气候变化领域集成服务门户(CCPortal): Inferring multilayer interactome networks shaping phenotypic plasticity and evolution

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DOI	10.1038/s41467-021-25086-5
	Inferring multilayer interactome networks shaping phenotypic plasticity and evolution
	Yang D.; Jin Y.; He X.; Dong A.; Wang J.; Wu R.
发表日期	2021
ISSN	2041-1723
卷号	12 期号:1
英文摘要	Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution. © 2021, The Author(s).
语种	英语
scopus关键词	ABC transporter; vancomycin; antiinfective agent; vancomycin; epistasis; evolution; game theory; genome; heritability; phenotype; phenotypic plasticity; Article; bacterial metabolism; causality; comparative study; computer model; controlled study; epistasis; Escherichia coli; fatty acid metabolism; game; gene mapping; genome-wide association study; microbial growth; nonhuman; phenotypic plasticity; population structure; predator prey interaction; protein protein interaction; quantitative trait locus; quantitative trait locus mapping; regulatory mechanism; single nucleotide polymorphism; Staphylococcus aureus; vancomycin resistance; adaptation; bacterial genome; chromosomal mapping; drug effect; epistasis; evolution; gene regulatory network; genetics; genome-wide association study; genotype; metabolism; phenotype; protein analysis; single nucleotide polymorphism; Escherichia coli; Excavata; Staphylococcus aureus; Adaptation, Physiological; Anti-Bacterial Agents; Biological Evolution; Chromosome Mapping; Epistasis, Genetic; Escherichia coli; Game Theory; Gene Regulatory Networks; Genome, Bacterial; Genome-Wide Association Study; Genotype; Phenotype; Polymorphism, Single Nucleotide; Protein Interaction Mapping; Quantitative Trait Loci; Staphylococcus aureus; Vancomycin
来源期刊	Nature Communications
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/251358
作者单位	Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China; Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China; Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA, United States
推荐引用方式 GB/T 7714	Yang D.,Jin Y.,He X.,et al. Inferring multilayer interactome networks shaping phenotypic plasticity and evolution[J],2021,12(1).
APA	Yang D.,Jin Y.,He X.,Dong A.,Wang J.,&Wu R..(2021).Inferring multilayer interactome networks shaping phenotypic plasticity and evolution.Nature Communications,12(1).
MLA	Yang D.,et al."Inferring multilayer interactome networks shaping phenotypic plasticity and evolution".Nature Communications 12.1(2021).