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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Coding Transcript-Derived Small Interfering RNAs: Their Biogenesis and Molecular Function in Arabidopsis.

Xintong Xu1, Nier Chen1, Xinwen Qing1

  • 1Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.

International Journal of Molecular Sciences
|February 27, 2026
PubMed
Summary
This summary is machine-generated.

Coding transcripts-derived small interfering RNAs (ct-siRNAs) are produced when RNA quality control is impaired, affecting gene expression and plant growth. This review explores ct-siRNA biogenesis, function, and consequences in plants.

Keywords:
DCL2DCL4EIN5/XRN4RDR6RQCSGS3SKI2ct-siRNAs

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Area of Science:

  • Plant Molecular Biology
  • RNA Biology
  • Genetics

Background:

  • Coding transcripts-derived small interfering RNAs (ct-siRNAs) are endogenous small RNAs involved in gene regulation.
  • Their biogenesis is linked to the RNA quality control (RQC) system and RNA-directed RNA polymerase 6 (RDR6).
  • ct-siRNAs accumulate when RNA metabolic pathways are perturbed, impacting plant phenotypes.

Purpose of the Study:

  • To review the biogenesis of ct-siRNAs under various RNA metabolic defective conditions.
  • To analyze the mechanisms of ct-siRNA action, including translation inhibition and mRNA cleavage.
  • To summarize the biological consequences of ct-siRNA accumulation on plant growth and stress responses.

Main Methods:

  • Literature review and comparative analysis of genetic contexts.
  • Examination of siRNA length and genetic background influence on regulatory outcomes.
  • Synthesis of current research on ct-siRNA function and impact.

Main Results:

  • ct-siRNAs are generated from aberrant mRNA fragments via RDR6 and DICER-LIKE proteins when RQC is impaired.
  • ct-siRNAs regulate gene expression through translation inhibition and/or mRNA cleavage.
  • Accumulation of ct-siRNAs is associated with impaired plant growth and stress adaptation.

Conclusions:

  • ct-siRNAs serve as a link between defective RNA metabolism and post-transcriptional gene silencing.
  • The regulatory effects of ct-siRNAs are context-dependent, influenced by siRNA length and genetic background.
  • Further research is needed to address current controversies and unsolved questions regarding ct-siRNAs.