Varicella-zoster virus expresses multiple small noncoding RNAs

Amos Markus; Linoy Golani; Nishant Kumar Ojha; Tatiana Borodiansky-Shteinberg; Paul R. Kinchington; Ronald S. Goldstein

doi:10.1128/JVI.01710-17

Varicella-zoster virus expresses multiple small noncoding RNAs

Amos Markus, Linoy Golani, Nishant Kumar Ojha, Tatiana Borodiansky-Shteinberg, Paul R. Kinchington, Ronald S. Goldstein

The Mina and Everard Goodman Faculty of Life Sciences

University of Pittsburgh

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Many herpesviruses express small noncoding RNAs (sncRNAs), including microRNAs (miRNAs), that may play roles in regulating lytic and latent infections. None have yet been reported in varicella-zoster virus (VZV; also known as human herpesvirus 3 [HHV-3]). Here we analyzed next-generation sequencing (NGS) data for small RNAs in VZV-infected fibroblasts and human embryonic stem cell-derived (hESC) neurons. Two independent bioinformatics analyses identified more than 20 VZV-encoded 20- to 24-nucleotide RNAs, some of which are predicted to have stemloop precursors potentially representing miRNAs. These sequences are perfectly conserved between viruses from three clades of VZV. One NGS-identified sequence common to both bioinformatics analyses mapped to the repeat regions of the VZV genome, upstream of the predicted promoter of the immediate early gene open reading frame 63 (ORF63). This miRNA candidate was detected in each of 3 independent biological repetitions of NGS of RNA from fibroblasts and neurons productively infected with VZV using TaqMan quantitative PCR (qPCR). Importantly, transfected synthetic RNA oligonucleotides antagonistic to the miRNA candidate significantly enhanced VZV plaque growth rates. The presence of 6 additional small noncoding RNAs was also verified by TaqMan qPCR in productively infected fibroblasts and ARPE19 cells. Our results show VZV, like other human herpesviruses, encodes several sncRNAs and miRNAs, and some may regulate infection of host cells.

Original language	English
Article number	e01710-17
Journal	Journal of Virology
Volume	91
Issue number	24
DOIs	https://doi.org/10.1128/JVI.01710-17
State	Published - 15 Dec 2017

Bibliographical note

Publisher Copyright:
© 2017 American Society for Microbiology.

Funding

This research was supported by NIH grants R01 AI122640 (P.R.K. and R.G.), R21 NS082662 (P.R.K. and R.G.), US-Israel Bi-National Science Foundation 2013072 (R.G. and P.R.K.). R.G. was also supported by Israel Science Foundation grant 254/16. P.R.K. also acknowledges an NEI CORE grant for Vison Research (EY08098) and unrestricted funds from Research to Prevent Blindness, Inc., and the Eye & Ear Foundation of Pittsburgh. We are very grateful to Noam Shomron (Tel Aviv University) for many helpful discussions that allowed us to pursue this project successfully, as well as reading of an earlier version of the manuscript. We also thank Dena Leshkowitz, Shlomit Gilad, and Sima Benjamin of The Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, for expert help and advice. Aryeh Weiss (Bar-Ilan University Faculty of Engineering) provided invaluable advice in the stitching of multiple micrographs. This research was supported by NIH grants R01 AI122640 (P.R.K. and R.G.), R21 NS082662 (P.R.K. and R.G.), US-Israel Bi-National Science Foundation 2013072 (R.G. and P.R.K.). R.G. was also supported by Israel Science Foundation grant 254/16. P.R.K. also acknowledges an NEI CORE grant for Vison Research (EY08098) and unrestricted funds from Research to Prevent Blindness, Inc., and the Eye & Ear Foundation of Pittsburgh

Funders	Funder number
US-Israel bi-national Science Foundation	2013072
National Institutes of Health	R21 NS082662, R01 AI122640
National Eye Institute	P30EY008098
Eye and Ear Foundation of Pittsburgh
Research to Prevent Blindness
Israel Science Foundation	254/16
Tel Aviv University

Keywords

MicroRNA
Noncoding RNA
Varicella-zoster virus

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10.1128/JVI.01710-17

Cite this

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title = "Varicella-zoster virus expresses multiple small noncoding RNAs",

abstract = "Many herpesviruses express small noncoding RNAs (sncRNAs), including microRNAs (miRNAs), that may play roles in regulating lytic and latent infections. None have yet been reported in varicella-zoster virus (VZV; also known as human herpesvirus 3 [HHV-3]). Here we analyzed next-generation sequencing (NGS) data for small RNAs in VZV-infected fibroblasts and human embryonic stem cell-derived (hESC) neurons. Two independent bioinformatics analyses identified more than 20 VZV-encoded 20- to 24-nucleotide RNAs, some of which are predicted to have stemloop precursors potentially representing miRNAs. These sequences are perfectly conserved between viruses from three clades of VZV. One NGS-identified sequence common to both bioinformatics analyses mapped to the repeat regions of the VZV genome, upstream of the predicted promoter of the immediate early gene open reading frame 63 (ORF63). This miRNA candidate was detected in each of 3 independent biological repetitions of NGS of RNA from fibroblasts and neurons productively infected with VZV using TaqMan quantitative PCR (qPCR). Importantly, transfected synthetic RNA oligonucleotides antagonistic to the miRNA candidate significantly enhanced VZV plaque growth rates. The presence of 6 additional small noncoding RNAs was also verified by TaqMan qPCR in productively infected fibroblasts and ARPE19 cells. Our results show VZV, like other human herpesviruses, encodes several sncRNAs and miRNAs, and some may regulate infection of host cells.",

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AU - Kinchington, Paul R.

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Varicella-zoster virus expresses multiple small noncoding RNAs

Abstract

Bibliographical note

Funding

Keywords

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