Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions

Xi Peng, Francesco Emiliani, Philip M. Smallwood, Amir Rattner, Hong Lei, Mark F. Sabbagh, Jeremy Nathans

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
JournaleLife
Volume7
DOIs
StatePublished - Oct 22 2018

Fingerprint

RNA Sequence Analysis
Polyribosomes
RNA
Proteins
Immobilized Proteins
High-Throughput Nucleotide Sequencing
Biological Science Disciplines
Brain
Peptides

Keywords

  • biochemistry
  • chemical biology
  • extracellular interactome
  • mouse
  • protocadherin
  • RNAseq
  • secretome

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions. / Peng, Xi; Emiliani, Francesco; Smallwood, Philip M.; Rattner, Amir; Lei, Hong; Sabbagh, Mark F.; Nathans, Jeremy.

In: eLife, Vol. 7, 22.10.2018.

Research output: Contribution to journalArticle

Peng, Xi ; Emiliani, Francesco ; Smallwood, Philip M. ; Rattner, Amir ; Lei, Hong ; Sabbagh, Mark F. ; Nathans, Jeremy. / Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions. In: eLife. 2018 ; Vol. 7.
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