TY - JOUR TI - Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions AU - Peng, Xi AU - Emiliani, Francesco AU - Smallwood, Philip M AU - Rattner, Amir AU - Lei, Hong AU - Sabbagh, Mark F AU - Nathans, Jeremy A2 - Bjorkman, Pamela J A2 - Cole, Philip A VL - 7 PY - 2018 DA - 2018/10/22 SP - e40982 C1 - eLife 2018;7:e40982 DO - 10.7554/eLife.40982 UR - https://doi.org/10.7554/eLife.40982 AB - Defining protein-protein interactions (PPIs) is central to the biological sciences. Here, we present a novel platform - Affinity Capture of Polyribosomes followed by RNA sequencing (ACAPseq) - for identifying PPIs. ACAPseq harnesses the power of massively parallel RNA sequencing (RNAseq) to quantify the enrichment of polyribosomes based on the affinity of their associated nascent polypeptides for an immobilized protein ‘bait’. This method was developed and tested using neonatal mouse brain polyribosomes and a variety of extracellular domains as baits. Of 92 baits tested, 25 identified one or more binding partners that appear to be biologically relevant; additional candidate partners remain to be validated. ACAPseq can detect binding to targets that are present at less than 1 part in 100,000 in the starting polyribosome preparation. One of the observed PPIs was analyzed in detail, revealing the mode of homophilic binding for Protocadherin-9 (PCDH9), a non-clustered Protocadherin family member. KW - secretome KW - extracellular interactome KW - RNAseq KW - protocadherin JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -