Comparative analysis of the transcriptome across distant species

Research output: Contribution to journalLetterpeer-review

Authors

  • Mark B Gerstein
  • Joel Rozowsky
  • Koon-Kiu Yan
  • Daifeng Wang
  • Chao Cheng
  • Carrie A Davis
  • LaDeana Hillier
  • Cristina Sisu
  • Jingyi Jessica Li
  • Baikang Pei
  • Arif O Harmanci
  • Michael O Duff
  • Sarah Djebali
  • Roger P Alexander
  • Burak H Alver
  • Raymond Auerbach
  • Kimberly Bell
  • Peter J Bickel
  • Max E Boeck
  • Nathan P Boley
  • Benjamin W Booth
  • Lucy Cherbas
  • Peter Cherbas
  • Chao Di
  • Alex Dobin
  • Jorg Drenkow
  • Brent Ewing
  • Gang Fang
  • Megan Fastuca
  • Elise A Feingold
  • Adam Frankish
  • Guanjun Gao
  • Peter J Good
  • Roderic Guigó
  • Ann Hammonds
  • Jen Harrow
  • Roger A Hoskins
  • Cédric Howald
  • Long Hu
  • Haiyan Huang
  • Tim J P Hubbard
  • Chau Huynh
  • Sonali Jha
  • Dionna Kasper
  • Masaomi Kato
  • Thomas C Kaufman
  • Robert R Kitchen
  • Erik Ladewig
  • Julien Lagarde

Colleges, School and Institutes

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.

Details

Original languageEnglish
Pages (from-to)445-448
Number of pages4
JournalNature
Volume512
Issue number7515
Publication statusPublished - 27 Aug 2014

Keywords

  • Animals, Caenorhabditis elegans/embryology, Chromatin/genetics, Cluster Analysis, Drosophila melanogaster/genetics, Gene Expression Profiling, Gene Expression Regulation, Developmental/genetics, Histones/metabolism, Humans, Larva/genetics, Models, Genetic, Molecular Sequence Annotation, Promoter Regions, Genetic/genetics, Pupa/genetics, RNA, Untranslated/genetics, Sequence Analysis, RNA, Transcriptome/genetics