title: Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
abstract: Intronic microRNAs (in-miRNAs) as a class of miRNA family that regulates gene expression are still poorly understood in plants. In this study, we systematically identified rice in-miRNAs by re-mining eight published small RNA-sequencing datasets of rice. Furthermore, based on the collected expression, annotation, and putative target data, we investigated the structures, potential functions, and expression features of these in-miRNAs and the expression patterns of their host genes. A total of 153 in-miRNAs, which account for over 1/4 of the total rice miRNAs, were identified. In silico expression analysis showed that most of them (∼63%) are tissue or stage-specific. However, a majority of their host genes, especially those containing clustered in-miRNAs, exhibit stable high-level expressions among 513 microarray datasets. Although in-miRNAs show diversity in function and mechanism, the DNA methylation directed by 24 nt in-miRNAs may be the main pathway that controls the expressions of target genes, host genes, and even themselves. These findings may enhance our understanding on special functions of in-miRNAs, especially in mediating DNA methylation that was concluded to affect the stability of expression and structure of host and target genes.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan, China.
authors.forename: Yong-ao
authors.initials: YA
authors.lastname: Tong
authors.forename: Hua
authors.initials: H
authors.lastname: Peng
authors.forename: Cheng
authors.initials: C
authors.lastname: Zhan
authors.forename: LinHong
authors.initials: L
authors.lastname: Fan
authors.forename: Taobo
authors.initials: T
authors.lastname: Ai
authors.forename: Shenghua
authors.initials: S
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D019175:DNA Methylation / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods; D007438:Introns / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D035683:MicroRNAs