High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
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DOI：
10.1101/gr.139618.112
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发表时间：
2013-01
期刊：
影响因子：
7
通讯作者：
Gingeras TR
中科院分区：
文献类型：
--
作者：
Batut P;Dobin A;Plessy C;Carninci P;Gingeras TR
许多真核基因具有多个具有不同表达特异性的替代启动子。因此，全面注释启动子和破译其各自的调控动力学是基因表达谱的应用程序和我们的调控复杂性的理解至关重要。我们介绍了RAMPAGE，一种新的启动子活性分析方法，结合了极其特异性的5′-完整的cDNA测序与集成的数据分析工作流程，以解决当前技术的局限性。RAMPAGE具有简化的方案，可快速轻松地生成高度多重测序文库，提供非常高的转录起始位点特异性，生成准确且可重复的启动子表达测量结果，并通过双端cDNA测序产生广泛的转录本连接性信息。我们使用RAMPAGE在全基因组研究的启动子活性在整个36个阶段的果蝇的生命周期，并在这里描述了一个全面的数据集，代表了第一个可用的发展时间进程的启动子的使用。我们发现>40%的发育表达基因具有至少两个启动子，并且替代启动子通常实施不同的调控程序。转座因子通过调控基因表达在宿主基因组的进化中起着重要作用，目前已发现至少有1300个启动子参与了D.黑腹菌数百个这样的启动子驱动注释基因的表达，并且转座子通常将它们自己的表达特异性赋予它们调节的基因。这些观察结果为转座子可能通过在其宿主基因组中分布定型的顺式调控模块来驱动调控创新的理论提供了支持。
Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5′-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
64.8
作者：
Graveley BR;Brooks AN;Carlson JW;Duff MO;Landolin JM;Yang L;Artieri CG;van Baren MJ;Boley N;Booth BW;Brown JB;Cherbas L;Davis CA;Dobin A;Li R;Lin W;Malone JH;Mattiuzzo NR;Miller D;Sturgill D;Tuch BB;Zaleski C;Zhang D;Blanchette M;Dudoit S;Eads B;Green RE;Hammonds A;Jiang L;Kapranov P;Langton L;Perrimon N;Sandler JE;Wan KH;Willingham A;Zhang Y;Zou Y;Andrews J;Bickel PJ;Brenner SE;Brent MR;Cherbas P;Gingeras TR;Hoskins RA;Kaufman TC;Oliver B;Celniker SE
通讯作者：
Celniker SE
影响因子：
30.8
作者：
Faulkner, Geoffrey J.;Kimura, Yasumasa;Carninci, Piero
通讯作者：
Carninci, Piero
影响因子：
14.8
作者：
Huang, Da Wei;Sherman, Brad T.;Lempicki, Richard A.
通讯作者：
Lempicki, Richard A.
影响因子：
7
作者：
Hoskins, Roger A.;Landolin, Jane M.;Celniker, Susan E.
通讯作者：
Celniker, Susan E.