A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
- 7 August 2008
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 18 (9) , 1456-1465
- https://doi.org/10.1101/gr.075572.107
Abstract
Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as post-transcriptional or transcriptional regulators in plants. miRNA function is essential for normal plant development and therefore is likely to be important in the growth of the rice grain. To investigate the roles of miRNAs in rice grain development, we carried out deep sequencing of the small RNA populations of rice grains at two developmental stages. In a data set of ∼5.5 million sequences, we found representatives of all 20 conserved plant miRNA families. We used an approach based on the presence of miRNA and miRNA* sequences to identify 39 novel, nonconserved rice miRNA families expressed in grains. Cleavage of predicted target mRNAs was confirmed for a number of the new miRNAs. We identified a putative mirtron, indicating that plants may also use spliced introns as a source of miRNAs. We also identified a miRNA-like long hairpin that generates phased 21 nt small RNAs, strongly expressed in developing grains, and show that these small RNAs act in trans to cleave target mRNAs. Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner.Keywords
This publication has 52 references indexed in Scilit:
- Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)Proceedings of the National Academy of Sciences, 2008
- Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativaGenome Research, 2008
- Mammalian Mirtron GenesMolecular Cell, 2007
- The Mirtron Pathway Generates microRNA-Class Regulatory RNAs in DrosophilaCell, 2007
- Intronic microRNA precursors that bypass Drosha processingNature, 2007
- A Mammalian microRNA Expression Atlas Based on Small RNA Library SequencingCell, 2007
- Role of RNA polymerase IV in plant small RNA metabolismProceedings of the National Academy of Sciences, 2007
- A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thalianaGenes & Development, 2006
- CSRDB: a small RNA integrated database and browser resource for cerealsNucleic Acids Research, 2006
- MicroRNAs in plantsGenes & Development, 2002