CrY2H-seq: A massively multiplexed assay for deep-coverage interactome mapping

Shelly A. Trigg, Renee M. Garza, Andrew MacWilliams, Joseph R. Nery, Anna Bartlett, Rosa Castanon, Adeline Goubil, Joseph Feeney, Ronan O'Malley, Shao-Shan Huang, Zhuzhu Z. Zhang, Mary Galli, Joseph R. Ecker

Research output: Contribution to journalArticle

Abstract

Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions. By performing ten independent screens testing a total of 36 million binary interaction combinations, and uncovering a network of 8,577 interactions among 1,453 transcription factors, we demonstrate CrY2H-seq?s improved screening capacity, efficiency, and sensitivity over those of existing technologies. The deep-coverage network resource we call AtTFIN-1 recapitulates one-third of previously reported interactions derived from diverse methods, expands the number of known plant transcription factor interactions by three-fold, and reveals previously unknown family-specific interaction module associations with plant reproductive development, root architecture, and circadian coordination.

Original languageEnglish (US)
Pages (from-to)819-825
Number of pages7
JournalNature Methods
Volume14
Issue number8
DOIs
StatePublished - Jul 28 2017

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Assays
Transcription Factors
Protein Interaction Mapping
Technology
Two-Hybrid System Techniques
Proteins
Plant Development
Electric fuses
DNA Sequence Analysis
Arabidopsis
Yeast
Screening
Yeasts
Costs and Cost Analysis
DNA
Testing
Costs
Cre recombinase

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Trigg, S. A., Garza, R. M., MacWilliams, A., Nery, J. R., Bartlett, A., Castanon, R., ... Ecker, J. R. (2017). CrY2H-seq: A massively multiplexed assay for deep-coverage interactome mapping. Nature Methods, 14(8), 819-825. https://doi.org/10.1038/nmeth.4343

CrY2H-seq : A massively multiplexed assay for deep-coverage interactome mapping. / Trigg, Shelly A.; Garza, Renee M.; MacWilliams, Andrew; Nery, Joseph R.; Bartlett, Anna; Castanon, Rosa; Goubil, Adeline; Feeney, Joseph; O'Malley, Ronan; Huang, Shao-Shan; Zhang, Zhuzhu Z.; Galli, Mary; Ecker, Joseph R.

In: Nature Methods, Vol. 14, No. 8, 28.07.2017, p. 819-825.

Research output: Contribution to journalArticle

Trigg, SA, Garza, RM, MacWilliams, A, Nery, JR, Bartlett, A, Castanon, R, Goubil, A, Feeney, J, O'Malley, R, Huang, S-S, Zhang, ZZ, Galli, M & Ecker, JR 2017, 'CrY2H-seq: A massively multiplexed assay for deep-coverage interactome mapping', Nature Methods, vol. 14, no. 8, pp. 819-825. https://doi.org/10.1038/nmeth.4343
Trigg SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R et al. CrY2H-seq: A massively multiplexed assay for deep-coverage interactome mapping. Nature Methods. 2017 Jul 28;14(8):819-825. https://doi.org/10.1038/nmeth.4343
Trigg, Shelly A. ; Garza, Renee M. ; MacWilliams, Andrew ; Nery, Joseph R. ; Bartlett, Anna ; Castanon, Rosa ; Goubil, Adeline ; Feeney, Joseph ; O'Malley, Ronan ; Huang, Shao-Shan ; Zhang, Zhuzhu Z. ; Galli, Mary ; Ecker, Joseph R. / CrY2H-seq : A massively multiplexed assay for deep-coverage interactome mapping. In: Nature Methods. 2017 ; Vol. 14, No. 8. pp. 819-825.
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