The DOI matches its Crossref record; 78 of the 78 references it cites were found in a registry or an index.
Affinity Capture and Identification of Host Cell Factors Associated with Hepatitis C Virus (+) Strand Subgenomic RNA
Open accessAbstract
Hepatitis C virus (HCV) infection leading to chronic hepatitis is a major factor in the causation of liver cirrhosis, hepatocellular carcinoma, and liver failure. This process may involve the interplay of various host cell factors, as well as the interaction of these factors with viral RNA and proteins. We report a novel strategy using a sequence-specific biotinylated peptide nucleic acid (PNA)-neamine conjugate targeted to HCV RNA for the in situ capture of subgenomic HCV (+) RNA, along with cellular and viral factors associated with it in MH14 host cells. Using this affinity capture system in conjunction with LC/MS/MS, we have identified 83 cellular factors and three viral proteins (NS5B, NS5A, and NS3-4a protease-helicase) associated with the viral genome. The capture was highly specific. These proteins were not scored with cured MH14 cells devoid of HCV replicons because of the absence of the target sequence in cells for the PNA-neamine probe and also because, unlike oligomeric DNA, cellular proteins have no affinity for PNA. The identified cellular factors belong to different functional groups, including signaling, oncogenic, chaperonin, transcriptional regulators, and RNA helicases as well as DEAD box proteins, ribosomal proteins, translational regulators/factors, and metabolic enzymes, that represent a diverse set of cellular factors associated with the HCV RNA genome. Small interfering RNA-mediated silencing of a diverse class of selected proteins in an HCV replicon cell line either enhanced or inhibited HCV replication/translation, suggesting that these cellular factors have regulatory roles in HCV replication.
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“To address this issue, a DNA mimic, termed peptide nucleic acid, was developed to replace the phosphate backbone with amide bonds, providing reduced nonspecific binding (83).”
From The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology (2014) · cites this paper as [83]
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Parsell, D. A., & Lindquist, S. (1993) · Annual Review of Genetics · doi:10.1146/annurev.ge.27.120193.002253 · Cited by 2,275
Internal ribosome entry site within hepatitis C virus RNA
Tsukiyama–Kohara, K., Iizuka, N., Kohara, M., & Nomoto, A. (1992) · Journal of Virology · doi:10.1128/jvi.66.3.1476-1483.1992 · Cited by 925
Pestova, T. V., Shatsky, I. N., Fletcher, S. P., Jackson, R. J., & Hellen, C. U. T. (1998) · Genes & Development · doi:10.1101/gad.12.1.67 · Cited by 729
Genome‐wide molecular profiles of HCV‐induced dysplasia and hepatocellular carcinoma†
Wurmbach, E., Chen, Y., Khitrov, G., Zhang, W., Roayaie, S., Schwartz, M., Fiel, M. I., Thung, S. N., Mazzaferro, V., Bruix, J., et al. (2007) · Hepatology · doi:10.1002/hep.21622 · Cited by 721
Cellular cofactors affecting hepatitis C virus infection and replication
Randall, G. C., Panis, M., Cooper, J. D., Tellinghuisen, T. L., Sukhodolets, K. E., Pfeffer, S., Landthaler, M., Landgraf, P., Kan, S., Lindenbach, B. D., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704894104 · Cited by 527
Overview of Hepatitis C Virus Genome Structure, Polyprotein Processing, and Protein Properties
Reed, K. E., & Rice, C. M. (2000) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-59605-6_4 · Cited by 507
Wang, C., Sarnow, P., & Siddiqui, A. (1993) · Journal of Virology · doi:10.1128/jvi.67.6.3338-3344.1993 · Cited by 440
Diamond, D. L., Syder, A. J., Jacobs, J., Sorensen, C. M., Walters, K., Proll, S. C., McDermott, J., Gritsenko, M. A., Zhang, Q., Zhao, R., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000719 · Cited by 429
Tommaso, L. D., Franchi, G., Park, Y. N., Fiamengo, B., Destro, A., Morenghi, E., Montorsi, M., Torzilli, G., Tommasini, M., Terracciano, L., et al. (2007) · Hepatology · doi:10.1002/hep.21531 · Cited by 425
A genome-wide genetic screen for host factors required for hepatitis C virus propagation
Li, Q.-S., Brass, A., Ng, A., Hu, Z.-Y., Xavier, R., Liang, T., & Elledge, S. (2009) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0907439106 · Cited by 391
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The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis
Mazeaud, C., Freppel, W., & Chatel‐Chaix, L. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00595 · Cited by 120
Protein–DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era
Cozzolino, F., Iacobucci, I., Monaco, V., & Monti, M. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00074 · Cited by 118
The Impact of Mass Spectrometry–Based Proteomics on Fundamental Discoveries in Virology
Greco, T. M., Diner, B. A., & Cristea, I. M. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085527 · Cited by 67
Identification of HNRNPK as Regulator of Hepatitis C Virus Particle Production
Poenisch, M., Metz, P., Blankenburg, H., Ruggieri, A., Lee, J., Rupp, D., Rebhan, I., Diederich, K., Kaderali, L., Domingues, F. S., et al. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004573 · Cited by 65
Chatel‐Chaix, L., Germain, M.-A., Motorina, A., Bonneil, É., Thibault, P., Baril, M., & Lamarre, D. (2013) · Journal of Virology · doi:10.1128/jvi.01474-13 · Cited by 61
Metadata
- Authors
- Upadhyay, A., Dixit, U., Manvar, D., Chaturvedi, N., & Pandey, V. N.
- Affiliations
- Rutgers New Jersey Medical School (US)
- Corresponding author
- Pandey, Virendra N.
- Venue
- Molecular & Cellular Proteomics
- Publisher
- Elsevier BV
- Published
- 2013-06
- Volume
- 12
- Issue
- 6
- Pages
- 1539-1552
- ISSN
- 1535-9476 (ISSN-L)
- PMC
- PMC3675812
- OpenAlex
- W2126789024
- Cited by
- 36
- References
- 78
- Citations by year
- 2026: 1 · 2023: 1 · 2022: 2 · 2021: 3 · 2020: 2 · 2019: 3 · 2018: 3 · 2017: 4 · 2016: 8 · 2015: 4 · 2014: 4 · 2013: 1
- FWCI
- 3.53
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular & Cellular Proteomics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of Allergy and Infectious Diseases (AI073703, R21AI073703)
- National Institute of Diabetes and Digestive and Kidney Diseases (R21DK083560, DK083560)
- Topics
- Health Sciences › Medicine › Hepatology › Hepatitis C virus research
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Virus Research Studies
- Keywords
- hepatitis C virus, subgenomic RNA, host cell factors, affinity capture, HCV replicon, NS5B, NS5A, viral replication, siRNA knockdown, RNA-protein interactions
- MeSH terms
- Viral Proteases, Chromatography, Affinity, Chromatography, Liquid, Framycetin, Humans, Replicon, RNA-Dependent RNA Polymerase, RNA, Viral, Serine Endopeptidases, Virus Replication, Gene Expression Regulation, Viral, Hepacivirus, Genome, Viral, Viral Nonstructural Proteins, Biotinylation, Protein Isoforms, Peptide Nucleic Acids, Hepatocytes, Nucleoside-Triphosphatase, Cell Line, Tumor, DEAD-box RNA Helicases, Tandem Mass Spectrometry, Host-Pathogen Interactions
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