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Method: A novel synthetic-genetic-array–based yeast one-hybrid system for high discovery rate and short processing time
- Chung-Shu Yeh,
- Zhifeng Wang,
- Fang Miao,
- Hongyan Ma,
- Chung-Ting Kao,
- Tzu-Shu Hsu,
- Jhong-He Yu,
- Er-Tsi Hung,
- Chia-Chang Lin,
- Chen-Yu Kuan,
- Ni-Chiao Tsai,
- Chenguang Zhou,
- Guan-Zheng Qu,
- Jing Jiang,
- Guifeng Liu,
- Jack P. Wang,
- Wei Li,
- Vincent L. Chiang,
- Tien-Hsien Chang,
- and Ying-Chung Jimmy Lin
Genome Res. August 2019 29: 1343-1351; Published in Advance June 11, 2019, doi:10.1101/gr.245951.118
...AJ. 2006b. Gateway-compatible yeast one-hybrid screens. CSH Protoc 2006. doi:10.1101/pdb.prot4590 ↵French S, Mangat C, Bharat A, Côté JP, Mori H, Brown ED. 2016. A robust platform for chemical genomics in bacterial systems. Mol Biol Cell 27: 1015–1025. doi:10.1091/mbc.E15-08-0573 ↵Fuxman Bass JI...
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Method: Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
- Shaleen Shrestha,
- Jared Allan Sewell,
- Clarissa Stephanie Santoso,
- Elena Forchielli,
- Sebastian Carrasco Pro,
- Melissa Martinez,
- and Juan Ignacio Fuxman Bass
Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
...experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false-positive and -negative predictions. To address these limitations, we developed an experimental approach based on enhanced yeast one-hybrid assays. The first...
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Method: An extended set of yeast-based functional assays accurately identifies human disease mutations
- Song Sun,
- Fan Yang,
- Guihong Tan,
- Michael Costanzo,
- Rose Oughtred,
- Jodi Hirschman,
- Chandra L. Theesfeld,
- Pritpal Bansal,
- Nidhi Sahni,
- Song Yi,
- Analyn Yu,
- Tanya Tyagi,
- Cathy Tie,
- David E. Hill,
- Marc Vidal,
- Brenda J. Andrews,
- Charles Boone,
- Kara Dolinski,
- and Frederick P. Roth
Genome Res. May 2016 26: 670-680; Published in Advance March 14, 2016, doi:10.1101/gr.192526.115
...evaluated in yeast (Jeong et al. 2007). In another study, mutagenesis of the human tumor suppressor gene HsTP53 was followed by the reverse yeast one-hybrid assay to identify variants that lose DNA-binding activity (Brachmann et al. 1996). Nearly all of the variants identified by this approach had also been...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
.... ↵ Deplancke, B. , Dupuy, D. , Vidal, M. , Walhout, A.J.M. ( 2004 ) A Gateway-compatible yeast one-hybrid system . Genome Res. 14 : 2093 – 2101 . ↵ Deplancke, B. , Mukhopadhyay, A. , Ao, W. , Elewa, A.M. , Grove, C.A. , Martinez, N.J. , Sequerra, R. , Doucette-Stam, L. , Reece-Hoyes, J.S. , Hope, I.A. , et al...
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REVIEW: Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
- Albertha J.M. Walhout
Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
...-throughput methods for protein–DNA interaction mapping. ( A ) protein–DNA interactions can be mapped using either TF- or gene-centered methods, as indicated by the arrows. Y1H, yeast one-hybrid assays; ChIP, chromatin-immunoprecipitations; PBM, protein binding microarray; B1H, bacterial one-hybrid system; Dam...
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LETTER: Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network
- Vanessa Vermeirssen,
- M. Inmaculada Barrasa,
- César A. Hidalgo,
- Jenny Aurielle B. Babon,
- Reynaldo Sequerra,
- Lynn Doucette-Stamm,
- Albert-László Barabási,
- and Albertha J.M. Walhout
Genome Res. July 2007 17: 1061-1071; Published in Advance May 18, 2007, doi:10.1101/gr.6148107
...systems, such methods are limited to TFs that are widely and highly expressed, and for which suitable antibodies are available. Gene-centered methods such as the Gateway-compatible yeast one-hybrid system (Y1H) provide a high-throughput, condition-independent approach for the systematic identification...
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Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- Lesley T. MacNeil and
- Albertha J.M. Walhout
Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
.... One of the few available gene-centered methods is the yeast one-hybrid (Y1H) system, which has been modified for use with large sets of genes and many TFs simultaneously (Deplancke et al. 2004, 2006; Vermeirssen et al. 2007b). The Y1H system has been used to delineate various medium...
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RESOURCE: A First Version of the Caenorhabditis elegans Promoterome
- Denis Dupuy,
- Qian-Ru Li,
- Bart Deplancke,
- Mike Boxem,
- Tong Hao,
- Philippe Lamesch,
- Reynaldo Sequerra,
- Stephanie Bosak,
- Lynn Doucette-Stamm,
- Ian A. Hope,
- David E. Hill,
- Albertha J.M. Walhout,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2169-2175; doi:10.1101/gr.2497604
.... A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. EMBO Rep. 2 : 821 -828. ↵ Deplancke, B., Dupuy, D., Vidal, M., and Walhout, A.J.M. 2004 . A Gateway-compatible yeast one-hybrid system. Genome Res . (this issue). ↵ Eimer, S., Donhauser, R., and Baumeister, R. 2002...
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PERSPECTIVE: ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List
- Michael A. Brasch,
- James L. Hartley,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2001-2009; doi:10.1101/gr.2769804
...., Dupuy, D., Vidal, M., and Walhout, A.J. 2004 . A Gateway-compatible yeast one-hybrid system. Genome Res. (this issue). ↵ Dorsett, Y. and Tuschl, T. 2004 . siRNAs: Applications in functional genomics and potential as therapeutics. Nat. Rev. Drug Discov. 3 : 318 -329. ↵ Dupuy, D., Li, Q.-R., Deplancke, B...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...powerful as additional Caenorhabditis sequences become available and as gene expression data are refined. Parallel to expression data and comparative analysis, investigators have attempted to identify the target sequence for known transcription factors. Using the yeast one-hybrid system, the motifs...

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