Interactome Projects at CCSB

H uman interactome mapping is the flagship project of CCSB. A first map of the human binary interactome (Rual et al Nature 2005) was obtained by yeast two-hybrid (Y2H) screening for direct, binary interactions within a "Space I" matrix of ~8,000 x 8,000 ORFs contained in Human ORFeome v1.1 (Rual et al Genome Res 2004). We have developed an empirical framework that quantitatively measures the parameters of screening completeness, assay sensitivity, sampling sensitivity, and precision, and used this framework to estimate the size of the human binary interactome as ~130,000 ± 32,000 binary interactions (Venkatesan et al Nat Methods 2009). Using a novel next-generation sequencing strategy to identify interaction pairs (Yu et al Nat Methods 2011), we have carried out a Y2H screen for interactions within a “Space II” matrix of ~13,000 x 13,000 ORFs contained in Human ORFeome v5.1. We report ~14,000 new direct, binary interactions (Rolland et al Cell 2014), bringing the total number of unique binary interactions to ~17,000. Mapping of the Reference human interactome has begun, with early release of Human ORF collection for binary interaction screening and binary protein-protein interactions from a small test search space being used to develop, optimize, and benchmark improvements to the mapping pipeline, as well as preliminary data. more

Viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations (Gulbahce et al PLoS Comput Biol 2012). We applied a systematic integrated pipeline to investigate at genome-scale perturbations of host interactome networks induced by individual gene products encoded by members of four functionally related, yet biologically distinct, families of DNA tumor viruses: polymaviruses, papillomaviruses, adenoviruses, and Epstein-Barr virus (Rozenblatt-Rosen et al Nature 2012). By yeast two-hybrid we screened 123 viral ORFs against ~13,000 human ORFs, obtaining 454 validated binary interactions between 53 viral proteins and 307 human target proteins. By tandem affinity purification followed by mass spectrometry (TAP-MS), we reproducibly mapped 3,787 viral-host co-complex associations involving 54 viral proteins and the products of 1,079 unambiguously identified host genes. more

Plants have unique features that evolved in response to environmental and ecological challenges. Accounts of the complex cellular networks that underlie plant-specific functions are missing. We reported a proteome-wide binary protein-protein interaction map from a search space size of ~8,000 x 8,000 ORFs for the interactome network of the plant Arabidopsis thaliana. This interactome map contains ~6,200 highly reliable interactions between ~2,700 proteins (Arabidopsis Interactome Mapping Consortium, Science 2011), representing ~2% of the full Arabidopsis biophysical binary interactome. more

Worm Interactome version 8 contains 3,864 binary protein-protein interactions for C. elegans assembled from the WI-2007 high-throughput yeast two-hybrid screen (1,816 new interactions reported in Simonis et al Nat Methods 2009); the WI-2004 high-throughput yeast two-hybrid screen (1,735 interactions reported in Li et al Science 2004); and a compendium of data from medium-throughput yeast two-hybrid screens (554 interactions). more

Yeast Interactome version 1 (CCSB-YI1) contains high-quality yeast two-hybrid protein-protein interactions for S. cerevisiae. It includes 1,809 interactions among 1,278 proteins, comprising ~10% of the complete yeast binary interactome estimated at ~18,000 ± 4,500 interactions (Yu et al Science 2008). To obtain a more comprehensive binary yeast interactome CCSB-YI1 was combined with Ito-core and Uetz-screen datasets to produce Y2H-union, which contains 2,930 binary interactions among 2,018 proteins, ~20% of the whole yeast binary interactome. more

Fragmentome: Many protein-protein interactions are mediated through independently folding modular domains. Proteome-wide efforts to model interactome networks have necessarily neglected the modular organization of proteins. We developed an experimental “fragmentome” strategy to efficiently identify interaction domains (Boxem et al Cell 2008). We used this strategy to generate a domain-based interactome network for proteins involved in C. elegans early embryonic cell divisions.