Abstract
BackgroundThe microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, relative fewer phasiRNA biogenesis pathways have been discovered in rice compared to other plant species, which limits the comprehensive understanding of phasiRNA biogenesis and the miRNA-derived regulatory network.ResultsIn this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further investigation of their regulatory function revealed that eleven novel phasiRNAs in 21-nt length recognized forty-one target genes. Most of these genes were involved in the growth and development of rice. In addition, five novel 24-nt phasiRNAs targeted to the promoter of an OsCKI1 gene and thereafter resulted in higher level of methylation in panicle, which implied their regulatory function in transcription of OsCKI1,which acted as a regulator of rice development.ConclusionsThese results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.
Highlights
The microRNAs(miRNA)-derived secondary phased small interfering RNAs participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants
Recent reports discovered that processing of 21-nt phasiRNAs mainly depends on OsDCL4, and OsDCL3 is required for biogenesis of 24-nt phasiRNAs in rice [20]
The six novel phasiRNAs biogenesis pathways that we discovered in three-week-old seedling were undetected in two-week-old seedling samples, which might be caused by the low expression level of phasiRNAs generated from these pathways in younger seedlings
Summary
The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. Two types of endogenous small RNAs, microRNAs (miRNAs) and small interfering RNAs (siRNAs), are highly abundant in plants. A small proportion of the fragments will survive and subsequently be processed into double-stranded RNA (dsRNA) by RNA-dependent RNA polymerase 6(RDR6) with the aid of Suppressor of Gene Silencing 3 (SGS3). These double-stranded fragments will further be cleaved by Dicer-like (DCL) proteins in different phased manners to produce a series of 21- or 24-nt siRNAs, termed phased small interfering RNAs (phasiRNAs) [8]
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