Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture

• Published in: Nature communications Vol. 9; no. 1; pp. 4408 - 13
• Main Authors: Perez-Perri, Joel I., Rogell, Birgit, Schwarzl, Thomas, Stein, Frank, Zhou, Yang, Rettel, Mandy, Brosig, Annika, Hentze, Matthias W.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 23.10.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/475; 631/45/500; 82/58; Adenosine - analogs & derivatives; Adenosine - metabolism; Amino Acids, Dicarboxylic - pharmacology; Binding; Contamination; Deoxyribonucleic acid; DNA; Genome; Humanities and Social Sciences; Humans; Jurkat Cells; multidisciplinary; N6-methyladenosine; Pharmacology; Poly A - metabolism; Protein Interaction Maps - drug effects; Proteins; Ribonucleic acid; RNA; RNA - metabolism; RNA, Ribosomal - metabolism; RNA-binding protein; RNA-Binding Proteins - metabolism; rRNA; Science; Science (multidisciplinary); TOR Serine-Threonine Kinases - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-06557-8

Following the realization that eukaryotic RNA-binding proteomes are substantially larger than anticipated, we must now understand their detailed composition and dynamics. Methods such as RNA interactome capture (RIC) have begun to address this need. However, limitations of RIC have been reported. Here we describe enhanced RNA interactome capture (eRIC), a method based on the use of an LNA-modified capture probe, which yields numerous advantages including greater specificity and increased signal-to-noise ratios compared to existing methods. In Jurkat cells, eRIC reduces the rRNA and DNA contamination by >10-fold compared to RIC and increases the detection of RNA-binding proteins. Due to its low background, eRIC also empowers comparative analyses of changes of RNA-bound proteomes missed by RIC. For example, in cells treated with dimethyloxalylglycine, which inhibits RNA demethylases, eRIC identifies m6A-responsive RNA-binding proteins that escape RIC. eRIC will facilitate the unbiased characterization of RBP dynamics in response to biological and pharmacological cues. RNA interactome capture allows the detailed investigation of RNA-bound proteomes. Here the authors describe enhanced RNA-interactome capture using LNA-modified probes for increased sensitivity and specificity.