Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
Barrasa, M. Inmaculada
Reece-Hoyes, John S.
Arda, H. Efsun
Grove, Christian A.
Martinez, Natalia Julia
Brent, Michael R.
Walhout, Albertha J. M.
Student AuthorsH. Efsun Arda; Christian A. Grove
UMass Chan AffiliationsProgram in Molecular Medicine
Program in Gene Function and Expression
Document TypeJournal Article
KeywordsAnimals; Caenorhabditis elegans; *Transcription, Genetic; Two-Hybrid System Techniques
Genetics and Genomics
Medicine and Health Sciences
MetadataShow full item record
AbstractYeast 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.
SourceNat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24. Link to article on publisher's site
Permanent Link to this Itemhttp://hdl.handle.net/20.500.14038/33778
Related ResourcesLink to Article in PubMed