Signal-dependent dynamics of transcription factor translocation controls gene expression

Nature Structural and Molecular Biology

Volumn 19, Issue 1, 2012, Pages 31-40

  Hao, Nan ^a,b   O'Shea, Erin K ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MSN2; UNCLASSIFIED DRUG;

AMPLITUDE MODULATION; ARTICLE; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; GENE TRANSLOCATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

ALGORITHMS; CELL NUCLEUS; CYTOPLASM; DNA-BINDING PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; KINETICS; LUMINESCENT PROTEINS; MICROSCOPY, FLUORESCENCE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; SINGLE-CELL ANALYSIS; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS;

SACCHAROMYCES CEREVISIAE;

EID: 84855424553     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2192     Document Type: Article

References (31)

1. Shaywitz, A.J. & Greenberg, M.E. CREB: a stimulus-induced transcription factor activated by a diverse array of extracellular signals. Annu. Rev. Biochem. 68, 821-861 (1999). (Pubitemid 29449210)
2. Hao, N., Zeng, Y., Elston, T.C. & Dohlman, H.G. Control of MAPK specificity by feedback phosphorylation of shared adaptor protein Ste50. J. Biol. Chem. 283, 33798-33802 (2008).
3. Skalhegg, B.S. & Tasken, K. Specificity in the cAMP/PKA signaling pathway. Differential expression, regulation, and subcellular localization of subunits of PKA. Front. Biosci. 5, D678-D693 (2000).
4. Behar, M. & Hoffmann, A. Understanding the temporal codes of intra-cellular signals. Curr. Opin. Genet. Dev. 20, 684-693 (2010).
5. Hoffmann, A., Levchenko, A., Scott, M.L. & Baltimore, D. The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298, 1241-1245 (2002). (Pubitemid 35285493)
6. Lee, T.K.et al. A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Sci. Signal. 2, ra65 (2009).
7. Ashall, L.et al. Pulsatile stimulation determines timing and specificity of NF-kappaB-dependent transcription. Science 324, 242-246 (2009).
8. Tay, S.et al. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466, 267-271 (2010).
9. Cai, L., Dalal, C.K. & Elowitz, M.B. Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455, 485-490 (2008).
10. Martínez-Pastor, M.T.et al. The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J. 15, 2227-2235 (1996). (Pubitemid 26141139)
11. Schmitt, A.P. & McEntee, K. Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 93, 5777-5782 (1996). (Pubitemid 26190756)
12. Görner, W.et al. Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev. 12, 586-597 (1998). (Pubitemid 28101020)
13. Görner, W.et al. Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor. EMBO J. 21, 135-144 (2002). (Pubitemid 34087082)
14. Hersen, P., McClean, M.N., Mahadevan, L. & Ramanathan, S. Signal processing by the HOG MAP kinase pathway. Proc. Natl. Acad. Sci. USA 105, 7165-7170 (2008). (Pubitemid 351754449)
15. Jacquet, M., Renault, G., Lallet, S., De Mey, J. & Goldbeter, A. Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae. J. Cell Biol. 161, 497-505 (2003). (Pubitemid 36578575)
16. Medvedik, O., Lamming, D.W., Kim, K.D. & Sinclair, D.A. MSN2 and MSN4 link calorie restriction and TOR to sirtuin-mediated lifespan extension in Saccharomyces cerevisiae. PLoS Biol. 5, e261 (2007).
17. Bishop, A.C.et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407, 395-401 (2000).
18. Sheff, M.A. & Thorn, K.S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 21, 661-670 (2004). (Pubitemid 38868184)
19. Shenton, D.et al. Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J. Biol. Chem. 281, 29011-29021 (2006). (Pubitemid 44507045)
20. Kim, H.D. & O'Shea, E.K. A quantitative model of transcription factor-activated gene expression. Nat. Struct. Mol. Biol. 15, 1192-1198 (2008).
21. Jessen, W.J., Hoose, S.A., Kilgore, J.A. & Kladde, M.P. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat. Struct. Mol. Biol. 13, 256-263 (2006). (Pubitemid 43348512)
22. Lam, F.H., Steger, D.J. & O'Shea, E.K. Chromatin decouples promoter threshold from dynamic range. Nature 453, 246-250 (2008). (Pubitemid 351667976)
23. Marshall, C.J. Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80, 179-185 (1995).
24. Giorgetti, L.et al. Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol. Cell 37, 418-428 (2010).
25. Geva-Zatorsky, N.et al. Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 2006.0033 (2006).
26. Loewer, A., Batchelor, E., Gaglia, G. & Lahav, G. Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling cells. Cell 142, 89-100 (2010).
27. Werner, S.L., Barken, D. & Hoffmann, A. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science 309, 1857-1861 (2005). (Pubitemid 41325096)
28. Hao, N.et al. Regulation of cell signaling dynamics by the protein kinase-scaffold Ste5. Mol. Cell 30, 649-656 (2008). (Pubitemid 351755062)
29. Capaldi, A.P.et al. Structure and function of a transcriptional network activated by the MAPK Hog1. Nat. Genet. 40, 1300-1306 (2008).
30. Zhou, X. & O'Shea, E.K. Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol. Cell 42, 826-836 (2011).
31. Gasch, A.P.et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257 (2000).