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- Title
Transcriptome-wide identification of microRNA targets in rice.
- Authors
Yong-Fang Li; Yun Zheng; Addo-Quaye, Charles; Li Zhang; Saini, Ajay; Jagadeeswaran, Guru; Axtell, Michael J.; Weixiong Zhang; Sunkar, Ramanjulu
- Abstract
MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis and rice ( Oryza sativa), respectively. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. In contrast with the well-characterized miRNA targets that are cleaved in Arabidopsis, only a few such targets have been confirmed in rice. To identify small RNA targets in rice, we applied the ‘degradome sequencing’ approach, which globally identifies the remnants of small RNA-directed target cleavage by sequencing the 5′ ends of uncapped RNAs. One hundred and sixty targets of 53 miRNA families (24 conserved and 29 rice-specific) and five targets of TAS3-small interfering RNAs (siRNAs) were identified. Surprisingly, an additional conserved target for miR398, which has not been reported so far, has been validated. Besides conserved homologous transcripts, 23 non-conserved genes for nine conserved miRNAs and 56 genes for 29 rice-specific miRNAs were also identified as targets. Besides miRNA targets, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.
- Publication
Plant Journal, 2010, Vol 62, Issue 5, p742
- ISSN
0960-7412
- Publication type
Academic Journal
- DOI
10.1111/j.1365-313X.2010.04187.x