计算生物学
相互作用体
生物
转录因子
蛋白质-蛋白质相互作用
交互网络
计算机科学
遗传学
基因
作者
Shelly A. Trigg,Renee M. Garza,Andrew MacWilliams,Joseph R. Nery,Anna Bartlett,Rosa Castanon,Adeline Goubil,Joseph Feeney,Ronan C. O’Malley,Shao‐shan Carol Huang,Zhuzhu Z. Zhang,Mary Galli,Joseph R. Ecker
出处
期刊:Nature Methods
[Springer Nature]
日期:2017-06-26
卷期号:14 (8): 819-825
被引量:147
摘要
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.
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