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

doi:10.7554/eLife.40982

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

School of Medicine

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

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 language	English (US)
Article number	e40982
Journal	eLife
Volume	7
DOIs	https://doi.org/10.7554/eLife.40982
State	Published - Oct 2018

ASJC Scopus subject areas

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

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10.7554/eLife.40982

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@article{d155a2b448274f809042ce17533ce937,

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

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 {\textquoteleft}bait{\textquoteright}. 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.",

author = "Xi Peng and Francesco Emiliani and Smallwood, {Philip M.} and Amir Rattner and Hong Lei and Sabbagh, {Mark F.} and Jeremy Nathans",

note = "Funding Information: Supported by the Arnold and Mabel Beckman Foundation, NEI/NIH (R01EY018637), the David Labovitz Fund, the Chinese Scholarship Council, and the Howard Hughes Medical Institute. Funding Information: The authors are grateful to Chris Cho and James Berger for assistance with protein structure visualization; Solomon Snyder for sharing his 96-well plate reader; Danelle Devenport, Elaine Fuchs, and Tadashi Uemura for CELSR cDNAs; Davide Comoletti for CNTN cDNAs; Woj Wojtowicz for sharing her collection of Fc fusion plasmids; the JHMI Deep sequencing core; Elena Pasquale for advice; and Allen Buskirk, Daniel Goldman, and Boris Zinshteyn for helpful comments on the manuscript. Supported by the Arnold and Mabel Beckman Foundation, NEI/NIH (R01EY018637), the David Labovitz Fund, the Chinese Scholarship Council, and the Howard Hughes Medical Institute. Publisher Copyright: {\textcopyright} Peng et al.",

year = "2018",

month = oct,

doi = "10.7554/eLife.40982",

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AU - Peng, Xi

AU - Emiliani, Francesco

AU - Smallwood, Philip M.

AU - Rattner, Amir

AU - Lei, Hong

AU - Sabbagh, Mark F.

AU - Nathans, Jeremy

N1 - Funding Information: Supported by the Arnold and Mabel Beckman Foundation, NEI/NIH (R01EY018637), the David Labovitz Fund, the Chinese Scholarship Council, and the Howard Hughes Medical Institute. Funding Information: The authors are grateful to Chris Cho and James Berger for assistance with protein structure visualization; Solomon Snyder for sharing his 96-well plate reader; Danelle Devenport, Elaine Fuchs, and Tadashi Uemura for CELSR cDNAs; Davide Comoletti for CNTN cDNAs; Woj Wojtowicz for sharing her collection of Fc fusion plasmids; the JHMI Deep sequencing core; Elena Pasquale for advice; and Allen Buskirk, Daniel Goldman, and Boris Zinshteyn for helpful comments on the manuscript. Supported by the Arnold and Mabel Beckman Foundation, NEI/NIH (R01EY018637), the David Labovitz Fund, the Chinese Scholarship Council, and the Howard Hughes Medical Institute. Publisher Copyright: © Peng et al.

PY - 2018/10

Y1 - 2018/10

N2 - 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.

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.

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

Abstract

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