Characterization and expression profiles of miRNAs in rice seeds

Small RNAs (sRNAs) are common and effective modulators of gene expression in eukaryotic organisms. To characterize the sRNAs expressed during rice seed development, massively parallel signature sequencing (MPSS) was performed, resulting in the obtainment of 797 399 22-nt sequence signatures, of whic...

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Bibliographic Details
Published in:Nucleic acids research 2009-02, Vol.37 (3), p.916-930
Main Authors: Xue, Liang-Jiao, Zhang, Jing-Jing, Xue, Hong-Wei
Format: Article
Language:English
Subjects:
Gene Expression Profiling
Gene Expression Regulation, Plant
Genome, Plant
MicroRNAs - chemistry
MicroRNAs - metabolism
Oryza - embryology
Oryza - genetics
Oryza - metabolism
Oryza sativa
Retroelements
RNA
RNA, Untranslated - classification
Seeds - genetics
Seeds - metabolism
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Summary:Small RNAs (sRNAs) are common and effective modulators of gene expression in eukaryotic organisms. To characterize the sRNAs expressed during rice seed development, massively parallel signature sequencing (MPSS) was performed, resulting in the obtainment of 797 399 22-nt sequence signatures, of which 111 161 are distinct ones. Analysis on the distributions of sRNAs on chromosomes showed that most sRNAs originate from interspersed repeats that mainly consist of transposable elements, suggesting the major function of sRNAs in rice seeds is transposon silencing. Through integrative analysis, 26 novel miRNAs and 12 miRNA candidates were identified. Further analysis on the expression profiles of the known and novel miRNAs through hybridizing the generated chips revealed that most miRNAs were expressed preferentially in one or two rice tissues. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated. In addition, differential accumulations of miRNAs and corresponding miRNA*s suggest the functions of miRNA*s other than being passenger strands of mature miRNAs, and in regulating the miRNA functions.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkn998