Nature Methods
- 4, 659 - 664 (2007)
Published online: 24 June 2007; | doi:10.1038/nmeth1063
Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mappingVanessa Vermeirssen1, 4, Bart Deplancke1, 4, M Inmaculada Barrasa1, 4, John S Reece-Hoyes1, 4, H Efsun Arda1, Christian A Grove1, Natalia J Martinez1, Reynaldo Sequerra2, Lynn Doucette-Stamm2, Michael R Brent3 & Albertha J M Walhout11
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. 2
Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA. 3
Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA. 4
These authors contributed equally to this work.
Correspondence should be addressed to marian.walhout@umassmed.edu Yeast one-hybrid (Y1H) assays provide a gene-centered method for the identification of interactions between gene promoters and regulatory transcription factors (TFs). To date, Y1H assays have involved library screens that are relatively expensive and laborious. We present two Y1H strategies that allow immediate prey identification: matrix assays that use an array of 755 individual Caenorhabditis elegans TFs, and smart-pool assays that use TF multiplexing. Both strategies simplify the Y1H pipeline and reduce the cost of protein-DNA interaction identification. We used a Steiner triple system (STS) to create smart pools of 4–25 TFs. Notably, we uniplexed a small number of highly connected TFs to allow efficient assay deconvolution. Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well.
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