Systematic discovery of endogenous human ribonucleoprotein complexes

Anna L Mallam, Wisath Sae-Lee, Jeffrey M Schaub, Fan Tu, Anna Battenhouse, Yu Jin Jang, Jonghwan Kim, Ilya J Finkelstein, Edward M Marcotte, Kevin Drew, BioRxiv (2018).
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Abstract

Ribonucleoprotein (RNP) complexes are important for many cellular functions but their prevalence has not been systematically investigated. We developed a proteome-wide fractionation-mass-spectrometry strategy called differential fractionation (DIF-FRAC) to discover RNP complexes by their sensitivity to RNase A treatment. Applying this to human cells reveals a set of 115 highly-stable endogenous RNPs, and a further 1,428 protein complexes whose subunits associate with RNA, thus indicating over 20% of all complexes are RNPs. We show RNP complexes either dissociate, change composition, or form stable protein-only complexes upon RNase A treatment, uncovering the biochemical role of RNA in complex formation. We combine these data into a resource, rna.MAP (rna.proteincomplexes.org), which demonstrates that well-studied complexes such as replication factor C (RFC) and centralspindlin exist as RNP complexes, providing new insight into their cellular functions. We apply our method to red blood cells and mouse embryonic stem cells to demonstrate its ability to identify cell-type specific roles for RNP complexes in diverse systems. Thus the methodology has the potential uncover RNP complexes in different human tissues, disease states and throughout all domains of life.