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Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping.
Vermeirssen, Vanessa; Deplancke, Bart; Barrasa, M Inmaculada; Reece-Hoyes, John S; Arda, H Efsun; Grove, Christian A; Martinez, Natalia J; Sequerra, Reynaldo; Doucette-Stamm, Lynn; Brent, Michael R; Walhout, Albertha J M.
Afiliación
  • Vermeirssen V; Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Nat Methods ; 4(8): 659-64, 2007 Aug.
Article en En | MEDLINE | ID: mdl-17589517
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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Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Transcripción Genética Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2007 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
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Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Transcripción Genética Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2007 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos