Analysis of RNA-Protein Interaction Networks Using RNP-MaP

Kaushik Saha; Gourisankar Ghosh

doi:10.1007/978-1-0716-3191-1_7

Analysis of RNA-Protein Interaction Networks Using RNP-MaP

Methods Mol Biol. 2023:2666:95-105. doi: 10.1007/978-1-0716-3191-1_7.

Authors

Kaushik Saha¹, Gourisankar Ghosh²

Affiliations

¹ Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
² Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA. gghosh@ucsd.edu.

PMID: 37166659
DOI: 10.1007/978-1-0716-3191-1_7

Abstract

RNA-protein interactions regulate a myriad of biological functions through formation of ribonucleoprotein complexes. These complexes may consist of one or more RNA-protein interaction network(s) providing additional layers of regulatory potential to the RNA. Moreover, since the protein-binding also regulates local and global structure of the RNA by structurally remodeling the latter, it is important to correlate RNA nucleotide flexibility with the site of protein-binding. We have discussed methods for chemical probing of structure of the RNA in the protein-free and protein-bound states in the preceding chapters. In this chapter, we describe a ribonucleoprotein mutational profiling (RNP-MaP) method for probing RNA-protein interaction networks.

Keywords: Mutational profiling; NHS-diazirine; Next-generation sequencing; RNA-protein interactions; RNP-MaP; UV cross-linking.

MeSH terms

Protein Binding
Protein Interaction Maps
RNA* / chemistry
Ribonucleoproteins* / metabolism

Substances

Ribonucleoproteins
RNA