PLoS ONE (Jan 2013)

Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.

  • Yong-ao Tong,
  • Hua Peng,
  • Cheng Zhan,
  • LinHong Fan,
  • Taobo Ai,
  • Shenghua Wang

DOI
https://doi.org/10.1371/journal.pone.0063938
Journal volume & issue
Vol. 8, no. 5
p. e63938

Abstract

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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.