Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes

• Published in: Cell reports (Cambridge) 2019-10, Vol.29 (5), p.1351-1368.e5
• Main Authors: Mallam, Anna L., Sae-Lee, Wisath, Schaub, Jeffrey M., Tu, Fan, Battenhouse, Anna, Jang, Yu Jin, Kim, Jonghwan, Wallingford, John B., Finkelstein, Ilya J., Marcotte, Edward M., Drew, Kevin
• Format: Article
• Language: English
• Subjects: Animals; biochemical fractionation; Cell Fractionation; DIF-FRAC; HEK293 Cells; Humans; interactome; mass spectrometry; Mice; Multiprotein Complexes - metabolism; Nucleic Acid Conformation; protein complexes; Proteome - metabolism; proteomics; RBP; Replication Protein C - metabolism; Reproducibility of Results; ribonucleoprotein complex; Ribonucleoproteins - metabolism; RNA - chemistry; RNA-binding protein; RNP
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2019.09.060

RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. We use our method to systematically identify cell-type-specific RNA-associated proteins in mouse embryonic stem cells and finally, distribute our resource, rna.MAP, in an easy-to-use online interface (rna.proteincomplexes.org). Our system thus provides a methodology for explorations across human tissues, disease states, and throughout all domains of life. [Display omitted] •DIF-FRAC systematically discovers ribonucleoprotein complexes•Identification of 1,428 RNP complexes (20% of known complexes)•RNP complexes fall into three categories: Apo-stable, structural, and compositional•Discovery of previously unknown roles for RNA in known protein complexes Ribonucleoprotein (RNP) complexes carry out many essential biological processes. Mallam et al. developed differential fractionation (DIF-FRAC), a proteomics method to systematically discover RNP complexes. Using their method, they discovered previously unknown RNP complexes, classified complexes by their RNA-dependent stability, and identified previously unknown roles for RNA in known protein complexes.