We report a genome-wide, multiscale approach to simultaneously measure the effect that the increased copy of each gene and/or operon has on a desired trait or phenotype. The method involves (i) growth selections on a mixture of several different plasmid-based genomic libraries of defined insert sizes or SCALEs, (ii) microarray studies of enriched plasmid DNA, and a (iii) mathematical multiscale analysis that precisely identifies the relevant genetic elements. This approach allows for identification of all single open reading frames and larger multigene fragments within a genomic library that alter the expression of a given phenotype. We have demonstrated this method in Escherichia coli by monitoring, in parallel, a population of >106 genomic library clones of different insert sizes, throughout continuous selections over a period of 100 generations.
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This work was supported by US National Institutes of Health grants R21 AI055773-01 and K25 AI064338 and National Science Foundation grant BES0228584. M.D.L. was supported by a National Institutes of Health F31 award A1056687. T.W. was supported by a US Department of Education Graduate Assistantship in Areas of National Need fellowship. We thank H. Marshall at the University of Colorado Microarray Facility, and P.D. Bevins for his help with this work.
University of Colorado has filed a patent on this method. M.D.L. and R.T.G. have started a company that is seeking a license on this technology. M.D.L. may be a future employee of this company.
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Lynch, M., Warnecke, T. & Gill, R. SCALEs: multiscale analysis of library enrichment. Nat Methods 4, 87–93 (2007). https://doi.org/10.1038/nmeth946
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