Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes

Byungil Kim, Sarah Arcos, Katherine Rothamel, Manuel Ascano

Published: 2020-12-01 DOI: 10.1038/s41596-020-00429-6

Viral crosslinking

Solid-phase purification

Ribonucleoprotein complexes

RNA virus genomes

Proteomics

AI 解读

Supplementary information

Supplementary Information

Supplementary Fig. 1.

Reporting Summary

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Phillips, S. L., Soderblom, E. J., Bradrick, S. S. & Garcia-Blanco, M. A. Identification of proteins bound to dengue viral RNA in vivo reveals new host proteins important for virus replication. MBio 7, e01865–15 (2016).
Lenarcic, E. M., Landry, D. M., Greco, T. M., Cristea, I. M. & Thompson, S. R. Thiouracil cross-linking mass spectrometry: a cell-based method to identify host factors involved in viral amplification. J. Virol. 87, 8697–8712 (2013).
Garcia-Moreno, M. et al. System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection. Mol. Cell 74, 196–211.e11 (2019).
Zhou, Y. & Routh, A. Mapping RNA-capsid interactions and RNA secondary structure within virus particles using next-generation sequencing. Nucleic Acids Res. 48, e12–e12 (2020).
Kim, B. et al. Discovery of widespread host protein interactions with the pre-replicated genome of CHIKV using VIR-CLASP. Mol. Cell 78, 624–640.e7 (2020).
Barrows, N. J. et al. Dual roles for the ER membrane protein complex in flavivirus infection: viral entry and protein biogenesis. Sci. Rep. 9, 9711 (2019).
Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010).
Favre, A. et al. 4-Thiouridine photosensitized RNA-protein crosslinking in mammalian cells. Biochem. Biophys. Res. Commun. 141, 847–854 (1986).
DeAngelis, M. M., Wang, D. G. & Hawkins, T. L. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 23, 4742–4743 (1995).
Licatalosi, D. D. et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456, 464–469 (2008).
Van Nostrand, E. L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016).
König, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915 (2010).
Ascano, M., Hafner, M., Cekan, P., Gerstberger, S. & Tuschl, T. Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip. Rev. RNA 3, 159–177 (2012).
Trendel, J. et al. The human RNA-binding proteome and its dynamics during translational arrest. Cell 176, 391–403.e19 (2019).
Asencio, C., Chatterjee, A. & Hentze, M. W. Silica-based solid-phase extraction of cross-linked nucleic acid-bound proteins. Life Sci. Alliance 1, e201800088 (2018).
Shchepachev, V. et al. Defining the RNA interactome by total RNA-associated protein purification. Mol. Syst. Biol. 15, e8689 (2019).
Berensmeier, S. Magnetic particles for the separation and purification of nucleic acids. Appl. Microbiol. Biotechnol. 73, 495–504 (2006).
Miller, C. et al. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol. Syst. Biol. 7, 458 (2011).
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280.e8 (2020).
Jiang, P., Liu, Y., Ma, H.-C., Paul, A. V. & Wimmer, E. Picornavirus morphogenesis. Microbiol. Mol. Biol. Rev. 78, 418–437 (2014).
Quail, M. A., Swerdlow, H. & Turner, D. J. Improved protocols for the illumina genome analyzer sequencing system. Curr. Protoc. Hum. Genet. Chapter 18, Unit 18, 2 (2009).
Telesnitsky, A. & Wolin, S. L. The host RNAs in retroviral particles. Viruses 8, 235 (2016).
Noda, T. et al. Importance of the 1+7 configuration of ribonucleoprotein complexes for influenza A virus genome packaging. Nat. Commun. 9, 54 (2018).
Kaur, P., Lee, R. C. H. & Chu, J. J. H. Infectious viral quantification of chikungunya virus-virus plaque assay. Methods Mol. Biol. 1426, 93–103 (2016).
Pedersen, I. R. Density gradient centrifugation studies on lymphocytic choriomeningitis virus and on viral ribonucleic acid. J. Virol. 6, 414–420 (1970).
Lim, C.-K. Virus isolation and preparation of sucrose-banded chikungunya virus samples for transmission electron microscopy. Methods Mol. Biol. 1426, 153–162 (2016).
Mortz, E., Krogh, T. N., Vorum, H. & Görg, A. Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis. Proteomics 1, 1359–1363 (2001).
Link, A. J. & Labaer, J. In-gel trypsin digest of gel-fractionated proteins. Cold Spring Harb. Protoc. 2009, pdb.prot5110–pdb.prot5110 (2009).
Smyth, G. K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article3 (2004).
Sysoev, V. O. et al. Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila. Nat. Commun. 7, 12128–11 (2016).
Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938–2940 (2017).
Dickson, A. M. et al. Dephosphorylation of HuR protein during alphavirus infection is associated with HuR relocalization to the cytoplasm. J. Biol. Chem. 287, 36229–36238 (2012).
Daffis, S. et al. 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature 468, 452–456 (2010).
Lex, A., Gehlenborg, N., Strobelt, H., Vuillemot, R. & Pfister, H. UpSet: visualization of intersecting sets. IEEE Trans. Vis. Comput. Graph 20, 1983–1992 (2014).

Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes

Supplementary information

Supplementary Information

Reporting Summary

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