Comparative analysis of the transcriptome across distant species

作者：Mark Gerstein, Joel Rozowsky, Koon‐Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander, B. Alver, Raymond K. Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alexander Dobin, Jörg Drenkow, Brent Ewing, Gang Fang, Megan Fastuca, Elise A. Feingold, Adam Frankish, Guanjun Gao, Peter J. Good, Roderic Guigó, Ann S. Hammonds, Jennifer Harrow, Roger A. Hoskins, Cédric Howald, Long Hu, Haiyan Huang, Tim Hubbard, Chau Huynh, Sonali Jha, Dionna M. Kasper, Masaomi Kato, Thomas C. Kaufman, Robert R. Kitchen, Erik Ladewig, Julien Lagarde, Eric C. Lai, Jing Leng, Zhi John Lu, Michael J. MacCoss, Gemma E. May, Rebecca McWhirter, Gennifer E. Merrihew, David M. Miller, A Mortazavi, Rabi Murad, Brian Oliver, Sara Olson, Peter J. Park, Michael J. Pazin, Norbert Perrimon, Dmitri D. Pervouchine, V Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary Saunders, Felix Schlesinger, Anurag Sethi, Frank J. Slack, William C. Spencer, Marcus H. Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen Thompson, Kenneth H. Wan, Guilin Wang, Huaien Wang, Kathie L. Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Y. Yip, Chris Zaleski, Yan Zhang, Henry Zheng, Steven E. Brenner, Brenton R. Graveley, S Celniker, T Gingeras, R Waterston · 发表于：Nature · 年份：2014 · DOI：10.1038/nature13424 · 被引用次数：326 · 研究领域：Genomics and Chromatin Dynamics、Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies

Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter. In this paper the modENCODE consortium reports on a comparative analysis of transcriptome data for human, worm and fly, revealing ancient, conserved features such as shared co-expression modules enriched in developmental genes. Expression patterns are used to align the stages in worm and fly development. Gene expression levels, both coding and non-coding, in all three organisms can be quantitatively predicted from chromatin features at the promoter using a model based on a single set of organism-independent parameters. The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features1,2,3,...