A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration

Troels K H Scheel; Joseph M Luna; Matthias Liniger; Eiko Nishiuchi; Kathryn Rozen-Gagnon; Amir Shlomai; Gaël Auray; Markus Gerber; John Fak; Irene Keller; Rémy Bruggmann; Robert B Darnell; Nicolas Ruggli; Charles M Rice

doi:10.1016/j.chom.2016.02.007

A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration

Troels K H Scheel, Joseph M Luna, Matthias Liniger, Eiko Nishiuchi, Kathryn Rozen-Gagnon, Amir Shlomai, Gaël Auray, Markus Gerber, John Fak, Irene Keller, Rémy Bruggmann, Robert B Darnell, Nicolas Ruggli, Charles M Rice

65 Citations (Scopus)

Abstract

Small non-coding RNAs have emerged as key modulators of viral infection. However, with the exception of hepatitis C virus, which requires the liver-specific microRNA (miRNA)-122, the interactions of RNA viruses with host miRNAs remain poorly characterized. Here, we used crosslinking immunoprecipitation (CLIP) of the Argonaute (AGO) proteins to characterize strengths and specificities of miRNA interactions in the context of 15 different RNA virus infections, including several clinically relevant pathogens. Notably, replication of pestiviruses, a major threat to milk and meat industries, critically depended on the interaction of cellular miR-17 and let-7 with the viral 3' UTR. Unlike canonical miRNA interactions, miR-17 and let-7 binding enhanced pestivirus translation and RNA stability. miR-17 sequestration by pestiviruses conferred reduced AGO binding and functional de-repression of cellular miR-17 targets, thereby altering the host transcriptome. These findings generalize the concept of RNA virus dependence on cellular miRNAs and connect virus-induced miRNA sequestration to host transcriptome regulation.

Original language	English
Journal	Cell Host & Microbe
Volume	19
Issue number	3
Pages (from-to)	409-23
Number of pages	15
ISSN	1931-3128
DOIs	https://doi.org/10.1016/j.chom.2016.02.007
Publication status	Published - 9 Mar 2016

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title = "A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration",

abstract = "Small non-coding RNAs have emerged as key modulators of viral infection. However, with the exception of hepatitis C virus, which requires the liver-specific microRNA (miRNA)-122, the interactions of RNA viruses with host miRNAs remain poorly characterized. Here, we used crosslinking immunoprecipitation (CLIP) of the Argonaute (AGO) proteins to characterize strengths and specificities of miRNA interactions in the context of 15 different RNA virus infections, including several clinically relevant pathogens. Notably, replication of pestiviruses, a major threat to milk and meat industries, critically depended on the interaction of cellular miR-17 and let-7 with the viral 3' UTR. Unlike canonical miRNA interactions, miR-17 and let-7 binding enhanced pestivirus translation and RNA stability. miR-17 sequestration by pestiviruses conferred reduced AGO binding and functional de-repression of cellular miR-17 targets, thereby altering the host transcriptome. These findings generalize the concept of RNA virus dependence on cellular miRNAs and connect virus-induced miRNA sequestration to host transcriptome regulation.",

author = "Scheel, {Troels K H} and Luna, {Joseph M} and Matthias Liniger and Eiko Nishiuchi and Kathryn Rozen-Gagnon and Amir Shlomai and Ga{\"e}l Auray and Markus Gerber and John Fak and Irene Keller and R{\'e}my Bruggmann and Darnell, {Robert B} and Nicolas Ruggli and Rice, {Charles M}",

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T1 - A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration

AU - Scheel, Troels K H

AU - Luna, Joseph M

AU - Liniger, Matthias

AU - Nishiuchi, Eiko

AU - Rozen-Gagnon, Kathryn

AU - Shlomai, Amir

AU - Auray, Gaël

AU - Gerber, Markus

AU - Fak, John

AU - Keller, Irene

AU - Bruggmann, Rémy

AU - Darnell, Robert B

AU - Ruggli, Nicolas

AU - Rice, Charles M

PY - 2016/3/9

Y1 - 2016/3/9

N2 - Small non-coding RNAs have emerged as key modulators of viral infection. However, with the exception of hepatitis C virus, which requires the liver-specific microRNA (miRNA)-122, the interactions of RNA viruses with host miRNAs remain poorly characterized. Here, we used crosslinking immunoprecipitation (CLIP) of the Argonaute (AGO) proteins to characterize strengths and specificities of miRNA interactions in the context of 15 different RNA virus infections, including several clinically relevant pathogens. Notably, replication of pestiviruses, a major threat to milk and meat industries, critically depended on the interaction of cellular miR-17 and let-7 with the viral 3' UTR. Unlike canonical miRNA interactions, miR-17 and let-7 binding enhanced pestivirus translation and RNA stability. miR-17 sequestration by pestiviruses conferred reduced AGO binding and functional de-repression of cellular miR-17 targets, thereby altering the host transcriptome. These findings generalize the concept of RNA virus dependence on cellular miRNAs and connect virus-induced miRNA sequestration to host transcriptome regulation.

AB - Small non-coding RNAs have emerged as key modulators of viral infection. However, with the exception of hepatitis C virus, which requires the liver-specific microRNA (miRNA)-122, the interactions of RNA viruses with host miRNAs remain poorly characterized. Here, we used crosslinking immunoprecipitation (CLIP) of the Argonaute (AGO) proteins to characterize strengths and specificities of miRNA interactions in the context of 15 different RNA virus infections, including several clinically relevant pathogens. Notably, replication of pestiviruses, a major threat to milk and meat industries, critically depended on the interaction of cellular miR-17 and let-7 with the viral 3' UTR. Unlike canonical miRNA interactions, miR-17 and let-7 binding enhanced pestivirus translation and RNA stability. miR-17 sequestration by pestiviruses conferred reduced AGO binding and functional de-repression of cellular miR-17 targets, thereby altering the host transcriptome. These findings generalize the concept of RNA virus dependence on cellular miRNAs and connect virus-induced miRNA sequestration to host transcriptome regulation.

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DO - 10.1016/j.chom.2016.02.007

M3 - Journal article

C2 - 26962949

SN - 1931-3128

VL - 19

SP - 409

EP - 423

JO - Cell Host & Microbe

JF - Cell Host & Microbe

IS - 3

ER -

A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration

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