Abstract
MicroRNAs (miRNAs) play important roles in plant development through regulation of gene expression by mRNA degradation or translational inhibition. Despite the fact that tomato (Solanum lycopersicum) is the model system for studying fleshy fruit development and ripening, only a few experimentally proven miRNA targets are known, and the role of miRNA action in these processes remains largely unknown. Here, by using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development, a total of 119 target genes of miRNAs were identified. Of these, 106 appeared to be new targets. A large part of the identified targets (56) coded for transcription factors. Auxin response factors, as well as two known ripening regulators, COLORLESS NON-RIPENING (CNR) and APETALA2a (SlAP2a), with developmentally regulated degradation patterns were identified. The levels of the intact messenger of both CNR and AP2a are actively modulated during ripening, by miR156/157 and miR172, respectively. Additionally, two TAS3-mRNA loci were identified as targets of miR390. Other targets such as ARGONAUTE 1 (AGO1), shown to be involved in miRNA biogenesis in other plant species, were identified, which suggests a feedback loop regulation of this process. In this study, it is shown that miRNA-guided cleavage of mRNAs is likely to play an important role in tomato fruit development and ripening
Original language | English |
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Pages (from-to) | 1863-1878 |
Journal | Journal of Experimental Botany |
Volume | 64 |
Issue number | 7 |
DOIs | |
Publication status | Published - 2013 |
Keywords
- solanum-lycopersicon
- small rnas
- flower development
- parallel analysis
- seed-germination
- sirna biogenesis
- leaf development
- mirna targets
- arabidopsis
- expression
Fingerprint Dive into the research topics of 'Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis'. Together they form a unique fingerprint.
Datasets
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Gene expression in three stages of ripening tomato fruit
de Maagd, R. (Creator) & Bovy, A. (Creator), Plant Research International, 5 Apr 2013
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42783
Dataset
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Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis
de Maagd, R. (Creator), Karlova, R. (Creator) & van Haarst, J. (Creator), Plant Research International, 12 Nov 2013
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42661
Dataset
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Comparison of tomato fruit gene expression data obtained by microarray analysis and by treatment of degradome sequencing data as an RNAseq experiment
de Maagd, R. (Creator), Plant Research International, 12 Nov 2013
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42784
Dataset