Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast
2012
Peng, Chien-Hua(Department of Resource Center for Clinical Research, Chang Gung Memorial Hospital) | Lin, Shu-Hsi(Institute of Bioinformatics and Structural Biology, National Tsing Hua University) | Peng, Shih-Chi(Department of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital and Chang Gung University) | Lyu, Ping-Chiang(Institute of Bioinformatics and Structural Biology, National Tsing Hua University) | Arita, Masanori(Department of Biophysics and Biochemistry, The University of Tokyo) | Tang, Chuan-Yi(Department of Computer Science, National Tsing Hua University)
Genetic robustness refers to a compensatory mechanism for buffering deleterious mutations or environmental variations. Gene duplication has been shown to provide such functional backups. However, the overall contribution of duplication-based buffering for genetic robustness is rather small. In this study, we investigated whether transcriptional compensation also exists among genes that share similar functions without sequence homology. A set of nonhomologous synthetic-lethal gene pairs was assessed by using a coexpression network, protein-protein interactions, and other types of genetic interactions in yeast. Our results are notably different from those of previous studies on buffering paralogs. The low expression similarity and the conditional coexpression alone do not play roles in identifying the functionally compensatory genes. Additional properties such as synthetic-lethal interaction, the ratio of shared common interacting partners, and the degree of coregulation were, at least in part, necessary to extract functional compensatory genes. Our network-based approach is applicable to select several well-documented cases of compensatory gene pairs and a set of new pairs. The results suggest that transcriptional reprogramming plays a limited role in functional compensation among nonhomologous genes. Our study aids in understanding the mechanism and features of functional compensation more in detail.
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