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A user-friendly platform for yeast two-hybrid library screening using next generation sequencing

Marie-Laure Erffelinck (UGent) , Bianca Ribeiro (UGent) , María Perassolo (UGent) , Laurens Pauwels (UGent) , Jacob Pollier (UGent) , Veronique Storme (UGent) and Alain Goossens (UGent)
(2018) PLOS ONE. 13(12).
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Abstract
Yeast two-hybrid (Y2H) is a well-established genetics-based system that uses yeast to selectively display binary protein-protein interactions (PPIs). To meet the current need to unravel complex PPI networks, several adaptations have been made to establish mediumto high-throughput Y2H screening platforms, with several having successfully incorporated the use of the next-generation sequencing (NGS) technology to increase the scale and sensitivity of the method. However, these have been to date mainly restricted to the use of fully annotated custom-made open reading frame (ORF) libraries and subject to complex downstream data processing. Here, a streamlined Y2H library screening strategy, based on integration of Y2H with NGS, called Y2H-seq, was developed, which allows efficient and reliable screening of Y2H cDNA libraries. To generate proof of concept, the method was applied to screen for interaction partners of two key components of the jasmonate signaling machinery in the model plant Arabidopsis thaliana, resulting in the identification of several previously reported as well as hitherto unknown interactors. Our Y2H-seq method offers a user-friendly, specific and sensitive screening method that allows identification of PPIs without prior knowledge of the organism's ORFs, thereby extending the method to organisms of which the genome has not entirely been annotated yet. The quantitative NGS readout allows to increase genome coverage, thereby overcoming some of the bottlenecks of current Y2H technologies, which will further strengthen the value of the Y2H technology as a discovery platform.
Keywords
TANDEM AFFINITY PURIFICATION, PROTEIN-PROTEIN INTERACTIONS, CO-REPRESSOR TOPLESS, SPLIT-UBIQUITIN, TRANSCRIPTION, INTERACTOME, COMPLEXES, SELECTION, NETWORK, SYSTEM

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Chicago
Erffelinck, Marie-Laure, Bianca Ribeiro, María Perassolo, Laurens Pauwels, Jacob Pollier, Veronique Storme, and Alain Goossens. 2018. “A User-friendly Platform for Yeast Two-hybrid Library Screening Using Next Generation Sequencing.” Plos One 13 (12).
APA
Erffelinck, M.-L., Ribeiro, B., Perassolo, M., Pauwels, L., Pollier, J., Storme, V., & Goossens, A. (2018). A user-friendly platform for yeast two-hybrid library screening using next generation sequencing. PLOS ONE, 13(12).
Vancouver
1.
Erffelinck M-L, Ribeiro B, Perassolo M, Pauwels L, Pollier J, Storme V, et al. A user-friendly platform for yeast two-hybrid library screening using next generation sequencing. PLOS ONE. 2018;13(12).
MLA
Erffelinck, Marie-Laure, Bianca Ribeiro, María Perassolo, et al. “A User-friendly Platform for Yeast Two-hybrid Library Screening Using Next Generation Sequencing.” PLOS ONE 13.12 (2018): n. pag. Print.
@article{8586584,
  abstract     = {Yeast two-hybrid (Y2H) is a well-established genetics-based system that uses yeast to selectively display binary protein-protein interactions (PPIs). To meet the current need to unravel complex PPI networks, several adaptations have been made to establish mediumto high-throughput Y2H screening platforms, with several having successfully incorporated the use of the next-generation sequencing (NGS) technology to increase the scale and sensitivity of the method. However, these have been to date mainly restricted to the use of fully annotated custom-made open reading frame (ORF) libraries and subject to complex downstream data processing. Here, a streamlined Y2H library screening strategy, based on integration of Y2H with NGS, called Y2H-seq, was developed, which allows efficient and reliable screening of Y2H cDNA libraries. To generate proof of concept, the method was applied to screen for interaction partners of two key components of the jasmonate signaling machinery in the model plant Arabidopsis thaliana, resulting in the identification of several previously reported as well as hitherto unknown interactors. Our Y2H-seq method offers a user-friendly, specific and sensitive screening method that allows identification of PPIs without prior knowledge of the organism's ORFs, thereby extending the method to organisms of which the genome has not entirely been annotated yet. The quantitative NGS readout allows to increase genome coverage, thereby overcoming some of the bottlenecks of current Y2H technologies, which will further strengthen the value of the Y2H technology as a discovery platform.},
  articleno    = {e0201270},
  author       = {Erffelinck, Marie-Laure and Ribeiro, Bianca and Perassolo, Mar{\'i}a and Pauwels, Laurens and Pollier, Jacob and Storme, Veronique and Goossens, Alain},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {12},
  pages        = {21},
  title        = {A user-friendly platform for yeast two-hybrid library screening using next generation sequencing},
  url          = {http://dx.doi.org/10.1371/journal.pone.0201270},
  volume       = {13},
  year         = {2018},
}

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