Abstract
“Smart-pooling” is a strategy to achieve high efficiency, sensitivity, and specificity in large-scale yeast two-hybrid screening. In smart-pooling, reagents are multiplexed in a highly redundant manner and the positives can be read out on the final selection plates without the requirement of any extra experimental steps. We have shown that the Shifted Transversal Design (STD), a powerful theoretical construction for smart-pooling, can be used in yeast two-hybrid interactome mapping. STD pooling can achieve similar levels of sensitivity and specificity as one-on-one array-based yeast two-hybrid, while the costs and workloads are much lower. This chapter focuses on the construction and usage of STD arrays for large-scale yeast two-hybrid interactome mapping.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Thierry-Mieg, N. (2006) Pooling in systems biology becomes smart, Nat Methods 3, 161–162.
Jin, F., Avramova, L., Huang, J., and Hazbun, T. (2007) A yeast two-hybrid smart-pool-array system for protein-interaction mapping, Nat Methods 4, 405–407.
Xin, X., Rual, J. F., Hirozane-Kishikawa, T., Hill, D. E., Vidal, M., Boone, C., and Thierry-Mieg, N. (2009) Shifted Transversal Design smart-pooling for high coverage interactome mapping, Genome Res 19, 1262–1269.
Vermeirssen, V., Deplancke, B., Barrasa, M. I., Reece-Hoyes, J. S., Arda, H. E., Grove, C. A., Martinez, N. J., Sequerra, R., Doucette-Stamm, L., Brent, M. R., and Walhout, A. J. (2007) Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping, Nat Methods 4, 659–664.
Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M., and Hannon, G. J. (2009) DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis, Genome Res 19, 1243–1253.
Prabhu, S., and Pe’er, I. (2009) Overlapping pools for high-throughput targeted resequencing, Genome Res 19, 1254–1261.
Thierry-Mieg, N. (2006) A new pooling strategy for high-throughput screening: the Shifted Transversal Design, BMC Bioinformatics 7, 28.
Thierry-Mieg, N., and Bailly, G. (2008) Interpool: interpreting smart-pooling results, Bioinformatics 24, 696–703.
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature 403, 623–627.
Acknowledgment
This work was supported by Canadian Cancer Society grant # 015311 awarded to CB.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Xin, X., Boone, C., Thierry-Mieg, N. (2012). Mapping Interactomes with High Coverage and Efficiency Using the Shifted Transversal Design. In: Suter, B., Wanker, E. (eds) Two Hybrid Technologies. Methods in Molecular Biology, vol 812. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-455-1_8
Download citation
DOI: https://doi.org/10.1007/978-1-61779-455-1_8
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-454-4
Online ISBN: 978-1-61779-455-1
eBook Packages: Springer Protocols