白质编码基因在五种小鼠组织中使用替代启动子。本文提出的启动子注释和ChIP-seq数据将有助于研究哺乳动物基因组中基因调控区域的特征。
Alternative promoters that are differentially used in various cellular contexts and tissue types add to the transcriptional complexity in mammalian genome. Identification of alternative promoters and the annotation of their activity in different tissues is one of the major challenges in understanding the transcriptional regulation of the mammalian genes and their isoforms. To determine the use of alternative promoters in different tissues, we performed ChIP-seq experiments using antibody against RNA Pol-II, in five adult mouse tissues (brain, liver, lung, spleen and kidney). Our analysis identified 38 639 Pol-II promoters, including 12 270 novel promoters, for both protein coding and non-coding mouse genes. Of these, 6384 promoters are tissue specific which are CpG poor and we find that only 34% of the novel promoters are located in CpG-rich regions, suggesting that novel promoters are mostly tissue specific. By identifying the Pol-II bound promoter(s) of each annotated gene in a given tissue, we found that 37% of the protein coding genes use alternative promoters in the five mouse tissues. The promoter annotations and ChIP-seq data presented here will aid ongoing efforts of characterizing gene regulatory regions in mammalian genomes.
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影响因子：
14.9
作者：
Blahnik KR;Dou L;O'Geen H;McPhillips T;Xu X;Cao AR;Iyengar S;Nicolet CM;Ludäscher B;Korf I;Farnham PJ
通讯作者：
Farnham PJ
影响因子：
46.9
作者：
Bajic, VB;Tan, SL;Sugano, S
通讯作者：
Sugano, S
影响因子：
7
作者：
Baek, Daehyun;Davis, Colleen;Green, Phil
通讯作者：
Green, Phil
影响因子：
3.5
作者：
Koyanagi, KO;Hagiwara, M;Imanishi, T
通讯作者：
Imanishi, T
影响因子：
12.3
作者：
Kawaji H;Severin J;Lizio M;Waterhouse A;Katayama S;Irvine KM;Hume DA;Forrest AR;Suzuki H;Carninci P;Hayashizaki Y;Daub CO
通讯作者：
Daub CO