메뉴 건너뛰기




Volumn 41, Issue 4, 2013, Pages

Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; ESTRADIOL; ESTROGEN RECEPTOR; HISTIDINE; PROTEIN VP16; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GAL4; TRANSCRIPTION FACTOR GCN4; TRANSCRIPTION FACTOR ZIF268; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

EID: 84876379604     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1313     Document Type: Article
Times cited : (122)

References (46)
  • 1
    • 84864751449 scopus 로고    scopus 로고
    • Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway
    • McIsaac, R.S., Petti, A.A., Bussemaker, H.J. and Botstein, D. (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol. Biol. Cell., 23, 2993-3007.
    • (2012) Mol. Biol. Cell. , vol.23 , pp. 2993-3007
    • McIsaac, R.S.1    Petti, A.A.2    Bussemaker, H.J.3    Botstein, D.4
  • 2
    • 80655144718 scopus 로고    scopus 로고
    • Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast
    • Hickman, M.J., Petti, A.A., Ho-Shing, O., Silverman, S.J., McIsaac, R.S., Lee, T.A. and Botstein, D. (2011) Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast. Mol. Biol. Cell., 22, 4192-4204.
    • (2011) Mol. Biol. Cell. , vol.22 , pp. 4192-4204
    • Hickman, M.J.1    Petti, A.A.2    Ho-Shing, O.3    Silverman, S.J.4    McIsaac, R.S.5    Lee, T.A.6    Botstein, D.7
  • 3
    • 0026778048 scopus 로고
    • Foreign gene expression in yeast: A review
    • Romanos, M.A., Scorer, C.A. and Clare, J.J. (1992) Foreign gene expression in yeast: a review. Yeast, 8, 423-488.
    • (1992) Yeast , vol.8 , pp. 423-488
    • Romanos, M.A.1    Scorer, C.A.2    Clare, J.J.3
  • 4
    • 0032785638 scopus 로고    scopus 로고
    • Copper ion inducible and repressible promoter systems in yeast
    • Labbe, S. and Thiele, D.J. (1999) Copper ion inducible and repressible promoter systems in yeast. Expr. Recombin. Genes Eukary. Sys., 306, 145-153.
    • (1999) Expr. Recombin. Genes Eukary. Sys. , vol.306 , pp. 145-153
    • Labbe, S.1    Thiele, D.J.2
  • 5
    • 0030838041 scopus 로고    scopus 로고
    • Use of conditional promoters for expression of heterologous proteins in Saccharomyces cerevisiae
    • Ronicke, V., Graulich, W., Mumberg, D., Muller, R. and Funk, M. (1997) Use of conditional promoters for expression of heterologous proteins in Saccharomyces cerevisiae. Cell Cycle Control, 283, 313-322.
    • (1997) Cell Cycle Control , vol.283 , pp. 313-322
    • Ronicke, V.1    Graulich, W.2    Mumberg, D.3    Muller, R.4    Funk, M.5
  • 6
    • 0032519306 scopus 로고    scopus 로고
    • An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast
    • Belli, G., Gari, E., Piedrafita, L., Aldea, M. and Herrero, E. (1998) An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. Nucleic Acids Res., 26, 942-947.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 942-947
    • Belli, G.1    Gari, E.2    Piedrafita, L.3    Aldea, M.4    Herrero, E.5
  • 8
    • 78649301379 scopus 로고    scopus 로고
    • RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 30-end processing in Saccharomyces cerevisiae
    • Alexander, R.D., Barrass, J.D., Dichtl, B., Kos, M., Obtulowicz, T., Robert, M.C., Koper, M., Karkusiewicz, I., Mariconti, L., Tollervey, D. et al. (2010) RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 30-end processing in Saccharomyces cerevisiae. RNA, 16, 2570-2580.
    • (2010) RNA , vol.16 , pp. 2570-2580
    • Alexander, R.D.1    Barrass, J.D.2    Dichtl, B.3    Kos, M.4    Obtulowicz, T.5    Robert, M.C.6    Koper, M.7    Karkusiewicz, I.8    Mariconti, L.9    Tollervey, D.10
  • 10
    • 0027240004 scopus 로고
    • Fusion of GAL4-VP16 to a steroid-binding domain provides a tool for gratuitous induction of galactose-responsive genes in yeast
    • Louvion, J.F., Havaux-Copf, B. and Picard, D. (1993) Fusion of GAL4-VP16 to a steroid-binding domain provides a tool for gratuitous induction of galactose-responsive genes in yeast. Gene, 131, 129-134.
    • (1993) Gene , vol.131 , pp. 129-134
    • Louvion, J.F.1    Havaux-Copf, B.2    Picard, D.3
  • 12
    • 77952280117 scopus 로고    scopus 로고
    • The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation
    • Klug, A. (2010) The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Quart. Rev. Biophys., 43, 1-21.
    • (2010) Quart. Rev. Biophys. , vol.43 , pp. 1-21
    • Klug, A.1
  • 13
    • 0028328872 scopus 로고
    • Zinc finger phage: Affinity selection of fingers with new DNA-binding specificities
    • Rebar, E.J. and Pabo, C.O. (1994) Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science, 263, 671-673.
    • (1994) Science , vol.263 , pp. 671-673
    • Rebar, E.J.1    Pabo, C.O.2
  • 14
    • 0034691202 scopus 로고    scopus 로고
    • A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions
    • Joung, J.K., Ramm, E.I. and Pabo, C.O. (2000) A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc. Natl Acad. Sci. USA, 97, 7382-7387.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 7382-7387
    • Joung, J.K.1    Ramm, E.I.2    Pabo, C.O.3
  • 15
    • 0032981699 scopus 로고    scopus 로고
    • Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 50-GNN-30 DNA target sequences
    • Segal, D.J., Dreier, B., Beerli, R.R. and Barbas, C.F. 3rd (1999) Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 50-GNN-30 DNA target sequences. Proc. Natl Acad. Sci. USA, 96, 2758-2763.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 2758-2763
    • Segal, D.J.1    Dreier, B.2    Beerli, R.R.3    Barbas Iii, C.F.4
  • 17
    • 0033524954 scopus 로고    scopus 로고
    • Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
    • Wolfe, S.A., Greisman, H.A., Ramm, E.I. and Pabo, C.O. (1999) Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol., 285, 1917-1934.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1917-1934
    • Wolfe, S.A.1    Greisman, H.A.2    Ramm, E.I.3    Pabo, C.O.4
  • 18
    • 0034693062 scopus 로고    scopus 로고
    • Chemically regulated zinc finger transcription factors
    • Beerli, R.R., Schopfer, U., Dreier, B. and Barbas, C.F. 3rd (2000) Chemically regulated zinc finger transcription factors. J. Biol. Chem., 275, 32617-32627.
    • (2000) J. Biol. Chem. , vol.275 , pp. 32617-32627
    • Beerli, R.R.1    Schopfer, U.2    Dreier, B.3    Barbas Iii, C.F.4
  • 19
    • 0034988731 scopus 로고    scopus 로고
    • A versatile framework for the design of ligand-dependent, transgene-specific transcription factors
    • Xu, L., Zerby, D., Huang, Y., Ji, H., Nyanguile, O.F., de los Angeles, J.E. and Kadan, M.J. (2001) A versatile framework for the design of ligand-dependent, transgene-specific transcription factors. Mol. Ther., 3, 262-273.
    • (2001) Mol. Ther. , vol.3 , pp. 262-273
    • Xu, L.1    Zerby, D.2    Huang, Y.3    Ji, H.4    Nyanguile, O.F.5    De Los Angeles, J.E.6    Kadan, M.J.7
  • 22
    • 34248559599 scopus 로고    scopus 로고
    • Gene splicing and mutagenesis by PCR-driven overlap extension
    • Heckman, K.L. and Pease, L.R. (2007) Gene splicing and mutagenesis by PCR-driven overlap extension. Nat. Protocols, 2, 924-932.
    • (2007) Nat. Protocols , vol.2 , pp. 924-932
    • Heckman, K.L.1    Pease, L.R.2
  • 23
    • 84864751060 scopus 로고    scopus 로고
    • Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway
    • Petti, A.A., McIsaac, R.S., Ho-Shing, O., Bussemaker, H.J. and Botstein, D. (2012) Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Mol. Biol. Cell., 23, 3008-3024.
    • (2012) Mol. Biol. Cell. , vol.23 , pp. 3008-3024
    • Petti, A.A.1    McIsaac, R.S.2    Ho-Shing, O.3    Bussemaker, H.J.4    Botstein, D.5
  • 24
    • 80655136471 scopus 로고    scopus 로고
    • Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function
    • Petti, A.A., Crutchfield, C.A., Rabinowitz, J.D. and Botstein, D. (2011) Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc. Natl Acad. Sci. USA, 108, E1089-E1098.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108
    • Petti, A.A.1    Crutchfield, C.A.2    Rabinowitz, J.D.3    Botstein, D.4
  • 25
    • 32444450670 scopus 로고    scopus 로고
    • Development Core Team R, Vienna, Austria, Vienna, Austria
    • Development Core Team, R. (2009) R Foundation for Statistical Computing, Vienna, Austria, Vienna, Austria.
    • (2009) R Foundation for Statistical Computing
  • 28
    • 0035024021 scopus 로고    scopus 로고
    • Validating clustering for gene expression data
    • Yeung, K.Y., Haynor, D.R. and Ruzzo, W.L. (2001) Validating clustering for gene expression data. Bioinformatics, 17, 309-318.
    • (2001) Bioinformatics , vol.17 , pp. 309-318
    • Yeung, K.Y.1    Haynor, D.R.2    Ruzzo, W.L.3
  • 33
    • 80555139629 scopus 로고    scopus 로고
    • Analysis of specific protein-DNA interactions by bacterial one-hybrid assay
    • Noyes, M.B. (2012) Analysis of specific protein-DNA interactions by bacterial one-hybrid assay. Methods Mol. Biol., 786, 79-95.
    • (2012) Methods Mol. Biol. , vol.786 , pp. 79-95
    • Noyes, M.B.1
  • 34
    • 43349107222 scopus 로고    scopus 로고
    • A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system
    • Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H. and Wolfe, S.A. (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res., 36, 2547-2560.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2547-2560
    • Noyes, M.B.1    Meng, X.2    Wakabayashi, A.3    Sinha, S.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 36
    • 0035914475 scopus 로고    scopus 로고
    • Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition
    • Miller, J.C. and Pabo, C.O. (2001) Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. J. Mol. Biol., 313, 309-315.
    • (2001) J. Mol. Biol. , vol.313 , pp. 309-315
    • Miller, J.C.1    Pabo, C.O.2
  • 37
    • 0020572457 scopus 로고
    • Positive regulation in the general amino acid control of Saccharomyces cerevisiae
    • Hinnebusch, A.G. and Fink, G.R. (1983) Positive regulation in the general amino acid control of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 80, 5374-5378.
    • (1983) Proc. Natl Acad. Sci. USA , vol.80 , pp. 5374-5378
    • Hinnebusch, A.G.1    Fink, G.R.2
  • 39
    • 35348955882 scopus 로고    scopus 로고
    • A universal framework for regulatory element discovery across all genomes and data types
    • Elemento, O., Slonim, N. and Tavazoie, S. (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell, 28, 337-350.
    • (2007) Mol. Cell , vol.28 , pp. 337-350
    • Elemento, O.1    Slonim, N.2    Tavazoie, S.3
  • 40
    • 77956126894 scopus 로고    scopus 로고
    • Xanthomonas AvrBs3 family-type III effectors: Discovery and function
    • Boch, J. and Bonas, U. (2010) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu. Rev. Phytopathol., 48, 419-436.
    • (2010) Annu. Rev. Phytopathol. , vol.48 , pp. 419-436
    • Boch, J.1    Bonas, U.2
  • 41
    • 72149090954 scopus 로고    scopus 로고
    • A simple cipher governs DNA recognition by TAL effectors
    • Moscou, M.J. and Bogdanove, A.J. (2009) A simple cipher governs DNA recognition by TAL effectors. Science, 326, 1501.
    • (2009) Science , vol.326 , pp. 1501
    • Moscou, M.J.1    Bogdanove, A.J.2
  • 43
    • 84867300642 scopus 로고    scopus 로고
    • Engineering synthetic TAL effectors with orthogonal target sites
    • Garg, A., Lohmueller, J.J., Silver, P.A. and Armel, T.Z. (2012) Engineering synthetic TAL effectors with orthogonal target sites. Nucleic Acids Res., 40, 7584-7595.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 7584-7595
    • Garg, A.1    Lohmueller, J.J.2    Silver, P.A.3    Armel, T.Z.4
  • 45
    • 80053347082 scopus 로고    scopus 로고
    • Light-based feedback for controlling intracellular signaling dynamics
    • Toettcher, J.E., Gong, D., Lim, W.A. and Weiner, O.D. (2011) Light-based feedback for controlling intracellular signaling dynamics. Nat. Methods, 8, 837-839.
    • (2011) Nat. Methods , vol.8 , pp. 837-839
    • Toettcher, J.E.1    Gong, D.2    Lim, W.A.3    Weiner, O.D.4
  • 46
    • 73349085934 scopus 로고    scopus 로고
    • An auxin-based degron system for the rapid depletion of proteins in nonplant cells
    • Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. and Kanemaki, M. (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods, 6, 917-922.
    • (2009) Nat. Methods , vol.6 , pp. 917-922
    • Nishimura, K.1    Fukagawa, T.2    Takisawa, H.3    Kakimoto, T.4    Kanemaki, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.