Use of cDNA Tiling Arrays for Identifying Protein Interactions Selected by In Vitro Display Technologies

Kenichi Horisawa, Nobuhide Doi, Hiroshi Yanagawa

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish
Article numbere0001646
JournalPLoS One
Volume3
Issue number2
DOIs
Publication statusPublished - 2008

Fingerprint

Oligonucleotide Array Sequence Analysis
Complementary DNA
Display devices
Technology
Messenger RNA
Transcription Factors
molecular cloning
Cloning
transcription factors
screening
Organism Cloning
application coverage
Screening
Proteins
proteins
oligonucleotides
open reading frames
binding proteins
Transcription
transcription (genetics)

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Use of cDNA Tiling Arrays for Identifying Protein Interactions Selected by In Vitro Display Technologies. / Horisawa, Kenichi; Doi, Nobuhide; Yanagawa, Hiroshi.

In: PLoS One, Vol. 3, No. 2, e0001646, 2008.

Research output: Contribution to journalArticle

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