Rice MicroRNA3’cytosine Addition And Its Possible Role In Rice Development

MicroRNA is a kind of20-24nt small noncoding RNAs that regulate gene expression at the post-transcriptional level via binding to complementary site in target mRNAs. In plant, the binding site between miRNA and mRNA is nearly perfect match, leading to the degradation of target mRNAs. Previous research has shown us that miRNA can participated in a lot of bioprocess thus as early development, cell proliferation, apoptosis, cell differentiation and flowering. Typically, miRNAs are annotated as a single defined sequence, but the fact is that,many miRNAs have several length and/or sequence variants, and this variants was named isomiRs. The most abundant form of isomiRs is3’nucleotide addition.IsomiRs were originally dismissed as experimental artifacts. However, massively parallel sequencing and sophisticated computational algorithms have now confidently identified a vast array of isomiRs in various species. Moreover, isomiRs have been demonstrated to associate actively with RISC and translational machinery, suggesting that isomiRs are capable of interacting with target mRNAs. Many studies have suggested that3’nucleotide addition is a mechanism for regulation of plant miRNA stability when they lose methylation. In both kingdoms, several studies have reached the consensus that adenylation increases stability, while uridylation boosts miRNA degradation. But few research have noticed the existence and the function of3’cytosine addition in rice.We analyze the rice(Oryza sativa) small RNA high throughput sequencing data from NCBI and find out that the average expression level of3’cytosine addition is more aboundant than adenylation. The expression level of3’ cytosine addition is significantly increased after oshenl and wAfl mutant, proved that the3’cytosine addition is one kind of truly exist post-transcriptional modification. Interestingly, a subset of miRNA loci appears to be frequently targeted for significant3’cytosine addition in rice, and the expression level of3’cytosine addition is not dependent on the expression level of miRNA locus. Comparison of the percentage of addition in the same miRNA locus across all analyzed rice organ revealed consistent correlation for uridine addition, but not for cytosine addition. Hints at the possibility that cytosine addition at miRNA loci fluctuates across cell types while uridine addition occurs at similar rates. The analysis of Ago IP data reveal that Ago4(but not AgoL) protein other has an enrichment effect on3’cytosine addition miRNA or associated with3cytosine addition activety.56miRNA with significant3cytosine addition in shoot and their3cytosine addition isomiRs were predicted to target359genes. The GO enrichment analysis was preformed by using all rice miRNA target as background. We found that these359genes are significantly enriched in19Gene Ontology (GO) terms, and over a half of the GO terms are related to development.