Access the full text.
Sign up today, get DeepDyve free for 14 days.
Lu (2005)
Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from ArabidopsisPlant Cell, 17
Adenot (2006)
DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7Curr. Biol., 16
Axtell (2008)
Evolution of plant microRNAs and their targetsTrends Plant Sci., 13
Morin (2008)
Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativaGenome Res., 18
Onodera (2005)
Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formationCell, 120
Fahlgren (2007)
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genesPLoS ONE, 2
Addo-Quaye (2008)
Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradomeCurr. Biol., 18
Axtell (2007)
Common functions for diverse small RNAs of land plantsPlant Cell, 19
Rajagopalan (2006)
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thalianaGenes Dev., 20
Barakat (2007)
Conservation and divergence of microRNAs in PopulusBMC Genomics, 8
Kawashima (2009)
Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell typesPlant J., 57
Moxon (2008a)
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripeningGenome Res., 18
Borsani (2005)
Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in ArabidopsisCell, 123
Schwab (2005)
Specific effects of microRNAs on the plant transcriptomeDev. Cell, 8
Aukerman (2003)
Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genesPlant Cell, 15
Arazi (2005)
Cloning and characterization of micro-RNAs from mossPlant J., 43
Fukuoka (2009)
Loss of function of a proline-containing protein confers durable disease resistance in riceScience, 325
Mallory (2008)
MicroRNA maturation and action - the expanding roles of ARGONAUTEsCurr. Opin. Plant Biol., 11
Gandikota (2007)
The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlingsPlant J., 49
Lu (2008)
Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)Proc. Natl Acad. Sci. USA, 105
Valoczi (2006)
Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissuesPlant J., 47
Herr (2005)
RNA polymerase IV directs silencing of endogenous DNAScience, 308
Vazquez (2004)
Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAsMol. Cell, 16
Jones-Rhoades (2004)
Computational identification of plant microRNAs and their targets, including a stress-induced miRNAMol. Cell, 14
Lacombe (2008)
Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in riceBMC Plant Biol., 8
Allen (2004)
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thalianaNat. Genet., 36
Wang (2009)
Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodulesBiochem. Biophys. Res. Commun., 378
Lu (2006)
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutantGenome Res., 16
Subramanian (2008)
Novel and nodulation-regulated microRNAs in soybean rootsBMC Genomics, 9
Zhu (2008)
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grainsGenome Res., 18
Floyd (2004)
Gene regulation: ancient microRNA target sequences in plantsNature, 428
Aung (2006)
pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target genePlant Physiol., 141
Brodersen (2008)
Widespread translational inhibition by plant miRNAs and siRNAsScience, 320
Velasco (2007)
A high quality draft consensus sequence of the genome of a heterozygous grapevine varietyPLoS ONE, 2
Phillips (2007)
The role of small RNAs in abiotic stressFEBS Lett., 581
Voinnet (2009)
Origin, biogenesis, and activity of plant microRNAsCell, 136
Kanno (2005)
Atypical RNA polymerase subunits required for RNA-directed DNA methylationNat. Genet., 37
Peragine (2004)
SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in ArabidopsisGenes Dev., 18
Carra (2009)
Cloning and characterization of small non-coding RNAs from grapePlant J., 59
Wu (2009)
Rice MicroRNA effector complexes and targetsPlant Cell, 21
Axtell (2005)
Antiquity of microRNAs and their targets in land plantsPlant Cell, 17
Chen (2003)
A microRNA as a translational repressor of APETALA2 in Arabidopsis flower developmentScience, 11
Allen (2005)
microRNA-directed phasing during trans-acting siRNA biogenesis in plantsCell, 121
Fattash (2007)
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolutionBMC Plant Biol., 7
Kurihara (2004)
Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functionsProc. Natl. Acad. Sci. USA, 101
Addo-Quaye (2009)
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targetsBioinformatics, 25
Zeenko (2002)
Eukaryotic elongation factor 1A interacts with the upstream pseudoknot domain in the 3′ untranslated region of tobacco mosaic virus RNAJ. Virol., 76
Lanet (2009)
Biochemical evidence for translational repression by Arabidopsis microRNAsPlant Cell, 21
German (2008)
Global identification of microRNA-target RNA pairs by parallel analysis of RNA endsNat. Biotechnol., 26
Yao (2007)
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)Genome Biol., 8
Moxon (2008b)
A toolkit for analysing large-scale plant small RNA datasetsBioinformatics, 24
Griffiths-Jones (2008)
miRBase: tools for microRNA genomicsNucleic Acids Res., 36
Jaillon (2007)
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phylaNature, 449
Brosnan (2009)
The long and the short of noncoding RNAsCurr. Opin. Cell Biol., 21
Calonje (2004)
Floral meristem identity genes are expressed during tendril development in grapevinePlant Physiol., 135
Jones-Rhoades (2006)
MicroRNAS and their regulatory roles in plantsAnnu. Rev. Plant Biol., 57
Puzey (2009)
Identification of conserved Aquilegia coerulea microRNAs and their targetsGene, 448
Lelandais-Briere (2009)
Genome-wide medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodulesPlant Cell, 21
Liu (2005)
Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in ricePlant Physiol., 139
Szittya (2008)
High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA familiesBMC Genomics, 9
Vazquez (2008)
Evolution of Arabidopsis MIR genes generates novel microRNA classesNucleic Acids Res., 36
In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post‐transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep‐sequencing, computational and molecular methods to identify, profile, and describe conserved and non‐conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non‐conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine‐specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue‐specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine‐specific miRNAs were identified by genomic‐scale high‐throughput sequencing of miRNA cleaved mRNAs.
The Plant Journal – Wiley
Published: Jun 1, 2010
Keywords: ; ; ; ;
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.