# Identification of the co-regulatory siRNAs of “miRNA→target” in Oryza sativa

## TL;DR

This study improves the rice miRNA-target database by identifying co-regulatory siRNAs and miRNA isoforms, revealing more complete regulatory relationships in rice.

## Contribution

The study introduces a method to discover co-regulatory siRNAs and miRNA isoforms, enhancing the completeness of the rice miRNA-target database.

## Key findings

- 86.2% of target genes in rice are co-regulated by one or more miRNAs/siRNAs.
- 30 miRNA isoforms and 12 siRNAs were identified as co-regulators involved in rice development and stress responses.
- Some miRNA isoforms showed higher expression levels than their parent miRNAs.

## Abstract

The current “small interfering RNA(siRNA)→Target” mining tools can only search for targets of known siRNAs, and cannot discover co-regulatory siRNAs of unknown sequences that may exist, which means that the “microRNA(miRNA)→Target” database obtained by these mining tools is incomplete. Using the previously developed sRNATargetDigger, we re-mined the rice “miRNA→Target” database supported by the degradome and found 86.2% of the target genes were co-regulated by one or more miRNAs\siRNAs. Besides the known miRNAs, 30 miRNA isoforms (isomiRs) and 12 siRNAs were identified to be involved in co-regulation, which play important roles in rice response to external auxin regulation, rice blast resistance, adventitious root formation, cold resistance, and tillering etc. Some isomiRs even have higher expression levels than miRNAs. In addition, we also found that the regulatory relationship between 51 miRNAs and 48 target genes in the original database could not be verified due to the low expression levels of miRNA, poor complementarity between miRNA and target, or no specific cleavage signal detected by degradome in the middle of the miRNA binding site in the targets. Four miRNAs (osa-miR530-5p,osa-miR319b,osa-miR172c and osa-miR395a) only found isomiRs involved in regulation. In addition, we also found a number of miRNA→target regulatory relationships missed in the database. This study improved the rice “miRNA→target” database which will contribute to the research of rice miRNA and molecular breeding.