Target cleavage and gene silencing by Argonautes with cityRNAs

Huaqun Zhang; GeunYoung Sim; Audrey C. Kehling; Vishal Annasaheb Adhav; Andrew Savidge; Benjamin Pastore; Wen Tang; Kotaro Nakanishi

Cell Reports (Oct 2024)

Target cleavage and gene silencing by Argonautes with cityRNAs

Huaqun Zhang,
GeunYoung Sim,
Audrey C. Kehling,
Vishal Annasaheb Adhav,
Andrew Savidge,
Benjamin Pastore,
Wen Tang,
Kotaro Nakanishi

Affiliations

Huaqun Zhang: Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
GeunYoung Sim: Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
Audrey C. Kehling: Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
Vishal Annasaheb Adhav: Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
Andrew Savidge: Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
Benjamin Pastore: Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
Wen Tang: Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
Kotaro Nakanishi: Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Corresponding author

Journal volume & issue: Vol. 43, no. 10
p. 114806

Abstract

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Summary: TinyRNAs (tyRNAs) are ≤17-nt guide RNAs associated with Argonaute proteins (AGOs), and certain 14-nt cleavage-inducing tyRNAs (cityRNAs) catalytically activate human Argonaute3 (AGO3). We present the crystal structure of AGO3 in complex with a cityRNA, 14-nt miR-20a, and its complementary target, revealing a different trajectory for the guide-target duplex from that of its ∼22-nt microRNA-associated AGO counterpart. cityRNA-loaded Argonaute2 (AGO2) and AGO3 enhance their endonuclease activity when the immediate 5′ upstream region of the tyRNA target site (UTy) includes sequences with low affinity for AGO. We propose a model where cityRNA-loaded AGO2 and AGO3 efficiently cleave fully complementary tyRNA target sites unless they directly recognize the UTy. To investigate their gene silencing, we devised systems for loading endogenous AGOs with specific tyRNAs and demonstrated that, unlike microRNAs, cityRNA-mediated silencing heavily relies on target cleavage. Our study uncovered that AGO exploits cityRNAs for target recognition differently from microRNAs and alters gene silencing.

CP: Molecular biology

Published in Cell Reports

ISSN: 2211-1247 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Biology (General)
Website: http://www.cell.com/cell-reports/home

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