Revealing posttranscriptional regulatory elements through network-level conservation

Chang S. Chan, Olivier Elemento, Saeed Tavazoie

Research output: Contribution to journalArticlepeer-review

67 Scopus citations

Abstract

We used network-level conservation between pairs of fly (Drosophila melanogaster/D. pseudoobscura) and worm (Caenorhabditis elegans/C. briggsae) genomes to detect highly conserved mRNA motifs in 39 untranslated regions. Many of these elements are complementary to the 59 extremity of known microRNAs (miRNAs), and likely correspond to their target sites. We also identify known targets of RNA-binding proteins, and many novel sites not yet known to be functional. Coherent sets of genes with similar function often bear the same conserved elements, providing new insights into their cellular functions. We also show that target sites for distinct miRNAs are often simultaneously conserved, suggesting combinatorial regulation by multiple miRNAs. A genome-wide search for conserved stem-loops, containing complementary sequences to the novel sites, revealed many new candidate miRNAs that likely target them. We also provide evidence that posttranscriptional networks have undergone extensive rewiring across distant phyla, despite strong conservation of regulatory elements themselves. Copyright:

Original languageEnglish (US)
Pages (from-to)564-578
Number of pages15
JournalPLoS computational biology
Volume1
Issue number7
DOIs
StatePublished - 2005
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

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