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Cited by 28RNA and protein synthesis mechanismsRNA Research and SplicingProtein Structure and Dynamics

Discovering RNA-Protein Interactome by Using Chemical Context Profiling of the RNA-Protein Interface

Open access
Parisien, Marc, Wang, Xiaoyun, Perdrizet, George, Lamphear, Corissa, Fierke, Carol A., Maheshwari, Ketan C., Wilde, Michael J., Sosnick, Tobin R. +1 more·2013·Cell Reports
DOI 10.1016/j.celrep.2013.04.010PMC PMC3769137
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Abstract

RNA-protein (RNP) interactions generally are required for RNA function. At least 5% of human genes code for RNA-binding proteins. Whereas many approaches can identify the RNA partners for a specific protein, finding the protein partners for a specific RNA is difficult. We present a machine-learning method that scores a protein's binding potential for an RNA structure by utilizing the chemical context profiles of the interface from known RNP structures. Our approach is applicable even when only a single RNP structure is available. We examined 801 mammalian proteins and find that 37 (4.6%) potentially bind transfer RNA (tRNA). Most are enzymes involved in cellular processes unrelated to translation and were not known to interact with RNA. We experimentally tested six positive and three negative predictions for tRNA binding in vivo, and all nine predictions were correct. Our computational approach provides a powerful complement to experiments in discovering new RNPs.

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  • A human tRNA microarray has been developed for tRNA quantification and has been applied in tRNA profiling in HIV-1, specific human tissues and tumor cells, and in identifying the complete interactome of tRNA-binding proteins.

    “A human tRNA microarray has been developed for tRNA quantification and has been applied in tRNA profiling in HIV-1 (51), as well as of specific human tissues and tumor cells, and in identifying the complete interactome of tRNA-binding proteins (136 -138).”

    From Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication (2019) · cites this paper as [138]

    The Experimental Procedures (UV CLIP-Chip; page not provided) say previously developed tRNA microarrays determine tRNA abundance, and this study used them to identify tRNAs bound to selected proteins. But the Results (Cognate versus Generic tRNA; page not provided) explicitly say the method will not identify all tRNA-binding proteins, so it does not support a complete interactome. This paper also does not establish the stated profiling of human tissues and tumor cells. (LLM, conf=0.91)

    Experimental — accuracy not yet measured

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Authors
Parisien, M., Wang, X., Perdrizet, G., Lamphear, C., Fierke, C. A., Maheshwari, K. C., Wilde, M. J., Sosnick, T. R., & Pan, T.
Affiliations
  • University of Chicago (US)
  • University of Michigan (US)
Corresponding author
  • Sosnick, Tobin R.
  • Pan, Tao
ORCID
Venue
Cell Reports
Publisher
Elsevier BV
Published
2013-05
Volume
3
Issue
5
Pages
1703-1713
ISSN
2211-1247 (ISSN-L)
DOI
10.1016/j.celrep.2013.04.010
PMC
PMC3769137
OpenAlex
W2165955313
Cited by
28
References
4
Citations by year
2026: 1 · 2025: 3 · 2024: 2 · 2023: 1 · 2021: 1 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 2 · 2016: 5 · 2015: 3 · 2014: 4 · 2013: 1
FWCI
1.94
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Reports (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • University of Chicago
  • National Institutes of Health
  • Natural Sciences and Engineering Research Council of Canada
  • National Institute of General Medical Sciences (R56GM057880, R01GM057880, GM57880)
  • National Center for Research Resources (S10RR029030)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
RNA-protein interactions, RNA-binding proteins, tRNA binding, protein binding prediction, machine learning, mammalian proteins
MeSH terms
Humans, Nucleic Acid Conformation, Protein Binding, RNA, Transfer, RNA-Binding Proteins, Computational Biology, Databases, Protein, HEK293 Cells, Nucleotide Motifs, Molecular Docking Simulation

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