Comparative analysis of the transcriptome across distant species

被引：200

作者：

Gerstein, Mark B. ^{[1
,2
,3
]}

Rozowsky, Joel ^{[1
,2
]}

Yan, Koon-Kiu ^{[1
,2
]}

Wang, Daifeng ^{[1
,2
]}

Cheng, Chao ^{[4
,5
]}

Brown, James B. ^{[6
,7
]}

Davis, Carrie A. ^{[8
]}

Hillier, LaDeana ^{[9
,10
]}

Sisu, Cristina ^{[1
,2
]}

Li, Jingyi Jessica ^{[7
,11
,12
]}

Pei, Baikang ^{[1
,2
]}

Harmanci, Arif O. ^{[1
,2
]}

Duff, Michael O. ^{[13
]}

Djebali, Sarah ^{[14
,15
]}

Alexander, Roger P. ^{[1
,2
]}

Alver, Burak H. ^{[16
]}

Auerbach, Raymond ^{[1
,2
]}

Bell, Kimberly ^{[8
]}

Bickel, Peter J. ^{[7
]}

Boeck, Max E. ^{[9
,10
]}

Boley, Nathan P. ^{[6
,17
]}

Booth, Benjamin W. ^{[6
]}

Cherbas, Lucy ^{[18
,19
]}

Cherbas, Peter ^{[18
,19
]}

Di, Chao ^{[20
]}

Dobins, Alex ^{[8
]}

Drenkows, Jorg ^{[8
]}

Ewing, Brent ^{[9
,10
]}

Fang, Gang ^{[1
,2
]}

Fastucas, Megan ^{[8
]}

Feingold, Elise A. ^{[21
]}

Frankish, Adam ^{[22
]}

Gao, Guanjun ^{[20
]}

Good, Peter J. ^{[21
]}

Guigo, Roderic ^{[14
,15
]}

Hammonds, Ann ^{[6
]}

Harrow, Jen ^{[22
]}

Hoskins, Roger A. ^{[6
]}

Howald, Cedric ^{[23
,24
]}

Hu, Long ^{[20
]}

Huang, Haiyan ^{[7
]}

Hubbard, Tim J. P. ^{[22
,25
]}

Huynh, Chau ^{[9
,10
]}

Jhas, Sonali ^{[8
]}

Kasper, Dionna ^{[26
]}

Kato, Masaomi ^{[27
]}

Kaufman, Thomas C. ^{[18
]}

Kitchen, Robert R. ^{[1
,2
]}

Ladewig, Erik ^{[28
]}

Lagarde, Julien ^{[14
,15
]}

机构：

[1] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA

[2] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

[3] Yale Univ, Dept Comp Sci, New Haven, CT 06511 USA

[4] Geisel Sch Med Dartmouth, Dept Genet, Hanover, NH 03755 USA

[5] Geisel Sch Med Dartmouth, Inst Quantitat Biomed Sci, Norris Cotton Canc Ctr, Lebanon, NH 03766 USA

[6] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA

[7] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[8] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[9] Dept Genome Sci, Seattle, WA 98195 USA

[10] Univ Washington, Sch Med, Seattle, WA 98195 USA

[11] Univ Calif Los Angeles, Dept Stat, Los Angeles, CA 90095 USA

[12] Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA 90095 USA

[13] Univ Connecticut, Ctr Hlth, Inst Syst Genom, Dept Genet & Dev Biol, Farmington, CT 06030 USA

[14] Ctr Genom Regulat, Barcelona 08003, Catalonia, Spain

[15] Univ Pompeu Fabra, Dept Ciencies Expt Salut, Barcelona 08003, Catalonia, Spain

[16] Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA

[17] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[18] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA

[19] Indiana Univ, Ctr Genom & Bioinformat, Bloomington, IN 47405 USA

[20] Tsinghua Univ, Sch Life Sci, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China

[21] NHGRI, NIH, Bethesda, MD 20892 USA

[22] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[23] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland

[24] Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland

[25] Kings Coll London, London WC2R 2LS, England

[26] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA

[27] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA

[28] Sloan Kettering Inst, New York, NY 10065 USA

[29] Carnegie Mellon Univ, Dept Biol Sci, Pittsburgh, PA 15213 USA

[30] Vanderbilt Univ, Dept Cell & Dev Biol, Nashville, TN 37232 USA

[31] Univ Calif Irvine, Irvine, CA 92697 USA

[32] Univ Calif Irvine, Ctr Complex Biol Syst, Irvine, CA 92697 USA

[33] NIDDK, Sect Dev Genom, Lab Cellular & Dev Biol, NIH, Bethesda, MD 20892 USA

[34] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[35] Harvard Univ, Sch Med, Drosophila RNAi Screening Ctr, Boston, MA 02115 USA

[36] Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA

[37] European Bioinformat Inst, Hinxton CB10 1SD, England

[38] Univ Pompeu Fabra, Ctr Genom Regulat, Bioinformat & Genom Programme, Barcelona 08003, Catalonia, Spain

[39] Univ Vienna, Theoret Biochem Grp TBI, Inst Theoret Chem, A-1090 Vienna, Austria

[40] Chinese Acad Sci, Shanghai Inst Biol Sci, CAS MPG Partner Inst Computat Biol, Key Lab Computat Biol, Shanghai 200031, Peoples R China

[41] Chinese Univ Hong Kong, Hong Kong Bioinformat Ctr, Shatin, Hong Kong, Peoples R China

[42] Chinese Univ Hong Kong, CUHK BGI Innovat Inst Trans Omics 5, Shatin, Hong Kong, Peoples R China

[43] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[44] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

来源：

NATURE | 2014年 / 512卷 / 7515期

基金：

英国惠康基金; 美国国家卫生研究院;

关键词：

GENE-EXPRESSION; LANDSCAPE; EVOLUTION; TISSUES; GENOME; CELLS;

D O I：

10.1038/nature13424

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 features(1-6). Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

引用

页码：445 / +

页数：13

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