# Coding Transcript-Derived Small Interfering RNAs: Their Biogenesis and Molecular Function in Arabidopsis

## TL;DR

This review explores how coding transcript-derived small interfering RNAs (ct-siRNAs) form in plants and how they affect gene regulation, growth, and stress responses.

## Contribution

The paper provides a comprehensive review of the biogenesis and molecular functions of ct-siRNAs in Arabidopsis under RNA metabolic defects.

## Key findings

- ct-siRNAs are generated from aberrant mRNAs processed by RDR6 and DCL proteins into 21-nt and 22-nt forms.
- Accumulation of ct-siRNAs leads to gene suppression and is linked to altered plant growth and stress responses.
- The regulatory effects of ct-siRNAs depend on their length and the genetic background of the plant.

## Abstract

Coding transcripts-derived small interfering RNAs (ct-siRNAs) have emerged as a special class of endogenous siRNAs and have been implicated in the regulation of gene expression in plants, particularly under conditions where RNA metabolic pathways are perturbed. When the RNA quality control (RQC) system is impaired, the aberrant mRNA fragments were converted to double stranded forms by RNA-directed RNA polymerase 6 (RDR6) with the assistance of Suppressor of Gene Silencing 3 (SGS3) and subsequently processed by DICER-LIKE proteins into 21-nt and 22-nt ct-siRNAs. The accumulation of ct-siRNAs and the resulting suppression of their cognate genes are usually associated with altered plant growth and stress response. In this review, we summarize our current understanding of the ct-siRNAs, particularly their biogenesis under different RNA metabolic defective conditions. Comparative analysis of these genetic contexts indicates that ct-siRNAs act through translation inhibition and/or mRNA cleavage, with regulatory outcomes influenced by siRNA length and genetic background. We further summarize the biological consequence of ct-siRNA accumulation, which are frequently associated with impaired plant growth and stress adaptation. Finally, we discuss current controversies on ct-siRNAs research and highlight key unsolved questions for future investigation. Collectively, this review highlights ct-siRNAs as a link between impaired RNA metabolisms and post-transcriptional gene silencing, with context-dependent effects on plant growth and stress responses.