Msn2 coordinates a stoichiometric gene expression program

Current Biology

Volumn 23, Issue 23, 2013, Pages 2336-2345

  Stewart Ornstein, Jacob ^a,b,c,d   Nelson, Christopher ^a,c   Derisi, Joe ^a,c   Weissman, Jonathan S ^b,c,d   El Samad, Hana ^a,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 2; DNA BINDING PROTEIN; MSN2 PROTEIN, S CEREVISIAE; RIBOSOME PROTEIN; RPS22A PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BIOLOGY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGICAL STRESS; PROMOTER REGION; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE;

BASE SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; CYCLIC NUCLEOTIDE PHOSPHODIESTERASES, TYPE 2; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; RIBOSOMAL PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS, DNA; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84889582936     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2013.09.043     Document Type: Article

References (40)

1. A.P. Gasch, P.T. Spellman, C.M. Kao, O. Carmel-Harel, M.B. Eisen, G. Storz, D. Botstein, and P.O. Brown Genomic expression programs in the response of yeast cells to environmental changes Mol. Biol. Cell 11 2000 4241 4257
2. I. Tirosh, A. Weinberger, M. Carmi, and N. Barkai A genetic signature of interspecies variations in gene expression Nat. Genet. 38 2006 830 834
3. D.P. Sangurdekar, F. Srienc, and A.B. Khodursky A classification based framework for quantitative description of large-scale microarray data Genome Biol. 7 2006 R32
4. A. Colman-Lerner, A. Gordon, E. Serra, T. Chin, O. Resnekov, D. Endy, C.G. Pesce, and R. Brent Regulated cell-to-cell variation in a cell-fate decision system Nature 437 2005 699 706
5. S. Takahashi, and P.M. Pryciak Membrane localization of scaffold proteins promotes graded signaling in the yeast MAP kinase cascade Curr. Biol. 18 2008 1184 1191
6. K.W. Rogers, and A.F. Schier Morphogen gradients: from generation to interpretation Annu. Rev. Cell Dev. Biol. 27 2011 377 407
7. L. Giorgetti, T. Siggers, G. Tiana, G. Caprara, S. Notarbartolo, T. Corona, M. Pasparakis, P. Milani, M.L. Bulyk, and G. Natoli Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs Mol. Cell 37 2010 418 428
8. L. Cai, C.K. Dalal, and M.B. Elowitz Frequency-modulated nuclear localization bursts coordinate gene regulation Nature 455 2008 485 490
9. J.R. Broach Nutritional control of growth and development in yeast Genetics 192 2012 73 105
10. E. Boy-Marcotte, C. Garmendia, H. Garreau, S. Lallet, L. Mallet, and M. Jacquet The transcriptional activation region of Msn2p, in Saccharomyces cerevisiae, is regulated by stress but is insensitive to the cAMP signalling pathway Mol. Genet. Genomics 275 2006 277 287
11. C. Zhu, K.J. Byers, R.P. McCord, Z. Shi, M.F. Berger, D.E. Newburger, K. Saulrieta, Z. Smith, M.V. Shah, and M. Radhakrishnan High-resolution DNA-binding specificity analysis of yeast transcription factors Genome Res. 19 2009 556 566
12. D.J. Huebert, P.F. Kuan, S. Keleş, and A.P. Gasch Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators Mol. Cell. Biol. 32 2012 1645 1653
13. A.P. Capaldi, T. Kaplan, Y. Liu, N. Habib, A. Regev, N. Friedman, and E.K. O'Shea Structure and function of a transcriptional network activated by the MAPK Hog1 Nat. Genet. 40 2008 1300 1306
14. N. Hao, and E.K. O'Shea Signal-dependent dynamics of transcription factor translocation controls gene expression Nat. Struct. Mol. Biol. 19 2012 31 39
15. W. Görner, E. Durchschlag, M.T. Martinez-Pastor, F. Estruch, G. Ammerer, B. Hamilton, H. Ruis, and C. Schüller Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity Genes Dev. 12 1998 586 597
16. J. Stewart-Ornstein, J.S. Weissman, and H. El-Samad Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae Mol. Cell 45 2012 483 493
17. T. Raveh-Sadka, M. Levo, U. Shabi, B. Shany, L. Keren, M. Lotan-Pompan, D. Zeevi, E. Sharon, A. Weinberger, and E. Segal Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast Nat. Genet. 44 2012 743 750
18. Y. Chi, M.J. Huddleston, X. Zhang, R.A. Young, R.S. Annan, S.A. Carr, and R.J. Deshaies Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase Genes Dev. 15 2001 1078 1092
19. E. Durchschlag, W. Reiter, G. Ammerer, and C. Schüller Nuclear localization destabilizes the stress-regulated transcription factor Msn2 J. Biol. Chem. 279 2004 55425 55432
20. S. Ghaemmaghami, W.K. Huh, K. Bower, R.W. Howson, A. Belle, N. Dephoure, E.K. O'Shea, and J.S. Weissman Global analysis of protein expression in yeast Nature 425 2003 737 741
21. P.M. Fordyce, D. Gerber, D. Tran, J. Zheng, H. Li, J.L. DeRisi, and S.R. Quake De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis Nat. Biotechnol. 28 2010 970 975
22. S.J. Maerkl, and S.R. Quake A systems approach to measuring the binding energy landscapes of transcription factors Science 315 2007 233 237
23. D.S. Wuttke, M.P. Foster, D.A. Case, J.M. Gottesfeld, and P.E. Wright Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity J. Mol. Biol. 273 1997 183 206
24. B.E. Bernstein, R.C. Hoffman, S. Horvath, J.R. Herriott, and R.E. Klevit Structure of a histidine-X4-histidine zinc finger domain: insights into ADR1-UAS1 protein-DNA recognition Biochemistry 33 1994 4460 4470
25. J.H. Laity, H.J. Dyson, and P.E. Wright DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers J. Mol. Biol. 295 2000 719 727
26. M. Kochoyan, H.T. Keutmann, and M.A. Weiss Alternating zinc fingers in the human male-associated protein ZFY: HX3H and HX4H motifs encode a local structural switch Biochemistry 30 1991 9396 9402
27. C.T. Harbison, D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, and J. Yoo Transcriptional regulatory code of a eukaryotic genome Nature 431 2004 99 104
28. D.J. Segal, B. Dreier, R.R. Beerli, and C.F. Barbas 3rd Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences Proc. Natl. Acad. Sci. USA 96 1999 2758 2763
29. H.S. Rhee, and B.F. Pugh Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution Cell 147 2011 1408 1419
30. F. Spitz, and E.E.M. Furlong Transcription factors: from enhancer binding to developmental control Nat. Rev. Genet. 13 2012 613 626
31. T. Gregor, E.F. Wieschaus, A.P. McGregor, W. Bialek, and D.W. Tank Stability and nuclear dynamics of the bicoid morphogen gradient Cell 130 2007 141 152
32. R.C. Yu, C.G. Pesce, A. Colman-Lerner, L. Lok, D. Pincus, E. Serra, M. Holl, K. Benjamin, A. Gordon, and R. Brent Negative feedback that improves information transmission in yeast signalling Nature 456 2008 755 761
33. A. Sadeh, N. Movshovich, M. Volokh, L. Gheber, and A. Aharoni Fine-tuning of the Msn2/4-mediated yeast stress responses as revealed by systematic deletion of Msn2/4 partners Mol. Biol. Cell 22 2011 3127 3138
34. X. Wang, H. Xu, S.W. Ha, D. Ju, and Y. Xie Proteasomal degradation of Rpn4 in Saccharomyces cerevisiae is critical for cell viability under stressed conditions Genetics 184 2010 335 342
35. G. Lahav, N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A.J. Levine, M.B. Elowitz, and U. Alon Dynamics of the p53-Mdm2 feedback loop in individual cells Nat. Genet. 36 2004 147 150
36. I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev Natural history and evolutionary principles of gene duplication in fungi Nature 449 2007 54 61
37. I. Tirosh, K.H. Wong, N. Barkai, and K. Struhl Extensive divergence of yeast stress responses through transitions between induced and constitutive activation Proc. Natl. Acad. Sci. USA 108 2011 16693 16698
38. N. Rhind, Z. Chen, M. Yassour, D.A. Thompson, B.J. Haas, N. Habib, I. Wapinski, S. Roy, M.F. Lin, and D.I. Heiman Comparative functional genomics of the fission yeasts Science 332 2011 930 936
39. U. Eser, M. Falleur-Fettig, A. Johnson, and J.M. Skotheim Commitment to a cellular transition precedes genome-wide transcriptional change Mol. Cell 43 2011 515 527
40. P.M. Fordyce, D. Pincus, P. Kimmig, C.S. Nelson, H. El-Samad, P. Walter, and J.L. DeRisi Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses Proc. Natl. Acad. Sci. USA 109 2012 E3084 E3093