NDLI: Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.

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Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Moxon, Simon Jing, Runchun Szittya, Gyorgy Schwach, Frank Rusholme Pilcher, Rachel L. Moulton, Vincent Dalmay, Tamas
Description	Country affiliation: United kingdom Author Affiliation: Moxon S ( School of Computing, University of East Anglia, Norwich NR4 7TJ, United Kingdom.)
Abstract	In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue-specific expression, which, combined with target gene validation results, suggests that miRNAs may play a role in fleshy fruit development. We also identified four new nonconserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This suggests that target prediction of plant short RNAs could have a high false-positive rate and must therefore be validated experimentally. We also found short RNAs from a Solanaceae-specific foldback transposon, which showed a miRNA/miRNA*-like distribution, suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae-specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
DOI	10.1101/gr.080127.108
Journal	Genome Research
Issue Number	10
Volume Number	18
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2008-10-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Genetics Lycopersicon Esculentum Micrornas Chemistry Rna, Plant Blotting, Northern Computational Biology Conserved Sequence Dna Transposable Elements Metabolism Gene Dosage Gene Expression Regulation, Plant Genes, Plant Genome, Plant Molecular Sequence Data Solanaceae Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

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Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.

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