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

Zhou, Yiyang; Routh, Andrew

doi:10.1093/nar/gkz1124

Cited by 23 publications

(38 citation statements)

References 74 publications

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“…Because a major activity of N SARS-CoV-2 is to encapsulate RNA, the immobile fraction observed by FRAP might represent the early stages of nucleocapsid assembly. Successful nucleocapsid formation, however, also depends on the specific sequence and secondary structure of viral RNA 18 and is therefore not expected for polyU. SARS-CoV-2 nucleocapsid protein associates with stress granules.…”

Section: Resultsmentioning

confidence: 99%

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

et al. 2020

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The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription, and is essential for viral replication. Here, we show that RNA induces cooperative liquid–liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid–liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.

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Section: Resultsmentioning

confidence: 99%

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

et al. 2020

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“…Because a major activity of N SARS-CoV-2 is to encapsulate RNA, the immobile fraction observed by FRAP might represent early stages of nucleocapsid assembly. Successful nucleocapsid formation, however, also depends on the specific sequence and secondary structure of viral RNA (Zhou and Routh, 2020) and is therefore not expected for polyU. associated with stress granules in HeLa cells.…”

Section: Time-dependent Transformation Of N Sars-cov-2 /Rna-dropletsmentioning

confidence: 99%

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Savastano

Opakua

Ranković

et al. 2020

Preprint

136

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The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription and is essential for viral replication. Here we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.

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“…Most recent studies have focused on RNA secondary structure prediction [2][3][4], and comparisons of RNA secondary structures have not yet been sufficiently studied. At the present stage, the comparison methods for RNA secondary structures are mainly divided into two types: alignment-based methods and alignment-free methods.…”

Section: Introductionmentioning

confidence: 99%

Graph-Based Analysis of RNA Secondary Structure Similarity Comparison

Yang

Liu

et al. 2021

Complexity

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In organisms, ribonucleic acid (RNA) plays an essential role. Its function is being discovered more and more. Due to the conserved nature of RNA sequences, its function mainly depends on the RNA secondary structure. The discovery of an approximate relationship between two RNA secondary structures helps to understand their functional relationship better. It is an important and urgent task to explore structural similarities from the graphical representation of RNA secondary structures. In this paper, a novel graphical analysis method based on the triple vector curve representation of RNA secondary structures is proposed. A combinational method involving a discrete wavelet transform (DWT) and fractal dimension with sliding window is introduced to analyze and compare the graphs derived from feature extraction; after that, the distance matrix is generated. Then, the distance matrix is analyzed by clustering and visualized as a clustering tree. RNA virus and noncoding RNA datasets are applied to perform experiments and analyze the clustering tree. The results show that the proposed method yields more accurate results in the comparison of RNA secondary structures.

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

Cited by 23 publications

References 74 publications

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Graph-Based Analysis of RNA Secondary Structure Similarity Comparison

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