Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing

Yiyang Zhou, Andrew Routh

Research output: Contribution to journalArticle

Abstract

To characterize RNA-capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: viral Photo-Activatable Ribonucleoside CrossLinking (vPAR-CL). In vPAR-CL, 4-thiouridine is incorporated into the encapsidated genomes of virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that vPAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant vPAR-CL signals across virus RNA genome, indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites coincide with previously identified functional RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining vPAR-CL and DMS-MaPseq reveals that the predominant RNA-capsid interaction sites favored double-stranded RNA regions. We disrupted secondary structures associated with vPAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA-capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.

Original languageEnglish (US)
Pages (from-to)e12
JournalNucleic acids research
Volume48
Issue number2
DOIs
StatePublished - Jan 24 2020

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Ribonucleosides
Capsid
Virion
RNA
Virus Replication
Genome
Virus Assembly
RNA Viruses
Thiouridine
Binding Sites
Cytidine
Nucleotide Motifs
Tropism
Double-Stranded RNA
Uridine
Viral RNA
Capsid Proteins
Viruses
Mutation

ASJC Scopus subject areas

  • Genetics

Cite this

Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. / Zhou, Yiyang; Routh, Andrew.

In: Nucleic acids research, Vol. 48, No. 2, 24.01.2020, p. e12.

Research output: Contribution to journalArticle

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