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Related Experiment Video

Updated: May 9, 2026

Substrate Generation for Endonucleases of CRISPR/Cas Systems

Substrate Generation for Endonucleases of CRISPR/Cas Systems

Published on: September 8, 2012

Cascading cis-cleavage on transcript from trans-acting siRNA-producing locus 3.

Changqing Zhang¹, Guangping Li, Jin Wang

¹College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China. zhang_chq2002@sohu.com

International Journal of Molecular Sciences

|July 17, 2013

Summary

Researchers discovered new ways small RNAs (sRNAs) are made from non-phased positions in grape TAS3 transcripts. This finding reveals a cascade of cis-cleavages, expanding knowledge beyond microRNA-directed production.

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Area of Science:

Molecular Biology
Genetics
Plant Science

Background:

Small RNA (sRNA) production is typically understood through microRNA-guided cleavage of trans-acting-siRNA-producing (TAS) transcripts, establishing phased sRNA patterns.
The mechanisms generating sRNAs from non-phased positions, independent of microRNA-directed cleavage, remain largely uncharacterized.

Purpose of the Study:

To investigate the production of sRNAs from non-phased positions in Vitis vinifera (grape) TAS3 transcripts.
To elucidate the mechanisms generating distinct sRNA patterns from non-phased cleavage events.

Main Methods:

Integrated high-throughput sRNA deep sequencing data with evolutionary conservation analysis.
Utilized genome-wide RNA degradome analysis to identify cis-cleavage events in TAS3 transcripts.
Analyzed sRNA phasing patterns generated by identified cleavage events.

Main Results:

Identified three novel cis-cleavage events within Vitis vinifera TAS3 transcripts.
These cis-cleavages form an orderly cascade, producing distinct phasing patterns of sRNAs in 21-nucleotide increments.
Observed conservation of some cascading cis-cleavage events in Arabidopsis thaliana, suggesting functional significance.

Conclusions:

Established that cis-cleavage events in TAS3 transcripts can generate orderly sRNA cascades and distinct phasing patterns.
Demonstrated a novel pathway for sRNA production from non-phased positions, distinct from microRNA-directed cleavage.
Enhanced understanding of the diverse mechanisms governing sRNA biogenesis in plants.