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Global insights into cellular organization and genome function require comprehensive understanding ofthe interactome networks that mediate genotypephenotype relationships1,2. Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRl'. With approximately 53,000 protein-protein interactions, HuRl has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration ofHuRl with genome3, transcriptome4 and proteome5 data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRl in identifying the specific subcellular roles of protein-protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRl is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes.
The reference human genome sequence has enabled systematic study of genetic6 and expression4 variability at the organism6, tissue4, cell type7 and single-cell level8. Despite advances in sequencing genomes, transcriptomes and proteomes, we still understand little about the cellular mechanisms that mediate phenotypic and tissue or cell type variability. A mechanistic understanding of cellular function and organization emerges from studying how genes and their products, primarily proteins, interact with each other, forming a dynamic interactome that drives biological function. Analogous to the reference human genome sequence9,10, a reference map of the human protein interactome, generated systematically and comprehensively, is needed to provide a scaffold for the unbiased proteome-wide study of biological mechanisms, generally and within specific cellular contexts.
It remains infeasible to assemble a reference interactome map by systematically identifying endogenous protein-protein interactions (PPIs) in thousands of physiological and pathological cellular contexts11,12. However, systematic affinity purification of exogenously expressed bait proteins in immortalized-cell contexts13 as well as binary PPI detection assays in cell models2,14 have generated biophysical human protein interactome maps of demonstrated high functional relevance. Specifically, yeast two-hybrid (Y2H) represents the only binary PPI assay that can be operated at sufficient throughput to systematically screen the human proteome for binary PPls. Using Y2H followed by validation in orthogonal assays, we previously generated Hl-ll-14 consisting of approximately 14,000 PPls involving 4,000 proteins from screening around 40% of the genome-by-genome search space2. ln contrast to curated interactions from hypothesis-driven small-scale studies and protein...