mRNA sequence features that contribute to translational regulation in Arabidopsis.

PubWeight™: 1.63‹?› | Rank: Top 4%

🔗 View Article (PMC 549406)

Published in Nucleic Acids Res on February 16, 2005

Authors

Riki Kawaguchi1, Julia Bailey-Serres

Author Affiliations

1: Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, CA 92521, USA.

Articles citing this

Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A (2009) 2.77

An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell (2007) 2.55

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol Syst Biol (2009) 1.86

Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot (2005) 1.82

Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol (2005) 1.66

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol (2010) 1.56

Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biol (2007) 1.49

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci U S A (2013) 1.48

The interface between metabolic and stress signalling. Ann Bot (2009) 1.32

Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29

Close spacing of AUG initiation codons confers dicistronic character on a eukaryotic mRNA. RNA (2006) 1.24

Plant L10 ribosomal proteins have different roles during development and translation under ultraviolet-B stress. Plant Physiol (2010) 1.16

Leaky scanning and reinitiation regulate BACE1 gene expression. Mol Cell Biol (2006) 1.11

Dynamic Light Regulation of Translation Status in Arabidopsis thaliana. Front Plant Sci (2012) 1.08

Diurnal changes of polysome loading track sucrose content in the rosette of wild-type arabidopsis and the starchless pgm mutant. Plant Physiol (2013) 1.07

Mutations in eIF5B confer thermosensitive and pleiotropic phenotypes via translation defects in Arabidopsis thaliana. Plant Cell (2017) 1.06

Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. Plant Physiol (2007) 1.02

Comparative genomic analysis of novel conserved peptide upstream open reading frames in Drosophila melanogaster and other dipteran species. BMC Genomics (2008) 1.01

Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics (2007) 0.98

Intron retention in the 5'UTR of the novel ZIF2 transporter enhances translation to promote zinc tolerance in arabidopsis. PLoS Genet (2014) 0.97

Dual location of the mitochondrial preprotein transporters B14.7 and Tim23-2 in complex I and the TIM17:23 complex in Arabidopsis links mitochondrial activity and biogenesis. Plant Cell (2012) 0.97

Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A (2014) 0.96

The immediate upstream region of the 5'-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana. Nucleic Acids Res (2013) 0.94

Post-transcriptional regulation of gene expression in plants during abiotic stress. Int J Mol Sci (2009) 0.94

Translational Regulation of Cytoplasmic mRNAs. Arabidopsis Book (2013) 0.93

A new plant protein interacts with eIF3 and 60S to enhance virus-activated translation re-initiation. EMBO J (2009) 0.92

Analysis of genome-wide changes in the translatome of Arabidopsis seedlings subjected to heat stress. PLoS One (2013) 0.90

Mechanism of cytoplasmic mRNA translation. Arabidopsis Book (2015) 0.89

Transcriptional regulation of ribosome components are determined by stress according to cellular compartments in Arabidopsis thaliana. PLoS One (2011) 0.88

Posttranscriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice. Plant Physiol (2012) 0.88

RNA decay and RNA silencing in plants: competition or collaboration? Front Plant Sci (2011) 0.85

Regulation of Translation Initiation under Abiotic Stress Conditions in Plants: Is It a Conserved or Not so Conserved Process among Eukaryotes? Comp Funct Genomics (2012) 0.84

The Arabidopsis translatome cell-specific mRNA atlas: Mining suberin and cutin lipid monomer biosynthesis genes as an example for data application. Plant Signal Behav (2010) 0.84

Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana. DNA Res (2011) 0.84

Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Sci (2013) 0.84

Internet Resources for Gene Expression Analysis in Arabidopsis thaliana. Curr Genomics (2008) 0.84

Germination Potential of Dormant and Nondormant Arabidopsis Seeds Is Driven by Distinct Recruitment of Messenger RNAs to Polysomes. Plant Physiol (2015) 0.82

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner. Nucleic Acids Res (2015) 0.81

The salicylic acid dependent and independent effects of NMD in plants. Plant Signal Behav (2012) 0.79

The 5' untranslated region of the soybean cytosolic glutamine synthetase β(1) gene contains prokaryotic translation initiation signals and acts as a translational enhancer in plants. Mol Genet Genomics (2012) 0.79

Transcriptomic landscape of Pueraria lobata demonstrates potential for phytochemical study. Front Plant Sci (2015) 0.77

Involvement of rRNA biosynthesis in the regulation of CUC1 gene expression and pre-meristematic cell mound formation during shoot regeneration. Front Plant Sci (2014) 0.77

Increased sucrose levels mediate selective mRNA translation in Arabidopsis. BMC Plant Biol (2014) 0.76

Transcriptional analysis of phloem-associated cells of potato. BMC Genomics (2015) 0.76

Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression. Int J Genomics (2015) 0.75

UV-B induction of the E3 ligase ARIADNE12 depends on CONSTITUTIVELY PHOTOMORPHOGENIC 1. Plant Physiol Biochem (2015) 0.75

Functional analysis of the Arabidopsis thaliana MUTE promoter reveals a regulatory region sufficient for stomatal-lineage expression. Planta (2016) 0.75

TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets. BMC Bioinformatics (2007) 0.75

Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives. J Exp Bot (2015) 0.75

Characterization of 5'UTR of rice ClpB-C/Hsp100 gene: evidence of its involvement in post-transcriptional regulation. Cell Stress Chaperones (2015) 0.75

Genes responding to water deficit in apple (Malus × domestica Borkh.) roots. BMC Plant Biol (2014) 0.75

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. G3 (Bethesda) (2016) 0.75

The promoter and the 5'-untranslated region of rice metallothionein OsMT2b gene are capable of directing high-level gene expression in germinated rice embryos. Plant Cell Rep (2014) 0.75

Auxin Signaling in Regulation of Plant Translation Reinitiation. Front Plant Sci (2017) 0.75

Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest. Nucleic Acids Res (2017) 0.75

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89

On finding all suboptimal foldings of an RNA molecule. Science (1989) 20.36

Integrating mRNA processing with transcription. Cell (2002) 9.74

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2003) 7.45

The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol (1995) 7.31

Frequent alternative splicing of human genes. Genome Res (1999) 6.68

Pushing the limits of the scanning mechanism for initiation of translation. Gene (2002) 6.47

RNA polymerase II and the integration of nuclear events. Genes Dev (2000) 6.16

Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15

An inspection of the domain between putative TATA box and translation start site in 79 plant genes. Nucleic Acids Res (1987) 5.93

Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol (1989) 5.52

Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90

RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. Proc Natl Acad Sci U S A (2003) 4.34

Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc Natl Acad Sci U S A (1999) 4.12

Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. Gene (1997) 4.02

Translational control by the 3'-UTR: the ends specify the means. Trends Biochem Sci (2003) 4.00

Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes. Cell (1980) 3.98

Regulation of fungal gene expression via short open reading frames in the mRNA 5'untranslated region. Mol Microbiol (2003) 3.61

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50

An mRNA cap binding protein, ABH1, modulates early abscisic acid signal transduction in Arabidopsis. Cell (2001) 3.50

Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nat Genet (2000) 2.79

Drought-inhibition of photosynthesis in C3 plants: stomatal and non-stomatal limitations revisited. Ann Bot (2002) 2.63

Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc Natl Acad Sci U S A (1999) 2.42

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics (2004) 2.22

Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol Cell Biol (2001) 2.17

Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci U S A (2002) 2.14

A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes. Gene Expr (1991) 2.13

Discovering common stem-loop motifs in unaligned RNA sequences. Nucleic Acids Res (2001) 2.12

New ways of initiating translation in eukaryotes? Mol Cell Biol (2001) 2.11

Translation control: bridging the gap between genomics and proteomics? Trends Biochem Sci (2001) 2.08

Global and specific translational control by rapamycin in T cells uncovered by microarrays and proteomics. J Biol Chem (2002) 2.08

Context sequences of translation initiation codon in plants. Plant Mol Biol (1997) 2.05

Starting the protein synthesis machine: eukaryotic translation initiation. Bioessays (2003) 2.00

Homodirectional changes in transcriptome composition and mRNA translation induced by rapamycin and heat shock. Nat Struct Biol (2003) 1.95

Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J (2004) 1.87

Translational efficiency is regulated by the length of the 3' untranslated region. Mol Cell Biol (1996) 1.87

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinformatics (2001) 1.74

Modulation of an RNA-binding protein by abscisic-acid-activated protein kinase. Nature (2002) 1.65

Determinants of translational fidelity and efficiency in vertebrate mRNAs. Biochimie (1994) 1.59

RNA diversity has profound effects on the translation of neuronal nitric oxide synthase. Proc Natl Acad Sci U S A (1999) 1.57

A reassessment of the translation initiation codon in vertebrates. Trends Genet (2001) 1.55

The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Mol Cell Proteomics (2003) 1.45

Transcription-coupled translation control of AML1/RUNX1 is mediated by cap- and internal ribosome entry site-dependent mechanisms. Mol Cell Biol (2000) 1.42

RNA-protein interactions in the control of stability and localization of messenger RNA (review). Int J Mol Med (2000) 1.40

Selective translation of cytoplasmic mRNAs in plants. Trends Plant Sci (1999) 1.40

Regulation of translational initiation in plants. Curr Opin Plant Biol (2002) 1.39

Regulation of Photosynthetic Rate of Two Sunflower Hybrids under Water Stress. Plant Physiol (1992) 1.36

Nuclear coupling: RNA processing reaches back to transcription. Nat Struct Biol (2002) 1.30

Effect of two consensus sequences preceding the translation initiator codon on gene expression in plant protoplasts. Plant Mol Biol (1992) 1.30

A delayed leaf senescence mutant is defective in arginyl-tRNA:protein arginyltransferase, a component of the N-end rule pathway in Arabidopsis. Plant J (2002) 1.28

RNA structure and the regulation of gene expression. Plant Mol Biol (1996) 1.27

In vivo evaluation of the context sequence of the translation initiation codon in plants. Plant Sci (2000) 1.25

Transcriptional activators control splicing and 3'-end cleavage levels. J Biol Chem (2003) 1.19

Protein-protein interactions required during translation. Plant Mol Biol (2002) 1.18

Diversity in translational regulation. Curr Opin Cell Biol (2001) 1.10

The role of 5'-leader length, secondary structure and PABP concentration on cap and poly(A) tail function during translation in Xenopus oocytes. Nucleic Acids Res (2000) 0.98

Genomic organization of the mouse peroxisome proliferator-activated receptor beta/delta gene: alternative promoter usage and splicing yield transcripts exhibiting differential translational efficiency. Biochem J (2002) 0.95

Coupling transcription to translation: a novel site for the regulation of eukaryotic gene expression. Int J Biochem Cell Biol (1996) 0.90

GPRM: A genetic programming approach to finding common RNA secondary structure elements. Nucleic Acids Res (2003) 0.86

Identification and characterization of a novel human cathepsin L splice variant. Gene (2002) 0.84

The length of 5'-untranslated leader sequences influences distribution of 3-hydroxy-3-methylglutaryl-coenzyme A reductase mRNA in polysomes: effects of lovastatin, oxysterols, and mevalonate. Arch Biochem Biophys (1995) 0.83

Differential translation of TOP mRNAs in rapamycin-treated human B lymphocytes. Biochim Biophys Acta (2003) 0.80

The 5'-untranslated region of the mouse glial cell line-derived neurotrophic factor gene regulates expression at both the transcriptional and translational levels. Brain Res Mol Brain Res (2001) 0.77

Articles by these authors

Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature (2006) 6.68

A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell (2006) 2.95

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A (2009) 2.77

RopGAP4-dependent Rop GTPase rheostat control of Arabidopsis oxygen deprivation tolerance. Science (2002) 2.18

Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants. Nature (2011) 2.06

Plant responses to hypoxia--is survival a balancing act? Trends Plant Sci (2004) 2.01

Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc Natl Acad Sci U S A (2008) 2.00

Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol (2008) 1.95

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J (2008) 1.92

Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J (2004) 1.87

Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann Bot (2005) 1.82

Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiol (2010) 1.79

Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol (2005) 1.66

Unraveling the tapestry of networks involving reactive oxygen species in plants. Plant Physiol (2008) 1.51

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci U S A (2013) 1.48

The submergence tolerance regulator SUB1A mediates crosstalk between submergence and drought tolerance in rice. Plant Cell (2011) 1.44

Flood adaptive traits and processes: an overview. New Phytol (2015) 1.39

Regulation of translational initiation in plants. Curr Opin Plant Biol (2002) 1.39

Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis cytosolic ribosomes. Plant Physiol (2005) 1.32

Isolation of plant polysomal mRNA by differential centrifugation and ribosome immunopurification methods. Methods Mol Biol (2009) 1.30

Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia. New Phytol (2011) 1.26

The roles of reactive oxygen species in plant cells. Plant Physiol (2006) 1.25

The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol (2010) 1.23

Regulated phosphorylation of 40S ribosomal protein S6 in root tips of maize. Plant Physiol (2003) 1.20

Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiol (2005) 1.14

Two Rumex species from contrasting hydrological niches regulate flooding tolerance through distinct mechanisms. Plant Cell (2013) 1.12

Profiling of translatomes of in vivo-grown pollen tubes reveals genes with roles in micropylar guidance during pollination in Arabidopsis. Plant Cell (2014) 1.11

Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice. Ann Bot (2008) 1.09

What makes species unique? The contribution of proteins with obscure features. Genome Biol (2006) 1.08

Dynamic Light Regulation of Translation Status in Arabidopsis thaliana. Front Plant Sci (2012) 1.08

Transient MPK6 activation in response to oxygen deprivation and reoxygenation is mediated by mitochondria and aids seedling survival in Arabidopsis. Plant Mol Biol (2011) 1.00

The submergence tolerance gene SUB1A delays leaf senescence under prolonged darkness through hormonal regulation in rice. Plant Physiol (2012) 0.99

Gene and enhancer trap transposable elements reveal oxygen deprivation-regulated genes and their complex patterns of expression in Arabidopsis. Ann Bot (2003) 0.97

Selective mRNA sequestration by OLIGOURIDYLATE-BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis. Proc Natl Acad Sci U S A (2014) 0.96

Expression of rice SUB1A and SUB1C transcription factors in Arabidopsis uncovers flowering inhibition as a submergence tolerance mechanism. Plant J (2011) 0.94

Comparison of GC-MS and NMR for metabolite profiling of rice subjected to submergence stress. J Proteome Res (2012) 0.92

Plant biology: Genetics of high-rise rice. Nature (2009) 0.91

Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. Plant Physiol (2012) 0.88

Posttranscriptional control of photosynthetic mRNA decay under stress conditions requires 3' and 5' untranslated regions and correlates with differential polysome association in rice. Plant Physiol (2012) 0.88

Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening. Physiol Plant (2013) 0.88

Characterization of distinct root and shoot responses to low-oxygen stress in Arabidopsis with a focus on primary C- and N-metabolism. Plant Cell Environ (2014) 0.87

Differential metabolic regulation governed by the rice SUB1A gene during submergence stress and identification of alanylglycine by 1H NMR spectroscopy. J Proteome Res (2011) 0.86

Cold shock protein 1 chaperones mRNAs during translation in Arabidopsis thaliana. Plant J (2013) 0.85

The Arabidopsis translatome cell-specific mRNA atlas: Mining suberin and cutin lipid monomer biosynthesis genes as an example for data application. Plant Signal Behav (2010) 0.84

Isolation and analysis of mRNAs from specific cell types of plants by ribosome immunopurification. Methods Mol Biol (2013) 0.81

Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes. Methods Mol Biol (2015) 0.78

Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation. Methods Mol Biol (2015) 0.76

Rapid immunopurification of ribonucleoprotein complexes of plants. Methods Mol Biol (2015) 0.75