Comparative Analysis of the Transcriptome Across Distant Species
Author
Gerstein, Mark B.
Rozowsky, Joel
Yan, Koon-Kiu
Wang, Daifeng
Cheng, Chao
Brown, James B.
Davis, Carrie A.
Hillier, LaDeana
Sisu, Cristina
Li, Jingyi Jessica
Pei, Baikang
Harmanci, Arif O.
Duff, Michael O.
Djebali, Sarah
Alexander, Roger P.
Auerbach, Raymond
Bell, Kimberly
Bickel, Peter J.
Boeck, Max E.
Boley, Nathan P.
Booth, Benjamin W.
Cherbas, Lucy
Cherbas, Peter
Di, Chao
Dobin, Alex
Drenkow, Jorg
Ewing, Brent
Fang, Gang
Fastuca, Megan
Feingold, Elise A.
Frankish, Adam
Gao, Guanjun
Good, Peter J.
Guigó, Roderic
Hammonds, Ann
Harrow, Jen
Hoskins, Roger A.
Howald, Cédric
Hu, Long
Huang, Haiyan
Hubbard, Tim J. P.
Huynh, Chau
Jha, Sonali
Kasper, Dionna
Kato, Masaomi
Kaufman, Thomas C.
Kitchen, Robert R.
Ladewig, Erik
Lagarde, Julien
Lai, Eric
Leng, Jing
Lu, Zhi
MacCoss, Michael
May, Gemma
McWhirter, Rebecca
Merrihew, Gennifer
Miller, David M.
Mortazavi, Ali
Murad, Rabi
Oliver, Brian
Olson, Sara
Pazin, Michael J.
Pervouchine, Dmitri
Reinke, Valerie
Reymond, Alexandre
Robinson, Garrett
Saunders, Gary I.
Schlesinger, Felix
Sethi, Anurag
Slack, Frank J.
Spencer, William C.
Stoiber, Marcus H.
Strasbourger, Pnina
Tanzer, Andrea
Thompson, Owen A.
Wan, Kenneth H.
Wang, Guilin
Wang, Huaien
Watkins, Kathie L.
Wen, Jiayu
Wen, Kejia
Xue, Chenghai
Yang, Li
Yip, Kevin
Zaleski, Chris
Zhang, Yan
Zheng, Henry
Brenner, Steven E.
Graveley, Brenton R.
Celniker, Susan E.
Gingeras, Thomas R.
Waterston, Robert
Published Version
https://doi.org/10.1038/nature13424Metadata
Show full item recordCitation
Gerstein, Mark B., Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis et al. "Comparative Analysis of the Transcriptome Across Distant Species." Nature 512, no. 7515 (2014): 445-448. DOI: 10.1038/nature13424Abstract
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 features1,2,3,4,5,6. 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.Other Sources
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737/Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAACitable link to this page
https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37372477
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