TY - JOUR
T1 - Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
AU - Vermeirssen, Vanessa
AU - Deplancke, Bart
AU - Barrasa, M. Inmaculada
AU - Reece-Hoyes, John S.
AU - Arda, H. Efsun
AU - Grove, Christian A.
AU - Martinez, Natalia J.
AU - Sequerra, Reynaldo
AU - Doucette-Stamm, Lynn
AU - Brent, Michael R.
AU - Walhout, Albertha J.M.
N1 - Funding Information:
We thank J. Dekker for critical reading of the manuscript; W. Harper (Harvard Medical School) for the Y187 yeast strain; N. Klitgord and M. Vidal (Dana-Farber Cancer Institute) for help with primer design; E. Méndez González (M-3 Informática, S.L.) for helpful suggestions regarding constraint programming and the sequencing staff at Agencourt Bioscience Corporation for technical assistance. This work was supported by BAEF fellowship for Biomedical and Biotechnology Research to V.V., and US National Institute of Diabetes and Digestive and Kidney Diseases grants (DK068429 and DK071713) to A.J.M.W.
PY - 2007/8
Y1 - 2007/8
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=34547624524&partnerID=8YFLogxK
U2 - 10.1038/nmeth1063
DO - 10.1038/nmeth1063
M3 - Article
C2 - 17589517
AN - SCOPUS:34547624524
SN - 1548-7091
VL - 4
SP - 659
EP - 664
JO - Nature Methods
JF - Nature Methods
IS - 8
ER -