Genome-wide analysis of 24-nt siRNAs dynamic variations during rice superior and inferior grain filling

PLoS One. 2013 Apr 12;8(4):e61029. doi: 10.1371/journal.pone.0061029. Print 2013.

Abstract

24 nt-siRNAs are the most abundant small interfering RNAs in rice grains aside from microRNAs. To investigate the roles that 24 nt-siRNAs played in the poor grain filling of rice inferior grains, dynamic variations of 24 nt-siRNAs in inferior grains were compared with those of superior grains by using small RNA deep sequencing technology. The results showed that 24 nt-siRNAs derived from multiple regions of rice genome, and the maintenance of the two strands of 24 nt-siRNA duplex was a non-random process. The amounts of 24 nt-siRNAs declined with the process of grain filling in both superior and inferior grains, but 24 nt-siRNAs in inferior grains was much higher than that of superior grains in each period we sampled. Bioinformatics prediction indicated that 24 nt-siRNAs targeted on more genes involved in most of the known KEGG rice pathways, such as the starch and sucrose biosynthesis pathway. Combined with digital gene expression profiling of target genes, 24 nt-siRNAs mapped on the antisense strands of exons were specifically investigated, but the abundance of 24 nt-siRNAs did not show negative correlations with their corresponding target genes. The results indicated that 24 nt-siRNAs were not involved in down-regulation of target genes. The potential biological meanings for this inconsistency were probably the results of methylation directed gene expression activation, or competition for small RNA stability methylation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Library
  • Genes, Plant
  • Genome, Plant / genetics*
  • High-Throughput Nucleotide Sequencing
  • Oryza / genetics*
  • RNA, Plant / genetics
  • RNA, Plant / metabolism*
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism*
  • Seeds / enzymology
  • Seeds / genetics*
  • Seeds / growth & development*

Substances

  • RNA, Plant
  • RNA, Small Interfering

Grants and funding

This work was supported by the National Natural Science Foundation of China (grant No. 31200973to HS), National Natural Science Foundation of China (grant No. 31271651 to QZ), and Supported Program for Innovative Research Team (in Science and Technology) in University of Henan Province (grant No 2010IRTSTHN005 to QZ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.