Transcriptional activators and activation mechanisms
Transcriptional activators are required to turn on the expression of genes in a eukaryotic cell. Activators bound to the enhancer can facilitate either the recruitment of RNA polymerase II to the promoter or its elongation. This article examines a few selected issues in understanding activator functions and activation mechanisms.
Keywords: activator, transcription, co-activator, enhancer, promoter, signal transduction, development
References
- Adams C.C., Workman J.L. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol Cell Biol. 1995; 15 :1405–1421. [PMC free article] [PubMed] [Google Scholar]
- Baird-Titus J.M., Clark-Baldwin K., Dave V., Caperelli C.A., Ma J., Rance M. The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. J Mol Biol. 2006; 356 :1137–1151. [PubMed] [Google Scholar]
- Bannister A.J., Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011; 21 :381–395. [PMC free article] [PubMed] [Google Scholar]
- Bauer D.C., Buske F.A., Bailey T.L. Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. BMC Bioinformatics. 2010; 11 :366. [PMC free article] [PubMed] [Google Scholar]
- Bertolino E., Singh H. POU/TBP cooperativity: a mechanism for enhancer action from a distance. Mol Cell. 2002; 10 :397–407. [PubMed] [Google Scholar]
- Blackwood E.M., Kadonaga J.T. Going the distance: a current view of enhancer action. Science. 1998; 281 :61–63. [PubMed] [Google Scholar]
- Blau J., Xiao H., McCracken S., O’Hare P., Greenblatt J., Bentley D. Three functional classes of transcriptional activation domains. Mol Cell Biol. 1996; 16 :2044–2055. [PMC free article] [PubMed] [Google Scholar]
- Boettiger A.N., Levine M. Synchronous and stochastic patterns of gene activation in the Drosophila embryo. Science. 2009; 325 :471–473. [PMC free article] [PubMed] [Google Scholar]
- Brent R. Building an artificial regulatory system to understand a natural one. Cell. 2004; 116 :S73–74. [PubMed] [Google Scholar]
- Brent R., Ptashne M. A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor. Cell. 1985; 43 :729–736. [PubMed] [Google Scholar]
- Brivanlou A.H., Darnell J.E., Jr. Signal transduction and the control of gene expression. Science. 2002; 295 :813–818. [PubMed] [Google Scholar]
- Bronstein R., Levkovitz L., Yosef N., Yanku M., Ruppin E., Sharan R., Westphal H., Oliver B., Segal D. Transcriptional regulation by CHIP/LDB complexes. PLoS Genet. 2010; 6 :e1001063. [PMC free article] [PubMed] [Google Scholar]
- Brooks C.L., Gu W. Ubiquitination, phosphorylation and acetylation: the molecular basis for p53 regulation. Curr Opin Cell Biol. 2003; 15 :164–171. [PubMed] [Google Scholar]
- Brown S.A., Imbalzano A.N., Kingston R.E. Activator-dependent regulation of transcriptional pausing on nucleosomal templates. Genes Dev. 1996; 10 :1479–1490. [PubMed] [Google Scholar]
- Bulger M., Groudine M. Looping versus linking: toward a model for long-distance gene activation. Genes Dev. 1999; 13 :2465–2477. [PubMed] [Google Scholar]
- Burz D.S., Pivera-Pomar R., Jackle H., Hanes S.D. Cooperative DNA-binding by Bicoid provides a mechanism for threshold-dependent gene activation in the Drosophila embryo. EMBO J. 1998; 17 :5998–6009. [PMC free article] [PubMed] [Google Scholar]
- Calhoun V.C., Levine M. Coordinate regulation of an extended chromosome domain. Cell. 2003; 113 :278–280. [PubMed] [Google Scholar]
- Calhoun V.C., Stathopoulos A., Levine M. Promoterproximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex. Proc Natl Acad Sci USA. 2002; 99 :9243–9247. [PMC free article] [PubMed] [Google Scholar]
- Carey M., Smale S.T. Transcriptional regulation in eukaryotes: Concepts, Strategies, and Techniques. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 2000. [Google Scholar]
- Chatterjee S., Struhl K. Connecting a promoter-bound protein to TBP bypasses the need for a transcriptional activation domain. Nature. 1995; 374 :820–822. [PubMed] [Google Scholar]
- Cheung D., Miles C., Kreitman M., Ma J. Scaling of the Bicoid morphogen gradient by a volume-dependent production rate. Development. 2011; 138 :2741–2749. [PMC free article] [PubMed] [Google Scholar]
- Chi T., Carey M. Assembly of the isomerized TFIIATFIID-TATA ternary complex is necessary and sufficient for gene activation. Gend Dev. 1996; 10 :2540–2550. [PubMed] [Google Scholar]
- Chopra V.S., Hendrix D.A., Core L.J., Tsui C., Lis J.T., Levine M. The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Mol Cell. 2011; 42 :837–844. [PMC free article] [PubMed] [Google Scholar]
- Chubb J.R., Liverpool T.B. Bursts and pulses: insights from single cell studies into transcriptional mechanisms. Curr Opin Genet Dev. 2010; 20 :478–484. [PubMed] [Google Scholar]
- Conaway R.C., Brower C.S., Conaway J.W. Emerging roles of ubiquitin in transcription regulation. Science. 2002; 296 :1254–1258. [PubMed] [Google Scholar]
- Core L.J., Waterfall J.J., Lis J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008; 322 :1845–1848. [PMC free article] [PubMed] [Google Scholar]
- Darnell J.E., Jr., Kerr I.M., Stark G.R. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science. 1994; 264 :1415–1421. [PubMed] [Google Scholar]
- Deng J., Wang W., Lu L.J., Ma J. A two-dimensional simulation model of the Bicoid gradient in Drosophila. PLoS ONE. 2010; 5 :e10275. [PMC free article] [PubMed] [Google Scholar]
- Dorsett D. Distant liaisons: long-range enhancer-promoter interactions in Drosophila. Curr Opin Genet Dev. 1999; 9 :505–514. [PubMed] [Google Scholar]
- Elowitz M.B., Levine A.J., Siggia E.D., Swain P.S. Stochastic gene expression in a single cell. Science. 2002; 297 :1183–1186. [PubMed] [Google Scholar]
- Farrell S., Simkovich N., Wu Y., Barberis A., Ptashne M. Gene activation by recruitment of the RNA polymerase II holoenzyme. Gend Dev. 1996; 10 :2359–2367. [PubMed] [Google Scholar]
- Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature. 1989; 340 :245–246. [PubMed] [Google Scholar]
- Foley K.P., Engel J.D. Individual stage selector element mutations lead to reciprocal changes in beta- vs. epsilon-globin gene transcription: genetic confirmation of promoter competition during globin gene switching. Genes Dev. 1992; 6 :730–744. [PubMed] [Google Scholar]
- Frankel N., Davis G.K., Vargas D., Wang S., Payre F., Stern D.L. Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature. 2010; 466 :490–493. [PMC free article] [PubMed] [Google Scholar]
- Frappier L., Verrijzer C.P. Gene expression control by protein deubiquitinases. Curr Opin Genet Dev. 2011; 21 :207–213. [PubMed] [Google Scholar]
- Garvie C.W., Wolberger C. Recognition of specific DNA sequences. Mol Cell. 2001; 8 :937–946. [PubMed] [Google Scholar]
- Giardina C., Lis J.T. DNA melting on yeast RNA polymerase II promoters. Science. 1993; 261 :759–762. [PubMed] [Google Scholar]
- Gill G. Something about SUMO inhibits transcription. Curr Opin Genet Dev. 2005; 15 :536–541. [PubMed] [Google Scholar]
- Golding I., Cox E.C. Eukaryotic transcription: what does it mean for a gene to be ‘on’? Curr Biol. 2006; 16 :R371–R373. [PubMed] [Google Scholar]
- Golding I., Paulsson J., Zawilski S.M., Cox E.C. Realtime kinetics of gene activity in individual bacteria. Cell. 2005; 123 :1025–1036. [PubMed] [Google Scholar]
- Gonzalez-Gouto E., Klages N., Strubin M. Synergistic and promoter-selective activation of transcription by recruitment of transcription factors TFIID and TFIIB. Proc Natl Acad Sci USA. 1997; 94 :8036–8041. [PMC free article] [PubMed] [Google Scholar]
- Gregor T., Tank D.W., Wieschaus E.F., Bialek W. Probing the limits to positional information. Cell. 2007; 130 :153–164. [PMC free article] [PubMed] [Google Scholar]
- Gregor T., Wieschaus E.F., McGregor A.P., Bialek W., Tank D. W. Stability and nuclear dynamics of the bicoid morphogen gradient. Cell. 2007; 130 :141–152. [PMC free article] [PubMed] [Google Scholar]
- Grimm O., Coppey M., Wieschaus E. Modelling the Bicoid gradient. Development. 2010; 137 :2253–2264. [PMC free article] [PubMed] [Google Scholar]
- Gu W., Roeder R.G. Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell. 1997; 90 :595–606. [PubMed] [Google Scholar]
- Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol. 2004; 11 :394–403. [PMC free article] [PubMed] [Google Scholar]
- Hampsey M. Molecular Genetics of the RNA polymerase II general transcription machinery. Microbiol Mol Biol Rev. 1998; 62 :465–503. [PMC free article] [PubMed] [Google Scholar]
- Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 1988; 55 :1137–1145. [PubMed] [Google Scholar]
- He F., Ren J., Wang W., Ma J. A multiscale investigation of bicoid-dependent transcriptional events in Drosophila embryos. PLoS ONE. 2011; 6 :e19122. [PMC free article] [PubMed] [Google Scholar]
- He F., Saunders T., Wen Y., Cheung D., Jiao R., ten Wolde P., Howard M., Ma J. Shaping a morphogen gradient for positional precision. Biophys J. 2010; 99 :697–707. [PMC free article] [PubMed] [Google Scholar]
- He F., Wen Y., Cheung D., Deng J., Lu L.J., Jiao R., Ma J. Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos. BMC Dev Biol. 2010; 10 :80. [PMC free article] [PubMed] [Google Scholar]
- He F., Wen Y., Deng J., Lin X., Lu J., Jiao R., Ma J. Probing intrinsic properties of a robust morphogen gradient in Drosophila. Dev Cell. 2008; 15 :558–567. [PMC free article] [PubMed] [Google Scholar]
- Herrera F.J., Triezenberg S.J. Molecular biology: what ubiquitin can do for transcription. Curr Biol. 2004; 14 :R622–R624. [PubMed] [Google Scholar]
- Hirose Y., Ohkuma Y. Phosphorylation of the C-terminal domain of RNA polymerase II plays central roles in the integrated events of eucaryotic gene expression. J Biochem. 2007; 141 :601–608. [PubMed] [Google Scholar]
- Ho L., Crabtree G.R. Chromatin remodelling during development. Nature. 2010; 463 :474–484. [PMC free article] [PubMed] [Google Scholar]
- Hobert O. Gene regulation: enhancers stepping out of the shadow. Curr Biol. 2010; 20 :R697–R699. [PubMed] [Google Scholar]
- Hong, J.W., Hendrix, D.A., and Levine, M.S. (2008). Shadow enhancers as a source of evolutionary novelty. Science (New York, NY 321, 1314. [PMC free article] [PubMed]
- Hope I.A., Struhl K. Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell. 1986; 46 :885–894. [PubMed] [Google Scholar]
- Jackson S.P., Tjian R. O-glycosylation of eukaryotic transcription factors: implications for mechanisms of transcriptional regulation. Cell. 1988; 55 :125–133. [PubMed] [Google Scholar]
- Kadonaga J.T. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell. 2004; 116 :247–257. [PubMed] [Google Scholar]
- Kaern M., Elston T.C., Blake W.J., Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet. 2005; 6 :451–464. [PubMed] [Google Scholar]
- Kamemura K., Hart G.W. Dynamic interplay between Oglycosylation and O-phosphorylation of nucleocytoplasmic proteins: a new paradigm for metabolic control of signal transduction and transcription. Prog Nucleic Acid Res Mol Biol. 2003; 73 :107–136. [PubMed] [Google Scholar]
- Keegan L., Gill G., Ptashne M. Separation of DNA binding from the transcriptional-activating function of a eukaryotic regulatory protein. Science. 1986; 231 :699–704. [PubMed] [Google Scholar]
- Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993; 365 :512–520. [PubMed] [Google Scholar]
- Klein C., Struhl K. Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo. Science. 1994; 266 :280–282. [PubMed] [Google Scholar]
- Kouzarides T. Chromatin modifications and their function. Cell. 2007; 128 :693–705. [PubMed] [Google Scholar]
- Krumm A., Meulia T., Brunvand M., Groudine M. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Gend Dev. 1992; 6 :2201–2213. [PubMed] [Google Scholar]
- Kuhn E.J., Geyer P.K. Genomic insulators: connecting properties to mechanism. Curr Opin Cell Biol. 2003; 15 :259–265. [PubMed] [Google Scholar]
- Levine M. Paused RNA polymerase II as a developmental checkpoint. Cell. 2011; 145 :502–511. [PMC free article] [PubMed] [Google Scholar]
- Levine M., Tjian R. Transcription regulation and animal diversity. Nature. 2003; 424 :147–151. [PubMed] [Google Scholar]
- Li B., Carey M., Workman J.L. The role of chromatin during transcription. Cell. 2007; 128 :707–719. [PubMed] [Google Scholar]
- Li J., Gilmour D.S. Promoter proximal pausing and the control of gene expression. Curr Opin Genet Dev. 2011; 21 :231–235. [PMC free article] [PubMed] [Google Scholar]
- Li X.Y., Virbasius A., Zhu X., Green M.R. Enhancement of TBP binding by activators and general transcription factors. Nature. 1999; 399 :605–609. [PubMed] [Google Scholar]
- Lipford J.R., Smith G.T., Chi Y., Deshaies R.J. A putative stimulatory role for activator turnover in gene expression. Nature. 2005; 438 :113–116. [PubMed] [Google Scholar]
- Lis J.T., Mason P., Peng J., Price D.H., Werner J. PTEFb kinase recruitment and function at heat shock loci. Genes Dev. 2000; 14 :792–803. [PMC free article] [PubMed] [Google Scholar]
- Liu J., He F., Ma J. Morphogen gradient formation and action: insights from studying Bicoid protein degradation. Fly (Austin) 2011; 5 :424–426. [PMC free article] [PubMed] [Google Scholar]
- Liu J., Ma J. Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos. Nat Cell Biol. 2011; 13 :22–29. [PMC free article] [PubMed] [Google Scholar]
- Lohr U., Chung H.R., Beller M., Jackle H. Bicoid: Morphogen function revisited. Fly (Austin) 2010; 4 :236–240. [PMC free article] [PubMed] [Google Scholar]
- Ma J. Actively seeking activating sequences. Cell. 2004; S116 :S75–S76. [PubMed] [Google Scholar]
- Ma J. Crossing the line between activation and repression. Trends Genet. 2005; 21 :54–59. [PubMed] [Google Scholar]
- Ma J., Ptashne M. A new class of yeast transcriptional activators. Cell. 1987; 51 :113–119. [PubMed] [Google Scholar]
- Ma J., Ptashne M. Deletion analysis of GAL4 defines two transcriptional activating segments. Cell. 1987; 48 :847–853. [PubMed] [Google Scholar]
- Ma J., Ptashne M. Converting a eukaryotic transcriptional inhibitor into an activator. Cell. 1988; 55 :443–446. [PubMed] [Google Scholar]
- Ma X., Yuan D., Diepold K., Scarborough T., Ma J. The Drosophila morphogenetic protein Bicoid binds DNA cooperatively. Development. 1996; 122 :1195–1206. [PubMed] [Google Scholar]
- Malik S., Roeder R.G. Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem Sci. 2000; 25 :277–283. [PubMed] [Google Scholar]
- Malik S., Roeder R.G. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet. 2010; 11 :761–772. [PMC free article] [PubMed] [Google Scholar]
- Mancebo H.S., Lee G., Flygare J., Tomassini J., Luu P., Zhu Y., Peng J., Blau C., Hazuda D., Price D., et al. P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro. Genes Dev. 1997; 11 :2633–2644. [PMC free article] [PubMed] [Google Scholar]
- Matthews J.M., Visvader J.E. LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins. EMBO Rep. 2003; 4 :1132–1137. [PMC free article] [PubMed] [Google Scholar]
- Meinhart A., Kamenski T., Hoeppner S., Baumli S., Cramer P. A structural perspective of CTD function. Genes Dev. 2005; 19 :1401–1415. [PubMed] [Google Scholar]
- Merika M., Thanos D. Enhanceosomes. Curr Opin Genet Dev. 2001; 11 :205–208. [PubMed] [Google Scholar]
- Morcillo P., Rosen C., Baylies M.K., Dorsett D. Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila. Genes Dev. 1997; 11 :2729–2740. [PMC free article] [PubMed] [Google Scholar]
- Muratani M., Kung C., Shokat K.M., Tansey W.P. The F box protein Dsg1/Mdm30 is a transcriptional coactivator that stimulates Gal4 turnover and cotranscriptional mRNA processing. Cell. 2005; 120 :887–899. [PubMed] [Google Scholar]
- Myers L.C., Kornberg R.D. Mediator of transcriptional regulation. Annu Rev Biochem. 2000; 69 :729–749. [PubMed] [Google Scholar]
- Naar A.M., Lemon B.D., Tjian R. Transcriptional coactivator complexes. Annu Rev Biochem. 2001; 70 :475–501. [PubMed] [Google Scholar]
- Narlikar G.J., Fan H.Y., Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell. 2002; 108 :475–487. [PubMed] [Google Scholar]
- Nechaev S., Adelman K. Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. Biochim Biophys Acta. 2011; 1809 :34–45. [PMC free article] [PubMed] [Google Scholar]
- Nechaev S., Fargo D.C., dos Santos G., Liu L., Gao Y., Adelman K. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science. 2010; 327 :335–338. [PMC free article] [PubMed] [Google Scholar]
- Nevado J., Gaudreau L., Adam M., Ptashne M. Transcriptional activation by artificial recruitment in mammalian cells. Proc Natl Acad Sci USA. 1999; 96 :2674–2677. [PMC free article] [PubMed] [Google Scholar]
- Nikolov D.B., Hu S.-H., Lin J., Gasch A., Hoffmann A., Horikoshi M., Chua N.-H., Roeder R.G., Burley S.K. Crystal structure of TFIID TATA-box binding protein. Nature. 1992; 360 :40–46. [PubMed] [Google Scholar]
- Nonet M., Sweetser D., Young R.A. Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II. Cell. 1987; 50 :909–915. [PubMed] [Google Scholar]
- Ong C.T., Corces V.G. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet. 2011; 12 :283–293. [PMC free article] [PubMed] [Google Scholar]
- Orphanides G., Lagrange T., Reinberg D. The general transcription factors of RNA polymerase II. Genes Dev. 1996; 10 :2657–2683. [PubMed] [Google Scholar]
- Ouyang J., Gill G. SUMO engages multiple corepressors to regulate chromatin structure and transcription. Epigenetics. 2009; 4 :440–444. [PubMed] [Google Scholar]
- Pare A., Lemons D., Kosman D., Beaver W., Freund Y., McGinnis W. Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting. Curr Biol. 2009; 19 :2037–2042. [PMC free article] [PubMed] [Google Scholar]
- Patikoglou G., Burley S.K. Eukaryotic transcription factor-DNA complexes. Annu Rev Biophys Biomol Struct. 1997; 26 :289–325. [PubMed] [Google Scholar]
- Perry M.W., Boettiger A.N., Bothma J.P., Levine M. Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol. 2010; 20 :1562–1567. [PMC free article] [PubMed] [Google Scholar]
- Peterlin B.M., Price D.H. Controlling the elongation phase of transcription with P-TEFb. Mol Cell. 2006; 23 :297–305. [PubMed] [Google Scholar]
- Peterson C.L., Workman J.L. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr Opin Genet Dev. 2000; 10 :187–192. [PubMed] [Google Scholar]
- Porcher A., Abu-Arish A., Huart S., Roelens B., Fradin C., Dostatni N. The time to measure positional information: maternal hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription. Development. 2010; 137 :2795–2804. [PubMed] [Google Scholar]
- Porcher A., Dostatni N. The bicoid morphogen system. Curr Biol. 2010; 20 :R249–R254. [PubMed] [Google Scholar]
- Prives C., Manley J.L. Why is p53 acetylated? Cell. 2001; 107 :815–818. [PubMed] [Google Scholar]
- Ptashne M. How eukaryotic transcriptional activators work. Nature. 1988; 335 :683–689. [PubMed] [Google Scholar]
- Ptashne M. Two “what if” experiments. Cell. 2004; S116 :S71–S72. [PubMed] [Google Scholar]
- Ptashne M., Gann A. Transcriptional activation by recruitment. Nature. 1997; 386 :569–577. [PubMed] [Google Scholar]
- Ptashne M., Gann A. Imposing specificity by localization: mechanism and evolution. Curr Biol. 1998; 8 :R812–R822. [PubMed] [Google Scholar]
- Ptashne M., Gann A.A.F. Activators and targets. Nature. 1990; 346 :329–331. [PubMed] [Google Scholar]
- Ranish J.A., Hahn S. Transcription: basal factors and activation. Curr Opin Genet Dev. 1996; 6 :151–158. [PubMed] [Google Scholar]
- Raser, J.M., and O’shea, E.K. (2005). Noise in gene expression: origins, consequences, and control. Science (New York, NY 309,2010–2013. [PMC free article] [PubMed]
- Rasmussen E.B., Lis J.T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc Natl Acad Sci USA. 1993; 90 :7923–7927. [PMC free article] [PubMed] [Google Scholar]
- Rasmussen E.B., Lis J.T. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J Mol Biol. 1995; 252 :522–535. [PubMed] [Google Scholar]
- Rougvie A.E., Lis J.T. The RNA polymerase II molecule at the 5′-end of the uninduced hsp70 genes of D. melanogaster is transcriptionally engaged. Cell. 1988; 54 :795–804. [PubMed] [Google Scholar]
- Ruthenburg A.J., Li H., Patel D.J., Allis C.D. Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol. 2007; 8 :983–994. [PMC free article] [PubMed] [Google Scholar]
- Sadowski I., Ma J., Triezenberg S., Ptashne M. GAL4-VP16 is an unusually potent transcriptional activator. Nature. 1988; 335 :563–564. [PubMed] [Google Scholar]
- Sharpe J., Nonchev S., Gould A., Whiting J., Krumlauf R. Selectivity, sharing and competitive interactions in the regulation of Hoxb genes. EMBO J. 1998; 17 :1788–1798. [PMC free article] [PubMed] [Google Scholar]
- Sims R.J., 3rd, Belotserkovskaya R., Reinberg D. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 2004; 18 :2437–2468. [PubMed] [Google Scholar]
- Sims R.J., 3rd, Mandal S.S., Reinberg D. Recent highlights of RNA-polymerase-II-mediated transcription. Curr Opin Cell Biol. 2004; 16 :263–271. [PubMed] [Google Scholar]
- Spellman P.T., Rubin G.M. Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol. 2002; 1 :5. [PMC free article] [PubMed] [Google Scholar]
- Spitz F., Gonzalez F., Duboule D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell. 2003; 113 :405–417. [PubMed] [Google Scholar]
- Stargell L.A., Struhl K. Mechanisms of transcriptional activation in vivo: two steps forward. Trends Genet. 1996; 12 :311–315. [PubMed] [Google Scholar]
- Thanos D., Maniatis T. Virus induction of human INFβ gene expression requires the assembly of an enhanceosome. Cell. 1995; 83 :1091–1100. [PubMed] [Google Scholar]
- To T.L., Maheshri N. Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science. 2010; 327 :1142–1145. [PubMed] [Google Scholar]
- Torigoi E., Bennani-Baiti I.M., Rosen C., Gonzalez K., Morcillo P., Ptashne M., Dorsett D. Chip interacts with diverse homeodomain proteins and potentiates bicoid activity in vivo. Proc Natl Acad Sci USA. 2000; 97 :2686–2691. [PMC free article] [PubMed] [Google Scholar]
- Travers A. Recognition of distorted DNA structures by HMG domains. Curr Opin Struct Biol. 2000; 10 :102–109. [PubMed] [Google Scholar]
- Triezenberg S.J., Kingsbury R.C., McKnight S.L. Functional dissection of VP16, the trans-activator of herpes simplex virus immediate early gene expression. Genes Dev. 1988; 2 :718–729. [PubMed] [Google Scholar]
- von der Lehr N., Johansson S., Wu S., Bahram F., Castell A., Cetinkaya C., Hydbring P., Weidung I., Nakayama K., Nakayama K.I., et al. The F-box protein Skp2 participates in c-Myc proteosomal degradation and acts as a cofactor for c-Myc-regulated transcription. Mol Cell. 2003; 11 :1189–1200. [PubMed] [Google Scholar]
- Wallace J.A., Felsenfeld G. We gather together: insulators and genome organization. Curr Opin Genet Dev. 2007; 17 :400–407. [PMC free article] [PubMed] [Google Scholar]
- Wang W., Carey M., Gralla J.D. Polymerase II promoter activation: Closed complex formation and ATP-driven start-site opening. Science. 1992; 255 :450–453. [PubMed] [Google Scholar]
- Wang X., Muratani M., Tansey W.P., Ptashne M. Proteolytic instability and the action of nonclassical transcriptional activators. Curr Biol. 2010; 20 :868–871. [PMC free article] [PubMed] [Google Scholar]
- Weake V.M., Workman J.L. Inducible gene expression: diverse regulatory mechanisms. Nat Rev Genet. 2010; 11 :426–437. [PubMed] [Google Scholar]
- West A.G., Gaszner M., Felsenfeld G. Insulators: many functions, many mechanisms. Genes Dev. 2002; 16 :271–288. [PubMed] [Google Scholar]
- Wu C. Chromatin remodeling and the control of gene expression. J Biol Chem. 1997; 272 :28171–28174. [PubMed] [Google Scholar]
- Wu J., Grunstein M. 25 years after the nucleosome model: chromatin modifications. Trends Biochem Sci. 2000; 25 :619–623. [PubMed] [Google Scholar]
- Wu R.C., Feng Q., Lonard D.M., O’Malley B.W. SRC-3 coactivator functional lifetime is regulated by a phospho-dependent ubiquitin time clock. Cell. 2007; 129 :1125–1140. [PubMed] [Google Scholar]
- Wyrick J.J., Holstege F.C., Jennings E.G., Causton H.C., Shore D., Grunstein M., Lander E.S., Young R.A. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature. 1999; 402 :418–421. [PubMed] [Google Scholar]
- Xiao H., Friesen J.D., Lis J.T. Recruiting TATA-binding protein to a promoter: transcriptional activation without an upstream activator. Mol Cell Biol. 1995; 15 :5757–5761. [PMC free article] [PubMed] [Google Scholar]
- Zeitlinger J., Stark A., Kellis M., Hong J.W., Nechaev S., Adelman K., Levine M., Young R.A. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet. 2007; 39 :1512–1516. [PMC free article] [PubMed] [Google Scholar]
- Zhou Q., Chen D., Pierstorff E., Luo K. Transcription elongation factor P-TEFb mediates Tat activation of HIV-1 transcription at multiple stages. EMBO J. 1998; 17 :3681–3691. [PMC free article] [PubMed] [Google Scholar]
- Zhu Y., Pe’ery T., Peng J., Ramanathan Y., Marshall N., Marshall T., Amendt B., Mathews M.B., Price D.H. Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev. 1997; 11 :2622–2632. [PMC free article] [PubMed] [Google Scholar]
- Zuniga A., Michos O., Spitz F., Haramis A.P., Panman L., Galli A., Vintersten K., Klasen C., Mansfield W., Kuc S., et al. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev. 2004; 18 :1553–1564. [PMC free article] [PubMed] [Google Scholar]