Degradome Sequencing for Plant miRNA Target Identification

MicroRNAs (miRNAs) are endogenous small noncoding RNAs that play crucial roles in the post-transcriptional regulation of gene expression in plants and animals. They function by binding to complementary mRNA molecules (targets) and acting as negative regulators of translation. This function is part of a complex web as a single miRNA might have several target genes and a single gene may be regulated by many miRNAs. Identification of these miRNA-target pairs is crucial to understanding the biology of the miRNA regulatory mechanism.

In plants, miRNAs exert negative regulatory control by binding to and causing cleavage of their targets at the position between nucleotides 10 and 11 of the miRNA. Recently, degradome sequencing, a modified 5'-rapid amplification of cDNA ends (RACE) performed with next-gen sequencing, has emerged as a comprehensive method of analyzing patterns of RNA degradation.  Deep sequencing of the 5’ ends of RNA degradation products allows identification of over-represented 5’ ends (miRNA cleavage sites) within and RNA sample. Matching cleavage sites to known miRNA sequences links miRNAs to their targets.

This poster will provide an overview of this emerging method for miRNA target identification, as well as case study examples to illustrate the usefulness of this latest application of next-gen sequencing technology to plant miRNA research.