Henan Engineering Laboratory for Rice and Key Laboratory of Physiology, Ecology and Genetics Improvement of Food Crop in Henan Province, Henan Agricultural University, Zhengzhou, China.
PLoS One. 2013 Apr 12;8(4):e61029. doi: 10.1371/journal.pone.0061029. Print 2013.
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.
24nt-siRNAs 是除 miRNA 之外在水稻籽粒中含量最丰富的小干扰 RNA。为了研究 24nt-siRNAs 在水稻弱势粒灌浆不良中的作用，本研究采用小 RNA 深度测序技术比较了弱势粒和强势粒中 24nt-siRNAs 的动态变化。结果表明，24nt-siRNAs 来源于水稻基因组的多个区域，24nt-siRNA 双链的两条链的维持是一个非随机的过程。在强势粒和弱势粒中，24nt-siRNAs 的含量随着灌浆过程的进行而逐渐下降，但在我们采样的每个时期，弱势粒中的 24nt-siRNAs 都明显高于强势粒。生物信息学预测表明，24nt-siRNAs 靶向参与大多数已知 KEGG 水稻途径的基因，如淀粉和蔗糖生物合成途径。结合靶基因的数字基因表达谱分析，特别研究了映射在外显子反义链上的 24nt-siRNAs，但 24nt-siRNAs 的丰度与其相应靶基因之间没有负相关关系。结果表明，24nt-siRNAs 不参与靶基因的下调。这种不一致的可能生物学意义可能是由于甲基化指导的基因表达激活，或对小 RNA 稳定性甲基化的竞争。
