Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data

Shigeo Fujimori, Naoya Hirai, Hiroyuki Ohashi, Kazuyo Masuoka, Akihiko Nishikimi, Yoshinori Fukui, Takanori Washio, Tomohiro Oshikubo, Tatsuhiro Yamashita, Etsuko Miyamoto-Sato

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Next-generation sequencing (NGS) has been applied to various kinds of omics studies, resulting in many biological and medical discoveries. However, high-throughput protein-protein interactome datasets derived from detection by sequencing are scarce, because protein-protein interaction analysis requires many cell manipulations to examine the interactions. The low reliability of the high-throughput data is also a problem. Here, we describe a cell-free display technology combined with NGS that can improve both the coverage and reliability of interactome datasets. The completely cell-free method gives a high-throughput and a large detection space, testing the interactions without using clones. The quantitative information provided by NGS reduces the number of false positives. The method is suitable for the in vitro detection of proteins that interact not only with the bait protein, but also with DNA, RNA and chemical compounds. Thus, it could become a universal approach for exploring the large space of protein sequences and interactome networks.

Original languageEnglish
Article number691
JournalScientific reports
Volume2
DOIs
Publication statusPublished - Nov 7 2012

Fingerprint

Technology
Proteins
Clone Cells
RNA
DNA
Datasets

All Science Journal Classification (ASJC) codes

  • General

Cite this

Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. / Fujimori, Shigeo; Hirai, Naoya; Ohashi, Hiroyuki; Masuoka, Kazuyo; Nishikimi, Akihiko; Fukui, Yoshinori; Washio, Takanori; Oshikubo, Tomohiro; Yamashita, Tatsuhiro; Miyamoto-Sato, Etsuko.

In: Scientific reports, Vol. 2, 691, 07.11.2012.

Research output: Contribution to journalArticle

Fujimori, S, Hirai, N, Ohashi, H, Masuoka, K, Nishikimi, A, Fukui, Y, Washio, T, Oshikubo, T, Yamashita, T & Miyamoto-Sato, E 2012, 'Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data', Scientific reports, vol. 2, 691. https://doi.org/10.1038/srep00691
Fujimori, Shigeo ; Hirai, Naoya ; Ohashi, Hiroyuki ; Masuoka, Kazuyo ; Nishikimi, Akihiko ; Fukui, Yoshinori ; Washio, Takanori ; Oshikubo, Tomohiro ; Yamashita, Tatsuhiro ; Miyamoto-Sato, Etsuko. / Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data. In: Scientific reports. 2012 ; Vol. 2.
@article{b05a0fcf47714280a504e5bc99acc40d,
title = "Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data",
abstract = "Next-generation sequencing (NGS) has been applied to various kinds of omics studies, resulting in many biological and medical discoveries. However, high-throughput protein-protein interactome datasets derived from detection by sequencing are scarce, because protein-protein interaction analysis requires many cell manipulations to examine the interactions. The low reliability of the high-throughput data is also a problem. Here, we describe a cell-free display technology combined with NGS that can improve both the coverage and reliability of interactome datasets. The completely cell-free method gives a high-throughput and a large detection space, testing the interactions without using clones. The quantitative information provided by NGS reduces the number of false positives. The method is suitable for the in vitro detection of proteins that interact not only with the bait protein, but also with DNA, RNA and chemical compounds. Thus, it could become a universal approach for exploring the large space of protein sequences and interactome networks.",
author = "Shigeo Fujimori and Naoya Hirai and Hiroyuki Ohashi and Kazuyo Masuoka and Akihiko Nishikimi and Yoshinori Fukui and Takanori Washio and Tomohiro Oshikubo and Tatsuhiro Yamashita and Etsuko Miyamoto-Sato",
year = "2012",
month = "11",
day = "7",
doi = "10.1038/srep00691",
language = "English",
volume = "2",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Next-generation sequencing coupled with a cell-free display technology for high-throughput production of reliable interactome data

AU - Fujimori, Shigeo

AU - Hirai, Naoya

AU - Ohashi, Hiroyuki

AU - Masuoka, Kazuyo

AU - Nishikimi, Akihiko

AU - Fukui, Yoshinori

AU - Washio, Takanori

AU - Oshikubo, Tomohiro

AU - Yamashita, Tatsuhiro

AU - Miyamoto-Sato, Etsuko

PY - 2012/11/7

Y1 - 2012/11/7

N2 - Next-generation sequencing (NGS) has been applied to various kinds of omics studies, resulting in many biological and medical discoveries. However, high-throughput protein-protein interactome datasets derived from detection by sequencing are scarce, because protein-protein interaction analysis requires many cell manipulations to examine the interactions. The low reliability of the high-throughput data is also a problem. Here, we describe a cell-free display technology combined with NGS that can improve both the coverage and reliability of interactome datasets. The completely cell-free method gives a high-throughput and a large detection space, testing the interactions without using clones. The quantitative information provided by NGS reduces the number of false positives. The method is suitable for the in vitro detection of proteins that interact not only with the bait protein, but also with DNA, RNA and chemical compounds. Thus, it could become a universal approach for exploring the large space of protein sequences and interactome networks.

AB - Next-generation sequencing (NGS) has been applied to various kinds of omics studies, resulting in many biological and medical discoveries. However, high-throughput protein-protein interactome datasets derived from detection by sequencing are scarce, because protein-protein interaction analysis requires many cell manipulations to examine the interactions. The low reliability of the high-throughput data is also a problem. Here, we describe a cell-free display technology combined with NGS that can improve both the coverage and reliability of interactome datasets. The completely cell-free method gives a high-throughput and a large detection space, testing the interactions without using clones. The quantitative information provided by NGS reduces the number of false positives. The method is suitable for the in vitro detection of proteins that interact not only with the bait protein, but also with DNA, RNA and chemical compounds. Thus, it could become a universal approach for exploring the large space of protein sequences and interactome networks.

UR - http://www.scopus.com/inward/record.url?scp=84868287528&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84868287528&partnerID=8YFLogxK

U2 - 10.1038/srep00691

DO - 10.1038/srep00691

M3 - Article

C2 - 23056904

AN - SCOPUS:84868287528

VL - 2

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 691

ER -