The chemistry of regulation of genes and other things

Journal of Biological Chemistry

Volumn 289, Issue 9, 2014, Pages 5417-5435

  Ptashne, Mark ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

AMINO TERMINAL SEQUENCE; BINDING SITE; BIOCHEMISTRY; DNA BINDING; DNA HELIX; DNA SEQUENCE; EUKARYOTE; FUNGAL GENE; GAL GENE; GAL4 GENE; GENE; GENE EXPRESSION; GENE FUNCTION; GENE INDUCTION; GENE ISOLATION; GENE PRODUCT; GENE SWITCHING; GENETIC REGULATION; HUMAN; KIT GENE; LYSOGENIZATION; MAMMAL CELL; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REPRESSOR GENE; REVIEW; TRANSCRIPTION REGULATION;

ACTIVATORS; COOPERATIVITY; DNA-BINDING PROTEIN; GENE REGULATION; GENETIC SWITCH; NUCLEOSOME; RECRUITMENT; REPRESSORS; SPECIFICITY; TRANSCRIPTION;

ANIMALS; GENE EXPRESSION REGULATION; HUMANS;

EID: 84895114683     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.X114.547323     Document Type: Review

References (105)

1. Ptashne, M. (2004) A Genetic Switch: Phage Lambda Revisited, 3rd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
2. Ptashne, M., and Gann, A. (2002) Genes & Signals, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
3. Ptashne, M. (2013) François Jacob (1920-2013). Cell 153, 1180-1182
4. Ptashne, M. (1967) Isolation of the λ phage repressor. Proc. Natl. Acad. Sci. U.S.A. 57, 306-313
5. Ptashne, M. (1967) Specific binding of the lambda phage repressor to lambda DNA. Nature 214, 232-234
6. Pirrotta, V., and Ptashne, M. (1969) Isolation of the 434 phage repressor. Nature 222, 541-544
7. Steinberg, R. A., and Ptashne, M. (1971) In vitro repression of RNA synthesis by purified lambda phage repressor. Nat. New Biol. 230, 76-80
8. Gilbert, W., and Müller-Hill, B. (1966) Isolation of the Lac repressor. Proc. Natl. Acad. Sci. U.S.A. 56, 1891-1898
9. Gilbert, W., and Müller-Hill, B. (1967) The lac operator is DNA. Proc. Natl. Acad. Sci. U.S.A. 58, 2415-2421
10. Maniatis, T., and Ptashne, M. (1973) Multiple repressor binding at the operators in bacteriophage λ. Proc. Natl. Acad. Sci. U.S.A. 70, 1531-1535
11. Anderson, W. F., Ohlendorf, D. H., Takeda, Y., and Matthews, B. W. (1981) Structure of the cro repressor from bacteriophage λ and its interaction with DNA. Nature 290, 754-758 (Pubitemid 11068043)
12. Pabo, C. O., and Lewis, M. (1982) The operator-binding domain of λ repressor: structure and DNA recognition. Nature 298, 443-447 (Pubitemid 12095621)
13. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M., and Harrison, S. C. (1988) Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 899-907
14. Wharton, R. P., and Ptashne, M. (1985) Changing the binding specificity of a repressor by redesigning an α-helix. Nature 316, 601-605 (Pubitemid 16238377)
15. Sauer, R. T., Yocum, R. R., Doolittle, R. F., Lewis, M., and Pabo, C. O. (1982) Homology among DNA-binding proteins suggests use of a conserved super-secondary structure. Nature 298, 447-451 (Pubitemid 12095622)
16. Laughon, A., and Scott, M. P. (1984) Sequence of a Drosophila segmentation gene: protein structure homology with DNA-binding proteins. Nature 310, 25-31 (Pubitemid 14077858)
17. Chadwick, P., Pirrotta, V., Steinberg, R., Hopkins, N., and Ptashne, M. (1970) The λ and 434 phage repressors. Cold Spring Harb. Symp. Quant. Biol. XXXV, 283-294
18. Pirrotta, V., Chadwick, P., and Ptashne, M. (1970) Active form of two coliphage repressors. Nature 227, 41-44
19. Maniatis, T., and Ptashne, M. (1973) Structure of the λ operators. Nature 246, 133-136
20. Maniatis, T., Ptashne, M., Backman, K., Kield, D., Flashman, S., Jeffrey, A., and Maurer, R. (1975) Recognition sequences of repressor and polymerase in the operators of bacteriophage λ. Cell 5, 109-113
21. Maniatis, T., Ptashne, M., Barrell, B. G., and Donelson, J. (1974) Sequence of a repressor-binding site in the DNA of bacteriophage λ. Nature 250, 394-397
22. Hopkins, N., and Ptashne, M. (1971) Genetics of virulence. in The Bacteriophage Lambda (Hershey, A. D., ed) Vol. 2, pp. 571-574, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
23. Johnson, A. D., Meyer, B. J., and Ptashne, M. (1979) Interactions between DNA-bound repressors govern regulation by the λ phage repressor. Proc. Natl. Acad. Sci. U.S.A. 76, 5061-5065 (Pubitemid 10231821)
24. Pabo, C. O., Sauer, R. T., Sturtevant, J. M., and Ptashne, M. (1979) The lambda repressor contains two domains. Proc. Natl. Acad. Sci. U.S.A. 76, 1608-1612 (Pubitemid 9175368)
25. Sauer, R. T., Pabo, C. O., Meyer, B. J., Ptashne, M., and Backman, K. C. (1979) Regulatory functions of the λ repressor reside in the amino-terminal domain. Nature 279, 396-400 (Pubitemid 9184716)
26. Whipple, F. W., Kuldell, N. H., Cheatham, L. A., and Hochschild, A. (1994) Specificity determinants for the interaction of λ repressor and P22 repressor dimers. Genes Dev. 8, 1212-1223 (Pubitemid 24163448)
27. Whipple, F. W., Hou, E. F., and Hochschild, A. (1998) Amino acid-amino acid contacts at the cooperativity interface of the bacteriophage λ and P22 repressors. Genes Dev. 12, 2791-2802 (Pubitemid 28420658)
28. Burz, D. S., and Ackers, G. K. (1994) Single-site mutations in the C-terminal domain of bacteriophage λ cI repressor alter cooperative interactions between dimers adjacently bound to OR. Biochemistry 33, 8406-8416 (Pubitemid 24242677)
29. Hochschild, A., and Ptashne, M. (1986) Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix. Cell 44, 681-687 (Pubitemid 16073963)
30. Griffith, J., Hochschild, A., and Ptashne, M. (1986) DNA loops induced by cooperative binding of λ repressor. Nature 322, 750-752 (Pubitemid 16074128)
31. Eisen, H., Brachet, P., Pereira da Silva, L., and Jacob, F. (1970) Regulation of repressor expression in λ. Proc. Natl. Acad. Sci. U.S.A. 66, 855-862
32. Heinemann, S. F., and Spiegelman, W. G. (1970) Control of transcription of the repressor gene in bacteriophage λ. Proc. Natl. Acad. Sci. U.S.A. 67, 1122-1129
33. Reichardt, L., and Kaiser, A. D. (1971) Control of λ repressor synthesis. Proc. Natl. Acad. Sci. U.S.A. 68, 2185-2189
34. Reichardt, L. F. (1975) Control of bacteriophage lambda repressor synthesis: regulation of the maintenance pathway of the cro and cI products. J. Mol. Biol. 93, 289-309
35. Guarente, L., Nye, J. S., Hochschild, A., and Ptashne, M. (1982) Mutant λ phage repressor with a specific defect in its positive control function. Proc. Natl. Acad. Sci. U.S.A. 79, 2236-2239 (Pubitemid 12093245)
36. Hochschild, A., Irwin, N., and Ptashne, M. (1983) Repressor structure and the mechanism of positive control. Cell 32, 319-325
37. R) of bacteriophage λ: III. λ repressor directly activates gene transcription. J. Mol. Biol. 139, 195-205
38. Bushman, F. D., and Ptashne, M. (1988) Turning λ Cro into a transcriptional activator. Cell 54, 191-197
39. Ptashne, M. (2007) On the use of the word 'epigenetic'. Curr. Biol. 17, R233-R236
40. Ptashne, M. (2013) Epigenetics: core misconcept. Proc. Natl. Acad. Sci. U.S.A. 110, 7101-7103
41. Neubauer, Z., and Calef, E. (1970) Immunity phase-shift in defective lysogens: non-mutational hereditary change of early regulation of λ prophage. J. Mol. Biol. 51, 1-13
42. - mutant LexA proteins. J. Mol. Biol. 210, 439-452
43. RM and efficient switching from lysogeny. Genes Dev. 15, 3013-3022
44. Dodd, I. B., Shearwin, K. E., Perkins, A. J., Burr, T., Hochschild, A., and Egan, J. B. (2004) Cooperativity in long-range gene regulation by the λ CI repressor. Genes Dev. 18, 344-354 (Pubitemid 38199258)
45. Schmeissner, U., Court, D., Shimatake, H., and Rosenberg, M. (1980) Promoter for the establishment of repressor synthesis in bacteriophage λ. Proc. Natl. Acad. Sci. U.S.A. 77, 3191-3195 (Pubitemid 10016920)
46. R3. Cell 47, 807-816
47. R3: their roles in mediating the effects of repressor and cro. J. Mol. Biol. 139, 163-194
48. Johnson, A., Meyer, B. J., and Ptashne, M. (1978) Mechanism of action of the cro protein of bacteriophage lambda. Proc. Natl. Acad. Sci. U.S.A. 75, 1783-1787 (Pubitemid 8344397)
49. Svenningsen, S. L., Costantino, N., Court, D. L., and Adhya, S. (2005) On the role of Cro in λ prophage induction. Proc. Natl. Acad. Sci. U.S.A. 102, 4465-4469
50. Johnson, A. D., Poteete, A. R., Lauer, G., Sauer, R. T., Ackers, G. K., and Ptashne, M. (1981) λ Repressor and cro-components of an efficient molecular switch. Nature 294, 217-223
51. Little, J. W. (2010) Evolution of complex gene regulatory circuits by addition of refinements. Curr. Biol. 20, R724-R734
52. Hershey, A. D. (ed) (1971) in The Bacteriophage Lambda, Vol. 2, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
53. Hendrix, R. W., Roberts, J. W., Stahl, F. W., and Weisberg, R. A. (eds) (1983) Lambda II, Cold Spring Harbor Press, Cold Spring Harbor, NY
54. Ptashne, M. (2007) On learning to write. Curr. Biol. 17, R394-R395
55. Ptashne, M. (2007) On speaking, writing and inspiration. Curr. Biol. 17, R348-R349
56. Giniger, E., Varnum, S. M., and Ptashne, M. (1985) Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell 40, 767-774 (Pubitemid 15240282)
57. Guarente, L., Yocum, R. R., and Gifford, P. (1982) A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site. Proc. Natl. Acad. Sci. U.S.A. 79, 7410-7414 (Pubitemid 13179117)
58. Keegan, L., Gill, G., and Ptashne, M. (1986) Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 231, 699-704 (Pubitemid 16104039)
59. Brent, R., and Ptashne, M. (1985) A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell 43, 729-736
60. Fischer, J. A., Giniger, E., Maniatis, T., and Ptashne, M. (1988) GAL4 activates transcription in Drosophila. Nature 332, 853-856
61. Kakidani, H., and Ptashne, M. (1988) GAL4 activates gene expression in mammalian cells. Cell 52, 161-167 (Pubitemid 18043595)
62. Ma, J., Przibilla, E., Hu, J., Bogorad, L., and Ptashne, M. (1988) Yeast activators stimulate plant gene expression. Nature 334, 631-633
63. Ma, J., and Ptashne, M. (1988) Converting a eukaryotic transcriptional inhibitor into an activator. Cell 55, 443-446
64. Fields, S., and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245-246 (Pubitemid 19171591)
65. Himmelfarb, H. J., Pearlberg, J., Last, D. H., and Ptashne, M. (1990) GAL11P: a yeast mutation that potentiates the effect of weak GAL4-derived activators. Cell 63, 1299-1309 (Pubitemid 120035078)
66. Barberis, A., Pearlberg, J., Simkovich, N., Farrell, S., Reinagel, P., Bamdad, C., Sigal, G., and Ptashne, M. (1995) Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell 81, 359-368
67. Wang, X., Muratani, M., Tansey, W. P., and Ptashne, M. (2010) Proteolytic instability and the action of nonclassical transcriptional activators. Curr. Biol. 20, 868-871
68. Farrell, S., Simkovich, N., Wu, Y., Barberis, A., and Ptashne, M. (1996) Gene activation by recruitment of the RNA polymerase II holoenzyme. Genes Dev. 10, 2359-2367 (Pubitemid 26322371)
69. Gill, G., and Ptashne, M. (1988) Negative effect of the transcriptional activator GAL4. Nature 334, 721-724
70. Kelleher, R. J., 3rd, Flanagan, P. M., and Kornberg, R. D. (1990) A novel mediator between activator proteins and the RNA polymerase II transcription apparatus. Cell 61, 1209-1215
71. Triezenberg, S. J., LaMarco, K. L., and McKnight, S. L. (1988) Evidence of DNA: protein interactions that mediate HSV-1 immediate early gene activation by VP16. Genes Dev. 2, 730-742
72. Ma, J., and Ptashne, M. (1987) A new class of yeast transcriptional activators. Cell 51, 113-119
73. Brzovic, P. S., Heikaus, C. C., Kisselev, L., Vernon, R., Herbig, E., Pacheco, D., Warfield, L., Littlefield, P., Baker, D., Klevit, R. E., and Hahn, S. (2011) The acidic transcription activator Gcn4 binds the Mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Mol. Cell 44, 942-953
74. Herbig, E., Warfield, L., Fish, L., Fishburn, J., Knutson, B. A., Moorefield, B., Pacheco, D., and Hahn, S. (2010) Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains. Mol. Cell. Biol. 30, 2376-2390
75. Reeves, W. M., and Hahn, S. (2005) Targets of the Gal4 transcription activator in functional transcription complexes. Mol. Cell. Biol. 25, 9092-9102 (Pubitemid 41429097)
76. Wu, Y., Reece, R. J., and Ptashne, M. (1996) Quantitation of putative activator-target affinities predicts transcriptional activating potentials. EMBO J. 15, 3951-3963 (Pubitemid 26289805)
77. Giniger, E., and Ptashne, M. (1987) Transcription in yeast activated by a putative amphipathic α helix linked to a DNA binding unit. Nature 330, 670-672 (Pubitemid 18005586)
78. Ruden, D. M., Ma, J., Li, Y., Wood, K., and Ptashne, M. (1991) Generating yeast transcriptional activators containing no yeast protein sequences. Nature 350, 250-252 (Pubitemid 21912212)
79. Giniger, E., and Ptashne, M. (1988) Cooperative DNA binding of the yeast transcriptional activator GAL4. Proc. Natl. Acad. Sci. U.S.A. 85, 382-386
80. Ruden, D. M., Ma, J., and Ptashne, M. (1988) No strict alignment is required between a transcriptional activator binding site and the "TATA box" of a yeast gene. Proc. Natl. Acad. Sci. U.S.A. 85, 4262-4266
81. Mapp, A. K., Ansari, A. Z., Ptashne, M., and Dervan, P. B. (2000) Activation of gene expression by small molecule transcription factors. Proc. Natl. Acad. Sci. U.S.A. 97, 3930-3935 (Pubitemid 30226064)
82. Struhl, K. (1999) Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98, 1-4
83. Bryant, G. O., Prabhu, V., Floer, M., Wang, X., Spagna, D., Schreiber, D., and Ptashne, M. (2008) Activator control of nucleosome occupancy in activation and repression of transcription. PLoS Biol. 6, 2928-2939
84. Wang, X., Bryant, G. O., Floer, M., Spagna, D., and Ptashne, M. (2011) An effect of DNA sequence on nucleosome occupancy and removal. Nat. Struct. Mol. Biol. 18, 507-509
85. Floer, M., Wang, X., Prabhu, V., Berrozpe, G., Narayan, S., Spagna, D., Alvarez, D., Kendall, J., Krasnitz, A., Stepansky, A., Hicks, J., Bryant, G. O., and Ptashne, M. (2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell 141, 407-418
86. Berrozpe, G., Bryant, G. O., Warpinski, K., and Ptashne, M. (2013) Regulation of a mammalian gene bearing a CpG island promoter and a distal enhancer. Cell Rep. 4, 445-453
87. Wang, X., Bai, L., Bryant, G. O., and Ptashne, M. (2011) Nucleosomes and the accessibility problem. Trends Genet. 27, 487-492
88. Polo, J. M., Anderssen, E., Walsh, R. M., Schwarz, B. A., Nefzger, C. M., Lim, S. M., Borkent, M., Apostolou, E., Alaei, S., Cloutier, J., Bar-Nur, O., Cheloufi, S., Stadtfeld, M., Figueroa, M. E., Robinton, D., Natesan, S., Melnick, A., Zhu, J., Ramaswamy, S., and Hochedlinger, K. (2012) A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617-1632
89. Wenick, A. S., and Hobert, O. (2004) Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Dev. Cell 6, 757-770 (Pubitemid 38745411)
90. Hammachi, F., Morrison, G. M., Sharov, A. A., Livigni, A., Narayan, S., Papapetrou, E. P., O'Malley, J., Kaji, K., Ko, M. S., Ptashne, M., and Brickman, J. M. (2012) Transcriptional activation by Oct4 is sufficient for the maintenance and induction of pluripotency. Cell Rep. 1, 99-109
91. Madhani, H. (2007) From a to α: Yeast as a Model for Cellular Differentiation, Cold Spring Harbor Laboratory Press, Cold Spring Harbor Laboratory Press, NY
92. Taberlay, P. C., Kelly, T. K., Liu, C. C., You, J. S., De Carvalho, D. D., Miranda, T. B., Zhou, X. J., Liang, G., and Jones, P. A. (2011) Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell 147, 1283-1294
93. Ptashne, M., and Gann, A. (1998) Imposing specificity by localization: mechanism and evolvability. Curr. Biol. 8, R897
94. Ptashne, M., and Gann, A. (2003) Signal transduction. Imposing specificity on kinases. Science 299, 1025-1027 (Pubitemid 36222917)
95. Ptashne, M., and Gann, A. (2001) Transcription initiation: imposing specificity by localization. Essays Biochem. 37, 1-15 (Pubitemid 33402952)
96. Ptashne, M., and Gann, A. (1998) Imposing specificity by localization: mechanism and evolvability. Curr. Biol. 8, R812-R822 (Pubitemid 29006656)
97. Davidson, E. H. (2006) The Regulatory Genome: Gene Regulatory Networks In Development And Evolution, 1st Ed., Academic Press, San Diego, CA
98. Ptashne, M. (2013) Faddish stuff: epigenetics and the inheritance of acquired characteristics. FASEB J. 27, 1-2
99. Ptashne, M. (2009) Binding reactions: epigenetic switches, signal transduction and cancer. Curr. Biol. 19, R234-R241
100. Ptashne, M., Hobert, O., and Davidson, E. (2010) Questions over the scientific basis of epigenome project. Nature 464, 487
101. Islam, K., Chen, Y., Wu, H., Bothwell, I. R., Blum, G. J., Zeng, H., Dong, A., Zheng, W., Min, J., Deng, H., and Luo, M. (2013) Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation. Proc. Natl. Acad. Sci. U.S.A. 110, 16778-16783
102. Furey, T. S., and Sethupathy, P. (2013) Genetics. Genetics driving epigenetics. Science 342, 705-706
103. Kilpinen, H., Waszak, S. M., Gschwind, A. R., Raghav, S. K., Witwicki, R. M., Orioli, A., Migliavacca, E., Wiederkehr, M., Gutierrez-Arcelus, M., Panousis, N. I., Yurovsky, A., Lappalainen, T., Romano-Palumbo, L., Planchon, A., Bielser, D., Bryois, J., Padioleau, I., Udin, G., Thurnheer, S., Hacker, D., Core, L. J., Lis, J. T., Hernandez, N., Reymond, A., Deplancke, B., and Dermitzakis, E. T. (2013) Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science 342, 744-747
104. Buganim, Y., Faddah, D. A., and Jaenisch, R. (2013) Mechanisms and models of somatic cell reprogramming. Nat. Rev. Genet. 14, 427-439
105. Graf, T., and Enver, T. (2009) Forcing cells to change lineages. Nature 462, 587-594