Skip to main content
eScholarship
Open Access Publications from the University of California

Comparative analysis of the transcriptome across distant species.

  • Author(s): 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
  • Alver, Burak H
  • 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 JP
  • 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
  • Park, Peter J
  • Pazin, Michael J
  • Perrimon, Norbert
  • Pervouchine, Dmitri
  • Reinke, Valerie
  • Reymond, Alexandre
  • Robinson, Garrett
  • Samsonova, Anastasia
  • 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
  • et al.

Published Web Location

http://www.nature.com/nature/journal/v512/n7515/full/nature13424.html
No data is associated with this publication.
Abstract

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. 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.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Item not freely available? Link broken?
Report a problem accessing this item