Journal Article

Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA

Weeks, Kevin M., Calabrese, J. Mauro, Mustoe, Anthony M., Weidmann, Chase A., Jariwala, Parth B.

2021

Overview

RNA–protein interaction networks govern many biological processes but are difficult to examine comprehensively. We devised ribonucleoprotein networks analyzed by mutational profiling (RNP-MaP), a live-cell chemical probing strategy that maps cooperative interactions among multiple proteins bound to single RNA molecules at nucleotide resolution. RNP-MaP uses a hetero-bifunctional crosslinker to freeze interacting proteins in place on RNA and then maps multiple bound proteins on single RNA strands by read-through reverse transcription and DNA sequencing. RNP-MaP revealed that RNase P and RMRP, two sequence-divergent but structurally related non-coding RNAs, share RNP networks and that network hubs define functional sites in these RNAs. RNP-MaP also identified protein interaction networks conserved between mouse and human XIST long non-coding RNAs and defined protein communities whose binding sites colocalize and form networks in functional regions of XIST. RNP-MaP enables discovery and efficient validation of functional protein interaction networks on long RNAs in living cells. Networks of proteins bound to single RNAs are identified by correlated chemical crosslinking.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/114 / 631/45 / 631/61 / Agriculture / Analysis / Animals / Binding sites / Bioinformatics / Biological activity / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biomedicine / Biotechnology / Composition / Crosslinked polymers / Crosslinking / Deoxyribonucleic acid / DNA / DNA sequencing / Genetic transcription / Hubs / Humans / Life Sciences / Methods / Network hubs / Non-coding RNA / Nucleotide sequence / Nucleotide sequencing / Nucleotides / Protein binding / Protein Interaction Maps / Proteins / Reproducibility of Results / Reverse transcription / Ribonuclease / Ribonuclease MRP / Ribonuclease P / Ribonuclease P - metabolism / Ribonucleic acid / Ribonucleoproteins - metabolism / RNA / RNA - metabolism / RNA, Long Noncoding - metabolism / RNA-Binding Proteins - metabolism / Scientific equipment and supplies industry