mRNA sequence features that contribute to translational regulation in Arabidopsis
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- @Article{Kawaguchi:2005:NAR,
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author = "Riki Kawaguchi and Julia Bailey-Serres",
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title = "mRNA sequence features that contribute to
translational regulation in Arabidopsis",
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journal = "Nucleic Acids Research",
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year = "2005",
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volume = "33",
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number = "3",
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pages = "955--965",
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keywords = "genetic algorithms, genetic programming",
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DOI = "doi:10.1093/nar/gki240",
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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.",
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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
Citations