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Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.

Publication ,  Journal Article
Bailey, MA; Martyr, JG; Hargrove, AE; Fitzgerald, MC
Published in: Analytical chemistry
February 2024

RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.

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Published In

Analytical chemistry

DOI

EISSN

1520-6882

ISSN

0003-2700

Publication Date

February 2024

Related Subject Headings

  • Analytical Chemistry
  • 4004 Chemical engineering
  • 3401 Analytical chemistry
  • 3205 Medical biochemistry and metabolomics
  • 0399 Other Chemical Sciences
  • 0301 Analytical Chemistry
 

Citation

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Bailey, M. A., Martyr, J. G., Hargrove, A. E., & Fitzgerald, M. C. (2024). Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Analytical Chemistry. https://doi.org/10.1021/acs.analchem.3c04978
Bailey, Morgan A., Justin G. Martyr, Amanda E. Hargrove, and Michael C. Fitzgerald. “Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.Analytical Chemistry, February 2024. https://doi.org/10.1021/acs.analchem.3c04978.
Bailey MA, Martyr JG, Hargrove AE, Fitzgerald MC. Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Analytical chemistry. 2024 Feb;
Bailey, Morgan A., et al. “Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.Analytical Chemistry, Feb. 2024. Epmc, doi:10.1021/acs.analchem.3c04978.
Bailey MA, Martyr JG, Hargrove AE, Fitzgerald MC. Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Analytical chemistry. 2024 Feb;
Journal cover image

Published In

Analytical chemistry

DOI

EISSN

1520-6882

ISSN

0003-2700

Publication Date

February 2024

Related Subject Headings

  • Analytical Chemistry
  • 4004 Chemical engineering
  • 3401 Analytical chemistry
  • 3205 Medical biochemistry and metabolomics
  • 0399 Other Chemical Sciences
  • 0301 Analytical Chemistry