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

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

Ting Peng  1 , Yanxiu Du, Jing Zhang, Junzhou Li, Yanxia Liu, Yafan Zhao, Hongzheng Sun, Quanzhi Zhao
Affiliations

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

Ting Peng et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Localization and length distribution of unambigously mapped siRNAs in rice grains.
A, location distribution; B, length distribution. The represents axis indicates the numbers of siRNA in each category.
Figure 2
Figure 2. Dynamic variation of 24 nt-siRNAs in superior and inferior grains.
The horizontal axis represents sample periods of superior and inferior grains, and the vertical axis represents number (in TPM) of 24 nt-siRNAs in each library.
Figure 3
Figure 3. Frequency of 24 nt-siRNAs and 24 nt-siRNA*s.
The horizontal axis represents 24 nt-siRNA pairs. The vertical axis represents frequency in TPM. Bars above and below the horizontal axis represent frequency of 24 nt-siRNA and 24 nt-siRNA*, respectively.
Figure 4
Figure 4. Frequency of 24 nt-siRNAs greater than 10TPM in the superior and inferior grains.
The horizontal axis indicates 24 nt-siRNA, and vertical axis indicates frequency in TPM. The siRNAs were arranged in the same order for the sake of comparison between superior and inferior grains of different stages. S indicates superior grain and I indicates inferior grain. DAF represents day after flowering.
See this image and copyright information in PMC

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