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Volumn 521, Issue 7552, 2015, Pages 344-347

Selection on noise constrains variation in a eukaryotic promoter

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTE; EVOLUTIONARY THEORY; GENE EXPRESSION; GENETIC DRIFT; GENETIC VARIATION; MUTATION; NOISE; PHENOTYPE; POLYMORPHISM;

EID: 84930221731     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14244     Document Type: Article
Times cited : (109)

References (46)
  • 1
    • 84888616764 scopus 로고    scopus 로고
    • A novel test for selection on cis-regulatory elements reveals positive and negative selection acting onmammalian transcriptional enhancers
    • Smith, J. D., McManus, K. F. & Fraser, H. B. A novel test for selection on cis-regulatory elements reveals positive and negative selection acting onmammalian transcriptional enhancers. Mol. Biol. Evol. 30, 2509-2518 (2013).
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 2509-2518
    • Smith, J.D.1    McManus, K.F.2    Fraser, H.B.3
  • 2
    • 18144405733 scopus 로고    scopus 로고
    • The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
    • Denver, D. R. et al. The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature Genet. 37, 544-548 (2005).
    • (2005) Nature Genet. , vol.37 , pp. 544-548
    • Denver, D.R.1
  • 3
    • 69249205499 scopus 로고    scopus 로고
    • Climbing mount probable: Mutation as a cause of nonrandomness in evolution
    • Stoltzfus, A. & Yampolsky, L. Y. Climbing mount probable: mutation as a cause of nonrandomness in evolution. J. Hered. 100, 637-647 (2009).
    • (2009) J. Hered. , vol.100 , pp. 637-647
    • Stoltzfus, A.1    Yampolsky, L.Y.2
  • 4
    • 84859619180 scopus 로고    scopus 로고
    • A test for selection employing quantitative trait locus and mutation accumulation data
    • Rice, D. P. D. & Townsend, J. P. J. A test for selection employing quantitative trait locus and mutation accumulation data. Genetics 190, 1533-1545 (2012).
    • (2012) Genetics , vol.190 , pp. 1533-1545
    • Rice, D.P.D.1    Townsend, J.P.J.2
  • 5
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser, J. M. & O'Shea, E. K. Control of stochasticity in eukaryotic gene expression. Science 304, 1811-1814 (2004).
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 6
    • 0022385984 scopus 로고
    • Differential expression of the three yeast glyceraldehyde-3-phosphate dehydrogenase genes
    • McAlister, L. & Holland, M. J. Differential expression of the three yeast glyceraldehyde-3-phosphate dehydrogenase genes. J. Biol. Chem. 260, 15019-15027 (1985).
    • (1985) J. Biol. Chem. , vol.260 , pp. 15019-15027
    • McAlister, L.1    Holland, M.J.2
  • 7
    • 39149125171 scopus 로고    scopus 로고
    • Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures
    • Pierce, S. E., Davis, R. W., Nislow, C. & Giaever, G. Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nature Protocols 2, 2958-2974 (2007).
    • (2007) Nature Protocols , vol.2 , pp. 2958-2974
    • Pierce, S.E.1    Davis, R.W.2    Nislow, C.3    Giaever, G.4
  • 8
    • 84887313970 scopus 로고    scopus 로고
    • Yeast Tdh3 (glyceraldehyde 3-phosphate dehydrogenase) is a Sir2-interacting factor that regulates transcriptional silencing and rDNA recombination
    • Ringel, A. E. et al. Yeast Tdh3 (glyceraldehyde 3-phosphate dehydrogenase) is a Sir2-interacting factor that regulates transcriptional silencing and rDNA recombination. PLoS Genet. 9, e1003871 (2013).
    • (2013) PLoS Genet. , vol.9 , pp. e1003871
    • Ringel, A.E.1
  • 9
    • 84859208133 scopus 로고    scopus 로고
    • Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: Frequency, effects and dominance
    • Gruber, J. D., Vogel, K., Kalay, G. & Wittkopp, P. J. Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects and dominance. PLoS Genet. 8, e1002497 (2012).
    • (2012) PLoS Genet. , vol.8 , pp. e1002497
    • Gruber, J.D.1    Vogel, K.2    Kalay, G.3    Wittkopp, P.J.4
  • 10
    • 62649089109 scopus 로고    scopus 로고
    • Population genomics of domestic and wild yeasts
    • Liti, G. et al. Population genomics of domestic and wild yeasts. Nature 458, 337-341 (2009).
    • (2009) Nature , vol.458 , pp. 337-341
    • Liti, G.1
  • 11
    • 62649126517 scopus 로고    scopus 로고
    • Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae
    • Schacherer, J., Shapiro, J. A., Ruderfer, D. M. & Kruglyak, L. Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458, 342-345 (2009).
    • (2009) Nature , vol.458 , pp. 342-345
    • Schacherer, J.1    Shapiro, J.A.2    Ruderfer, D.M.3    Kruglyak, L.4
  • 12
    • 48249133274 scopus 로고    scopus 로고
    • A genome-wide view of the spectrum ofspontaneous mutations in yeast
    • Lynch, M. et al. A genome-wide view of the spectrum ofspontaneous mutations in yeast. Proc. Natl Acad. Sci. USA 105, 9272-9277 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 9272-9277
    • Lynch, M.1
  • 13
    • 71849118573 scopus 로고    scopus 로고
    • High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
    • Patwardhan, R. P. et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nature Biotechnol. 27, 1173-1175 (2009).
    • (2009) Nature Biotechnol. , vol.27 , pp. 1173-1175
    • Patwardhan, R.P.1
  • 14
    • 84863229330 scopus 로고    scopus 로고
    • Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
    • Melnikov, A. et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature Biotechnol. 30, 271-279 (2012).
    • (2012) Nature Biotechnol. , vol.30 , pp. 271-279
    • Melnikov, A.1
  • 15
    • 84863230316 scopus 로고    scopus 로고
    • Massively parallel functional dissection of mammalian enhancers in vivo
    • Patwardhan, R. P. et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnol. 30, 265-270 (2012).
    • (2012) Nature Biotechnol. , vol.30 , pp. 265-270
    • Patwardhan, R.P.1
  • 16
    • 84869853147 scopus 로고    scopus 로고
    • Complex effects of nucleotide variants in a mammalian cis-regulatory element
    • Kwasnieski, J. & Mogno, I. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc. Natl Acad. Sci. USA 109, 19498-19503 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 19498-19503
    • Kwasnieski, J.1    Mogno, I.2
  • 17
    • 0028411171 scopus 로고
    • The UAS of the yeast GAPDH promoter consists of multiple general functional elements including RAP1 and GRF2 binding sites
    • Yagi, S., Yagi, K., Fukuoka, J. & Suzuki, M. The UAS of the yeast GAPDH promoter consists of multiple general functional elements including RAP1 and GRF2 binding sites. J. Vet. Med. Sci. 56, 235-244 (1994).
    • (1994) J. Vet. Med. Sci. , vol.56 , pp. 235-244
    • Yagi, S.1    Yagi, K.2    Fukuoka, J.3    Suzuki, M.4
  • 18
    • 0026650525 scopus 로고
    • Characterization of the DNA-binding activity of GCR1: In vivo evidence for two GCR1-binding sitesinthe upstreamactivating sequenceofTPI of Saccharomyces cerevisiae
    • Baker, H. V. et al. Characterization of the DNA-binding activity of GCR1: in vivo evidence for two GCR1-binding sitesinthe upstreamactivating sequenceofTPI of Saccharomyces cerevisiae. Mol. Cell. Biol. 12, 2690-2700 (1992).
    • (1992) Mol. Cell. Biol. , vol.12 , pp. 2690-2700
    • Baker, H.V.1
  • 19
    • 84870562146 scopus 로고    scopus 로고
    • Noise-meanrelation shipinmutated promoters
    • Hornung, G. et al. Noise-meanrelation shipinmutated promoters. GenomeRes. 22, 2409-2417 (2012).
    • (2012) GenomeRes. , vol.22 , pp. 2409-2417
    • Hornung, G.1
  • 20
    • 42949131308 scopus 로고    scopus 로고
    • Selectionto minimise noise inliving systems and its implications for the evolution of gene expression
    • Lehner, B. Selectionto minimise noise inliving systems and its implications for the evolution of gene expression. Mol. Syst. Biol. 4, 1-6 (2008).
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 1-6
    • Lehner, B.1
  • 22
    • 79955613183 scopus 로고    scopus 로고
    • Impactofgeneexpressionnoiseonorganismalfitnessandthe efficacy of natural selection
    • Wang, Z. & Zhang, J. Impactofgeneexpressionnoiseonorganismalfitnessandthe efficacy of natural selection. Proc. Natl Acad. Sci. USA 108, E67-E76 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. E67-E76
    • Wang, Z.1    Zhang, J.2
  • 23
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S. Cerevisiae reveals the architecture of biological noise
    • Newman, J. R. S. et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840-846 (2006).
    • (2006) Nature , vol.441 , pp. 840-846
    • Newman, J.R.S.1
  • 24
    • 34547519199 scopus 로고    scopus 로고
    • Evolution of chromosome organization driven by selection for reduced gene expression noise
    • Batada, N. & Hurst, L. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nature Genet. 39, 945-949 (2007).
    • (2007) Nature Genet. , vol.39 , pp. 945-949
    • Batada, N.1    Hurst, L.2
  • 25
    • 69249106061 scopus 로고    scopus 로고
    • Positive selection for elevated gene expression noise in yeast
    • Zhang, Z., Qian, W. & Zhang, J. Positive selection for elevated gene expression noise in yeast. Mol. Syst. Biol. 5, 1-12 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 1-12
    • Zhang, Z.1    Qian, W.2    Zhang, J.3
  • 26
    • 77954960062 scopus 로고    scopus 로고
    • Phenotypic robustness conferred by apparently redundant transcriptional enhancers
    • Frankel, N. et al. Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466, 1-5 (2010).
    • (2010) Nature , vol.466 , pp. 1-5
    • Frankel, N.1
  • 27
    • 77956521381 scopus 로고    scopus 로고
    • Shadow enhancers foster robustness of Drosophila gastrulation
    • Perry, M. W., Boettiger, A. N., Bothma, J. P. & Levine, M. Shadow enhancers foster robustness of Drosophila gastrulation. Curr. Biol. 20, 1562-1567 (2010).
    • (2010) Curr. Biol. , vol.20 , pp. 1562-1567
    • Perry, M.W.1    Boettiger, A.N.2    Bothma, J.P.3    Levine, M.4
  • 28
    • 0028003496 scopus 로고
    • The arrival of the fittest: Toward a theory of biological organization
    • Fontana, W. & Buss, L. ''The arrival of the fittest'': toward a theory of biological organization. Bull. Math. Biol. 56, 1-64 (1994).
    • (1994) Bull. Math. Biol. , vol.56 , pp. 1-64
    • Fontana, W.1    Buss, L.2
  • 30
    • 80054796108 scopus 로고    scopus 로고
    • Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures
    • Taly, J.-F. et al. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nature Protocols 6, 1669-1682 (2011).
    • (2011) Nature Protocols , vol.6 , pp. 1669-1682
    • Taly, J.-F.1
  • 31
    • 78649319201 scopus 로고    scopus 로고
    • WebPRANK: A phylogeny-aware multiple sequence aligner with interactive alignment browser
    • Löytynoja, A. & Goldman, N. webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinform. 11, 579 (2010).
    • (2010) BMC Bioinform. , vol.11 , pp. 579
    • Löytynoja, A.1    Goldman, N.2
  • 32
    • 80052293238 scopus 로고    scopus 로고
    • Microbe domestication and the identification of the wild genetic stockoflager-brewing yeast
    • Libkind, D. et al. Microbe domestication and the identification of the wild genetic stockoflager-brewing yeast. Proc. Natl Acad. Sci. USA108, 14539-14544 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 14539-14544
    • Libkind, D.1
  • 33
    • 84883006832 scopus 로고    scopus 로고
    • The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus
    • Scannell, D. R. et al. The awesome power of yeast evolutionary genetics: new genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3 1, 11-25 (2011).
    • (2011) G3 , vol.1 , pp. 11-25
    • Scannell, D.R.1
  • 34
    • 84873036642 scopus 로고    scopus 로고
    • High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome
    • Liti, G. et al. High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genom. 14, 69 (2013).
    • (2013) BMC Genom. , vol.14 , pp. 69
    • Liti, G.1
  • 35
    • 84868206362 scopus 로고    scopus 로고
    • Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity
    • Wang, Q.-M., Liu, W.-Q., Liti, G., Wang, S.-A. & Bai, F.-Y. Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol. Ecol. 21, 5404-5417 (2012).
    • (2012) Mol. Ecol. , vol.21 , pp. 5404-5417
    • Wang, Q.-M.1    Liu, W.-Q.2    Liti, G.3    Wang, S.-A.4    Bai, F.-Y.5
  • 37
    • 0033771358 scopus 로고    scopus 로고
    • TCS: A computer program to estimate gene genealogies
    • Clement, M., Posada, D. & Crandall, K. A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9, 1657-1659 (2000).
    • (2000) Mol. Ecol. , vol.9 , pp. 1657-1659
    • Clement, M.1    Posada, D.2    Crandall, K.A.3
  • 38
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: Calculating evolutionary conservationinsequence and structureofproteins and nucleic acids
    • Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservationinsequence and structureofproteins and nucleic acids. Nucleic Acids Res. 38, W529-W533 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. W529-W533
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5
  • 39
    • 84876783002 scopus 로고    scopus 로고
    • Saccharomyces diversity and evolution: A budding model genus
    • Hittinger, C. T. Saccharomyces diversity and evolution: a budding model genus. Trends Genet. 29, 309-317 (2013).
    • (2013) Trends Genet. , vol.29 , pp. 309-317
    • Hittinger, C.T.1
  • 40
    • 3042722019 scopus 로고    scopus 로고
    • Evolutionary changes in cis and trans gene regulation
    • Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Evolutionary changes in cis and trans gene regulation. Nature 430, 85-88 (2004).
    • (2004) Nature , vol.430 , pp. 85-88
    • Wittkopp, P.J.1    Haerum, B.K.2    Clark, A.G.3
  • 43
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla, G., Murray, A., Tollervey, D. & Plotkin, J. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255-258 (2009).
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.2    Tollervey, D.3    Plotkin, J.4
  • 44
    • 67649488081 scopus 로고    scopus 로고
    • FlowClust: A Bioconductor package for automated gating of flow cytometry data
    • Lo, K., Hahne, F., Brinkman, R. R. & Gottardo, R. flowClust: a Bioconductor package for automated gating of flow cytometry data. BMC Bioinform. 10, 145 (2009).
    • (2009) BMC Bioinform. , vol.10 , pp. 145
    • Lo, K.1    Hahne, F.2    Brinkman, R.R.3    Gottardo, R.4
  • 45
    • 65949097067 scopus 로고    scopus 로고
    • FlowCore: A Bioconductor package for high throughput flow cytometry
    • Hahne, F. et al. flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinform. 10, 106 (2009).
    • (2009) BMC Bioinform. , vol.10 , pp. 106
    • Hahne, F.1


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