Journal Article

CAPRI enables comparison of evolutionarily conserved RNA interacting regions

Manke, Thomas, Ramírez, Fidel, Shvedunova, Maria, Akhtar, Asifa, Panhale, Amol, Richter, Florian M., Mittler, Gerhard

2019

Overview

RNA-protein complexes play essential regulatory roles at nearly all levels of gene expression. Using in vivo crosslinking and RNA capture, we report a comprehensive RNA-protein interactome in a metazoan at four levels of resolution: single amino acids, domains, proteins and multisubunit complexes. We devise CAPRI, a method to map RNA-binding domains (RBDs) by simultaneous identification of RNA interacting crosslinked peptides and peptides adjacent to such crosslinked sites. CAPRI identifies more than 3000 RNA proximal peptides in Drosophila and human proteins with more than 45% of them forming new interaction interfaces. The comparison of orthologous proteins enables the identification of evolutionary conserved RBDs in globular domains and intrinsically disordered regions (IDRs). By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence. Comprehensive characterisation of RNA-protein interactions requires different levels of resolution. Here, the authors present an integrated mass spectrometry-based approach that allows them to define the Drosophila RNA-protein interactome from the level of multisubunit complexes down to the RNA-binding amino acid.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 101/47 / 631/337/475 / 631/45/500 / 631/45/612/1230 / 82/1 / 82/58 / Amino acid composition / Amino acid sequence / Amino Acid Sequence - genetics / Amino acids / Animals / Cell Line / Conserved sequence / Conserved Sequence - genetics / Cross-Linking Reagents - chemistry / Crosslinking / Divergence / Drosophila / Evolution, Molecular / Evolutionary conservation / Fruit flies / Gene expression / Humanities and Social Sciences / Humans / Interfaces / multidisciplinary / Nucleotide sequence / Peptides / Peptides - chemistry / Peptides - genetics / Protein Binding - genetics / Proteins / Proteome - genetics / Proteomics - methods / Ribonucleic acid / RNA / RNA - chemistry / RNA - metabolism / RNA-Binding Motifs - genetics / RNA-Binding Proteins - chemistry / RNA-Binding Proteins - genetics / Science / Science (multidisciplinary)