Common effects of acidic activators on large-scale chromatin structure and transcription

Molecular and Cellular Biology

Volumn 25, Issue 3, 2005, Pages 958-968

  Carpenter, Anne E ^a,c   Memedula, Sevinci ^a   Plutz, Matthew J ^a   Belmont, Andrew S ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b B107 CLSL ^*  (United States)

^c WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; ACID; CYAN FLUORESCENT PROTEIN; HYBRID PROTEIN; MAMMALIAN TARGET OF RAPAMYCIN; PEPTIDE; PROTEIN VP16; RAPAMYCIN; UNCLASSIFIED DRUG; VIRUS PROTEIN; YELLOW FLUORESCENT PROTEIN;

ANIMAL CELL; ARTICLE; CHROMATIN CONDENSATION; CHROMATIN STRUCTURE; CONTROLLED STUDY; DIMERIZATION; DNA SEQUENCE; FLUORESCENCE MICROSCOPY; HYDROPHOBICITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN MOTIF; TRANSCRIPTION INITIATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; ANTIBIOTICS, ANTINEOPLASTIC; CHO CELLS; CHROMATIN; CRICETINAE; CRICETULUS; GREEN FLUORESCENT PROTEINS; HERPES SIMPLEX VIRUS PROTEIN VMW65; MOLECULAR SEQUENCE DATA; SIROLIMUS; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC;

ANIMALIA; MAMMALIA;

EID: 12844272896     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.3.958-968.2005     Document Type: Article

References (54)

1. Aris, J. P., and G. Blobel. 1991. cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera. Proc. Natl. Acad. Sci. USA 88:931-935.
2. Belmont, A. S. 2001. Visualizing chromosome dynamics with GFP. Trends Cell Biol. 11:250-257.
3. Berger, S. L. 2002. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12:142-148.
4. Berger, S. L., W. D. Cress, A. Cress, S. J. Triezenberg, and L. Guarente. 1990. Selective inhibition of activated but not basal transcription by the acidic activation domain of VP16: evidence for transcriptional adaptors. Cell 61:1199-1208.
5. Carpenter, A. E., A. Ashouri, and A. S. Belmont. 2004. Automated microscopy identifies estrogen receptor subdomains with large-scale chromatin structure unfolding activity. Cytometry 58A:157-166.
6. Carpenter, A. E., and A. S. Belmont. 2004. Direct visualization of transcription factor induced chromatin remodeling and cofactor recruitment in vivo. Methods Enzymol. 375:366-381.
7. Chambeyron, S., and W. A. Bickmore. 2004. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 18:1119-1130.
8. Cress, W. D., and S. J. Triezenberg. 1991. Critical structural elements of the VP16 transcriptional activation domain. Science 251:87-90.
9. Denisenko, O. N., and K. Bomsztyk. 1997. The product of the murine homolog of the Drosophila extra sex combs gene displays transcriptional repressor activity. Mol. Cell. Biol. 17:4707-4717.
10. Dunker, A. K., J. D. Lawson, C. J. Brown, R. M. Williams, P. Romero, J. S. Oh, C. J. Oldfield, A. M. Campen, C. M. Ratliff, K. W. Hipps, J. Ausio, M. S. Nissen, R. Reeves, C. Kang, C. R. Kissinger, R. W. Bailey, M. D. Griswold, W. Chiu, E. C. Garner, and Z. Obradovic. 2001. Intrinsically disordered protein. J. Mol. Graph. Model. 19:26-59.
11. Engelman, D. M., T. A. Steitz, and A. Goldman. 1986. Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem. 15:321-353.
12. Erkine, A. M., and D. S. Gross. 2003. Dynamic chromatin alterations triggered by natural and synthetic activation domains. J. Biol. Chem. 278:7755-7764.
13. Frangioni, J. V., L. M. LaRiccia, L. C. Cantley, and M. R. Montminy. 2000. Minimal activators that bind to the KIX domain of p300/CBP identified by phage display screening. Nat. Biotechnol. 18:1080-1085.
14. Ge, H., and R. G. Roeder. 1994. Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class 11 genes. Cell 78:513-523.
15. Goodrich, J. A., T. Hoey, C. J. Thut, A. Admon, and R. Tjian. 1993. Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB. Cell 75:519-530.
16. Gugneja, S., C. M. Virbasius, and R. C. Scarpulla. 1996. Nuclear respiratory factors 1 and 2 utilize similar glutamine-containing clusters of hydrophobic residues to activate transcription. Mol. Cell. Biol. 16:5708-5716.
17. Hall, D. B., and K. Struhl. 2002. The VP16 activation domain interacts with multiple transcriptional components as determined by protein-protcin cross-linking in vivo. J. Biol. Chem. 277:46043-46050.
18. Hassan, A. H., K. E. Neely, M. Vignali, J. C. Reese, and J. L. Workman. 2001. Promoter targeting of chromatin-modifying complexes. Front. Biosci. 6: D1054-D1064.
19. Ingles, C. J., M. Shales, W. D. Cress, S. J. Triezenberg, and J. Greenblatt. 1991. Reduced binding of TFIID to transcriptionally compromised mutants of VP16. Nature 351:588-590.
20. Janicki, S. M., T. Tsukamoto, S. E. Salghetti, W. P. Tansey, R. Sachidanandam, K. V. Prasanth, T. Ried, Y. Shav-Tal, E. Bertrand, R. H. Singer, and D. L. Spector. 2004. From silencing to gene expression: real-time analysis in single cells. Cell 116:683-698.
21. Klein, J., M. Nolden, S. L. Sanders, J. Kirchner, P. A. Weil, and K. Melcher, 2003. Use of a genetically introduced cross-linker to identify interaction sites of acidic activators within native transcription factor IID and SAGA. J. Biol. Chem. 278:6779-6786.
22. Kobayashi, N., T. G. Boyer, and A. J. Berk. 1995. A class of activation domains interacts directly with TFIIA and stimulates TFIIA-TFIID-promoter complex assembly. Mol. Cell. Biol. 15:6465-6473.
23. Kunzler, M., G. H. Braus, O. Georgiev, K. Seipel, and W. Schaffner. 1994. Functional differences between mammalian transcription activation domains at the yeast GAL1 promoter. EMBO J. 13:641-645.
24. Li, G., G. Sudlow, and A. S. Belmont. 1998. Interphase cell cycle dynamics of a late-replicating, heterochromatic homogeneously staining region: precise choreography of condensation/decondensation and nuclear positioning. J. Cell Biol. 140:975-989.
25. Li, R. 1999. Stimulation of DNA replication in Saccharomyces cerevisiae by a glutamine- and proline-rich transcriptional activation domain. J. Biol. Chem. 274:30310-30314.
26. Liberles, S. D., S. T. Diver, D. J. Austin, and S. L. Schreiber. 1997. Inducible gene expression and protein translocation using nontoxic ligands identified by a mammalian three-hybrid screen. Proc. Natl. Acad. Sci. USA 94:7825-7830.
27. Lin, Y. S., I. Ha, E. Maldonado, D. Reinberg, and M. R. Green. 1991. Binding of general transcription factor TFIIB to an acidic activating region. Nature 353:569-571.
28. Littell, R. C., G. A. Milliken, W. W. Stroup, and R. D. Wolfinger. 1996. SAS system for mixed models. SAS Institute, Inc., Cary, N.C.
29. Ma, J., and M. Ptashne. 1987. Deletion analysis of GAL4 defines two transcriptional activating segments. Cell 48:847-853.
30. Melcher, K. 2000. The strength of acidic activation domains correlates with their affinity for both transcriptional and non-transcriptional proteins. J. Mol. Biol. 301:1097-1112.
31. Mitchell, P. J., and R. Tjian. 1989. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 245:371-378.
32. Muller, W. G., D. Walker, G. L. Hager, and J. G. McNally. 2001. Large-scale chromatin decondensation and recondensation regulated by transcription from a natural promoter. J. Cell Biol. 154:33-48.
33. Nedialkov, Y. A., and S. J. Triezenberg. 2004. Quantitative assessment of in vitro interactions implicates TATA-binding protein as a target of the VP16C transcriptional activation region. Arch. Biochem. Biophys. 425:77-86.
34. Neely, K. E., A. H. Hassan, C. E. Brown, L. Howe, and J. L. Workman. 2002. Transcription activator interactions with multiple SWI/SNF subunits. Mol. Cell. Biol. 22:1615-1625.
35. Nye, A. C. 2003. Effects of transcriptional activators on large-scale chromatin structure. Ph.D. thesis. University of Illinois, Urbana-Champaign.
36. Nye, A. C., R. R. Rajendran, D. L. Stenoien, M. A. Mancini, B. S. Katzenellenbogen, and A. S. Belmont. 2002. Alteration of large-scale chromatin structure by estrogen receptor. Mol. Cell. Biol. 22:3437-3449.
37. Ptashne, M., and A. Gann. 1997. Transcriptional activation by recruitment. Nature 386:569-577.
38. Regier, J. L., F. Shen, and S. J. Triezenberg. 1993. Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP16 transcriptional activator. Proc. Natl. Acad. Sci. USA 90:883-887.
39. Schmitz, M. L., and P. A. Baeuerle. 1991. The p65 subunit is responsible for the strong transcription activating potential of NF-kappa B. EMBO J. 10:3805-3817.
40. Schmitz, M. L., M. A. dos Santos Silva, H. Altmann, M. Czisch, T. A. Holak, and P. A. Baeuerle. 1994. Structural and functional analysis of the NF-κB p65 C terminus. An acidic and modular transactivation domain with the potential to adopt an alpha-helical conformation. J. Biol. Chem. 269:25613-25620.
41. Seipel, K., O. Georgiev, and W. Schaffner. 1992. Different activation domains stimulate transcription from remote ('enhancer') and proximal ('promoter') positions. EMBO J. 11:4961-4968.
42. Seipel, K., O. Georgiev, and W. Schaffner. 1994. A minimal transcription activation domain consisting of a specific array of aspartic acid and leucine residues. Biol. Chem. Hoppe-Seyler 375:463-470.
43. Shen, F., S. J. Triezenberg, P. Hensley, D. Porter, and J. R. Knutson. 1996. Transcriptional activation domain of the herpesvirus protein VP16 becomes conformationally constrained upon interaction with basal transcription factors. J. Biol. Chem. 271:4827-4837.
44. Sullivan, S. M., P. J. Horn, V. A. Olson, A. H. Koop, W. Niu, R. H. Ebright, and S. J. Triezenberg. 1998. Mutational analysis of a transcriptional activation region of the VP16 protein of herpes simplex virus. Nucleic Acids Res. 26:4487-4496.
45. Tanaka, M., and W. Herr. 1994. Reconstitution of transcriptional activation domains by reiteration of short peptide segments reveals the modular organization of a glutamine-rich activation domain. Mol. Cell. Biol. 14:6056-6067.
46. Triezenberg, S. J., R. C. Kingsbury, and S. L. McKnight. 1988. Functional dissection of VP16, the trans-activator of herpes simplex virus immediate early gene expression. Genes Dev. 2:718-729.
47. Tsukamoto, T., N. Hashiguchi, S. M. Janicki, T. Tumbar, A. S. Belmont, and D. L. Spector. 2000. Visualization of gene activity in living cells. Nat. Cell Biol. 2:871-878.
48. Tumbar, T., G. Sudlow, and A. S. Belmont. 1999. Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain. J. Cell Biol. 145:1341-1354.
49. Uesugi, M., O. Nyanguile, H. Lu, A. J. Levine, and G. L. Verdine. 1997. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. Science 277:1310-1313.
50. Utley, R. T., K. Ikeda, P. A. Grant, J. Cote, D. J. Steger, A. Eberharter, S. John, and J. L. Workman. 1998. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 394:498-502.
51. Uversky, V. N. 2002. Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11:739-756.
52. Wright, P. E., and H. J. Dyson. 1999. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293:321-331.
53. Xiao, H., A. Pearson, B. Coulombe, R. Truant, S. Zhang, J. L. Regier, S. J. Triezenberg, D. Reinberg, O. Flores, and C. J. Ingles. 1994. Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53. Mol. Cell. Biol 14:7013-7024.
54. Ye, Q., Y. F. Hu, H. Zhong, A. C. Nye, A. S. Belmont, and R. Li. 2001. BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations. J. Cell Biol. 155:911-921.