Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
Interdisciplinary Graduate Program
Program in Gene Function and Expression; Program in Molecular Medicine
Genetics and Genomics | Life Sciences | Medicine and Health Sciences
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.
DOI of Published Version
Nat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24. Link to article on publisher's site
Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ. (2007). Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. GSBS Student Publications. https://doi.org/10.1038/nmeth1063. Retrieved from https://escholarship.umassmed.edu/gsbs_sp/439