Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
Authors
Vermeirssen, VanessaDeplancke, Bart
Barrasa, M. Inmaculada
Reece-Hoyes, John S.
Arda, H. Efsun
Grove, Christian A.
Martinez, Natalia Julia
Sequerra, Reynaldo
Doucette-Stamm, Lynn
Brent, Michael R.
Walhout, Albertha J. M.
Student Authors
H. Efsun Arda; Christian A. GroveDocument Type
Journal ArticlePublication Date
2007-06-26Keywords
Animals; Caenorhabditis elegans; *Transcription, Genetic; Two-Hybrid System TechniquesGenetics and Genomics
Life Sciences
Medicine and Health Sciences
Metadata
Show full item recordAbstract
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.Source
Nat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24. Link to article on publisher's siteDOI
10.1038/nmeth1063Permanent Link to this Item
http://hdl.handle.net/20.500.14038/33778PubMed ID
17589517Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1038/nmeth1063