A comprehensive survey of degradation and 3' end modification of plant microRNAs by deep sequencing
The degradation and 3' end modification of plant microRNAs (miRNAs) play crucial roles in regulating miRNA function and stability. However, the process and mechanism of miRNA degradation and 3' end modification has, to date, been poorly characterized. Here, we report that analysis of the two small RNA libraries constructed from two hickory floral differentiation stages by deep sequencing obtained a large number of truncated miRNAs and miRNAs with 3' end modifications. The presence of so many truncated miRNAs suggests that plant miRNAs may be degraded through the 5' to 3' and 3' to 5' ends simultaneously, but the probability of miRNAs being truncated from the 3' end was higher than from the 5' end. Single- or double-nucleotide 3' additions to miRNAs has been observed in many families. In this study, the 3' addition of adenine to miRNA was the most common, accounting for more than 50% of all miRNA 3' end modification in both small RNA libraries, followed by uridine addition. This suggests that the 3' end modification of miRNAs shows a bias towards adenine and uridine in plants. Furthermore, we observed that both truncated miRNA and isomiR expressions associated with mature miRNAs. Our study provides more information regarding the degradation and 3' end modification of miRNAs in plants. Overall design: Examination of 2 different female flower buds