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

Scientific Reports 2, 691 doi:10.1038/srep00691
Shigeo Fujimori, Naoya Hirai, Hiroyuki Ohashi, Kazuyo Masuoka, Akihiko Nishikimi, Yoshinori Fukui, Takanori Washio, Tomohiro Oshikubo, Tatsuhiro Yamashita, Etsuko Miyamoto-Sato
Division of Interactome Medical Sciences, The Institute of Medical Science, The University of Tokyo, Division of Immunogenetics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, RIKEN GENESIS Co., Ltd., Production Solution Business Office, Production Solution Division II, Solution Department I, Fujitsu Advanced Engineering Limited, BioIT Business Development Unit, Fujitsu Limited, Human Genome Center, The Institute of Medical Science, The University of Tokyo.

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.