mRNA sequence features that contribute to translational regulation in Arabidopsis

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@Article{Kawaguchi:2005:NAR,
  author =       "Riki Kawaguchi and Julia Bailey-Serres",
  title =        "mRNA sequence features that contribute to
                 translational regulation in Arabidopsis",
  journal =      "Nucleic Acids Research",
  year =         "2005",
  volume =       "33",
  number =       "3",
  pages =        "955--965",
  keywords =     "genetic algorithms, genetic programming",
  DOI =          "doi:10.1093/nar/gki240",
  abstract =     "DNA microarrays were used to evaluate the regulation
                 of the proportion of individual mRNA species in
                 polysomal complexes in leaves of Arabidopsis thaliana
                 under control growth conditions and following a mild
                 dehydration stress (DS). The analysis determined that
                 the percentage of an individual gene transcript in
                 polysomes (ribosome loading) ranged from over 95 to
                 <5percent. DS caused a decrease in ribosome loading
                 from 82 to 72percent, with maintained polysome
                 association for over 60percent of the mRNAs with an
                 increased abundance. To identify sequence features
                 responsible for translational regulation, ribosome
                 loading values and features of full-length mRNA
                 sequences were compared. mRNAs with extreme length or
                 high GU content in the 5'-untranslated regions
                 (5'-UTRs) were generally poorly translated. Under DS,
                 mRNAs with both a high GC content in the 5'-UTR and
                 long open reading frame showed a significant impairment
                 in ribosome loading. Evaluation of initiation A+1UG
                 codon context revealed distinctions in the frequency of
                 adenine in nucleotides -10 to -1 (especially at -4 and
                 -3) in mRNAs with different ribosome loading values.
                 Notably, the mRNA features that contribute to
                 translational regulation could not fully explain the
                 variation in ribosome loading, indicating that
                 additional factors contribute to translational
                 regulation in Arabidopsis.",
  notes =        "PMID: {"}despite considerable effort, we were unable
                 to identify motifs that augment or impair ribosome
                 loading under DS using publicly available motif explore
                 programs [e.g. MEME, GPRM \cite{Yuh-JyhHu:2003:NAR} and
                 SLASH (52)] (data not shown).{"}",
}

Genetic Programming entries for Riki Kawaguchi Julia Bailey-Serres

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