use of cdna tiling arrays for identifying protein interactions selected by in vitro display technologies利用cdna花砖阵列识别蛋白质交互选择体外显示技术.pdfVIP

Use of cDNA Tiling Arrays for Identifying Protein Interactions Selected by In Vitro Display Technologies Kenichi Horisawa, Nobuhide Doi, Hiroshi Yanagawa* Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan Abstract In vitro display technologies such as mRNA display are powerful screening tools for protein interaction analysis, but the final cloning and sequencing processes represent a bottleneck, resulting in many false negatives. Here we describe an application of tiling array technology to identify specifically binding proteins selected with the in vitro virus (IVV) mRNA display technology. We constructed transcription-factor tiling (TFT) arrays containing ,1,600 open reading frame sequences of known and predicted mouse transcription-regulatory factors (334,372 oligonucleotides, 50-mer in length) to analyze cDNA fragments from mRNA-display screening for Jun-associated proteins. The use of the TFT arrays greatly increased the coverage of known Jun-interactors to 28% (from 14% with the cloning and sequencing approach), without reducing the accuracy (,75%). This method could detect even targets with extremely low expression levels (less than a single mRNA copy per cell in whole brain tissue). This highly sensitive and reliable method should be useful for high-throughput protein interaction analysis on a genome-wide scale. Citation: Horisawa K, Doi N, Yanagawa H (2008) Use of cDNA Tiling Arrays for Identifying Protein Interactions Selected by In Vitro Display Technologies. PLoS ONE 3(2): e1646. doi:10.1371/journal.pone.0001646 ´ ´ Editor: Stephen W. Michnick, Universite de Montreal, Canada Received October 21, 2007; Accepted January 28, 2008; Published February 20, 2008 Copyright: 2008 Horisawa et al. This