Transcriptional activation triggers deposition and removal of the histone variant H3.3

Genes and Development

Volumn 19, Issue 7, 2005, Pages 804-814

  Schwartz, Brian E ^a   Ahmad, Kami ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Chromatin; Drosophila; H3.3; Histone; Nucleosome; Transcription

Indexed keywords

DNA; HEAT SHOCK PROTEIN 70; HISTONE; HISTONE H3; HISTONE H3.3; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN STRUCTURE; DNA STRAND; DROSOPHILA; EUKARYOTIC CELL; GENE; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN LOCALIZATION; PROTEIN STABILITY; TRANSCRIPTION INITIATION;

ANIMALS; CHROMATIN; DROSOPHILA; GENES, REPORTER; HISTONES; HSP70 HEAT-SHOCK PROTEINS; RECOMBINANT FUSION PROTEINS; TRANSCRIPTION, GENETIC;

EID: 17044394787     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1259805     Document Type: Article

References (46)

1. Adkins, M.W., Howar, S.R., and Tyler, J.K. 2004. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell 14: 657-666.
2. Ahmad, K. and Henikoff, S. 2001. Centromeres arc specialized replication domains in heterochromatin. J. Cell Biol. 153: 101-110.
3. -. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9: 1191-1200.
4. Altheim, B.A. and Schultz, M.C. 1999. Histone modification governs the cell cycle regulation of a replication-independent chromatin assembly pathway in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 96: 1345-1350.
5. Andrulis, E.D., Guzman, E., Doring, P., Werner, J., and Lis, J.T. 2000. High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: Roles in promoter proximal pausing and transcription elongation. Genes & Dev. 14: 2635-2649.
6. Boeger, H., Griesenbeck, J., Strattan, J.S., and Kornberg, R.D. 2003. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell 11: 1587-1598.
7. Campbell, R.E., Tour, O., Palmer, A.E., Steinbach, P.A., Baird, G.S., Zacharias, D.A., and Tsien, R.Y. 2002. A monomeric red fluorescent protein. Proc. Natl. Acad. Sci. 99: 7877-7882.
8. Collins, K.A., Furuyama, S., and Biggins, S. 2004. Proteolysis contributes to the exclusive centromere localization of the yeast Cse4/CENP-A histone H3 variant. Curr. Biol. 14: 1968-1972.
9. Cusick, M.E., Lee, K.S., DePamphilis, M.L., and Wassarman, P.M. 1983. Structure of chromatin at deoxyribonucleic acid replication forks: Nuclease hypersensitivity results from both prenucleosomal deoxyribonucleic acid and an immature chromatin structure. Biochemistry 22: 3873-3884.
10. Doenecke, D., Albig, W., Bode, C., Drabent, B., Franke, K., Gavenis, K., and Witt, O. 1997. Histones: Genetic diversity and tissue-specific gene expression. Histochem. Cell Biol. 107: 1-10.
11. Gunjan, A. and Verreault, A. 2003. A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell 115: 537-549.
12. Henikoff, S., Ahmad, K., Platero, J.S., and van Steensel, B. 2000. Heterochromatic deposition of centromeric histone H3-like proteins. Proc. Natl. Acad. Sci. 97: 716-721.
13. Jackson, V. 1987. Deposition of newly synthesized histones: New histones H2A and H2B do not deposit in the same nucleosomc with new histones H3 and H4. Biochemistry 26:2315-2325.
14. Jamrich, M., Greenleaf, A.L., and Bautz, E.K. 1977. Localization of RNA polymerase in polytene chromosomes of Drosophila melanogaster. Proc. Natl. Acad. Sci. 74: 2079-2083.
15. Janicki, S.M., Tsukamoto, T., Salghetti, S.E., Tansey, W.P., Sachidanandam, R., Prasanth, K.V., Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R.H., et al. 2004. From silencing to gene expression: Real-time analysis in single cells. Cell 116: 683-698.
16. Kimura, H. and Cook, P.R. 2001. Kinetics of core histones in living human cells: Little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153: 1341-1353.
17. Korge, G. 1975. Chromosome puff activity and protein synthesis in larval salivary glands of Drosophila melanogaster. Proc. Natl. Acad. Sci. 72: 4550-4554.
18. Kouskouti, A. and Talianidis, I. 2005. Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J. 24: 347-357.
19. Leach, T.J., Mazzeo, M., Chotkowski, H.L., Madignn, J.P., Wotring, M.G., and Glaser, R.L. 2000. Histone H2A.Z is widely but nonrandomly distributed in chromosomes of Drosophila melanogaster. J. Biol. Chem. 275: 23267-23272.
20. Malik, H.S. and Henikoff, S. 2003. Phylogenomics of the nucleosome. Nat. Struct. Biol. 10: 882-891.
21. McKittrick, E., Gafken, P.R., Ahmad, K., and Henikoff, S. 2004. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl. Acad. Sci. 101: 1525-1530.
22. Mizuguchi, G., Shen, X., Landry, J., Wu, W., Sen, S., and Wu, C. 2004. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303: 343-348.
23. Narlikar, G.J., Fan, H.Y., and Kingston, R.E. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487.
24. Nowak, S.J. and Corces, V.G. 2000. Phosphorylation of histone H3 correlates with transcriptionally active loci. Genes & Dev. 14: 3003-3013.
25. Park, J.M., Werner, T., Kim, J.M., Lis, J.T., and Kim, Y.J. 2001. Mediator, not holoenzyme, is directly recruited to the heat shock promoter by HSF upon heat shock. Mol. Cell 8: 9-19.
26. Pina, B. and Suau, P. 1987. Changes in histones H2A and H3 variant composition in differentiating and mature rat brain cortical neurons. Dev. Biol. 123: 51-58.
27. Polach, K.J. and Widom, J. 1996. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258: 800-812.
28. Ray-Gallet, D., Quivy, J.P., Scamps, C., Martini, E.M., Lipinski, M., and Almouzni, G. 2002. HIRA is critical for a nucleosome assembly pathway independent of DNA synthesis. Mol. Cell 9: 1091-1100.
29. Redon, C., Pilch, D., Rogakou, E., Sedelnikova, O., Newrock, K., and Bonner, W. 2002. Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12: 162-169.
30. Reinke, H. and Horz, W. 2003. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11: 1599-1607.
31. Rio, D.C. and Rubin, G.M. 1985. Transformation of cultured Drosophila melanogaster cells with a dominant selectable marker. Mol. Cell. Biol. 5: 1833-1838.
32. Rubin, G.M. and Spradling, A.C. 1983. Vectors for P element-mediated gene transfer in Drosophila. Nucleic Acids Res. 11: 6341-6351.
33. Schwabish, M.A. and Struhl, K. 2004. Evidence for eviction and rapid deposition of histories upon transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 24: 10111-10117.
34. Schwartz, B.E., Werner, J.K., and Lis, J.T. 2004. Indirect immunofluorescent labeling of Drosophila polytene chromosomes: Visualizing protein interactions with chromatin in vivo. Methods Enzymol. 376: 393-404.
35. Segraves, W.A. and Hogness, D.S. 1990. The E75 ecdysone-inducible gene responsible for the 75B early puff in Drosophila encodes two new members of the steroid receptor superfamily. Genes & Dev. 4: 204-219.
36. Shibahara, K. and Stillman, B. 1999. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell 96: 575-585.
37. Smith, S.T., Petruk, S., Sedkov, Y., Cho, E., Tillib, S., Canaani, E., and Mazo, A. 2004. Modulation of heat shock gene expression by the TAC1 chromatin-modifying complex. Nat. Cell Biol. 6: 162-167.
38. Solomon, M.J., Larsen, P.L., and Varshavsky, A. 1988. Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene. Cell 53: 937-947.
39. Staehling-Hampton, K., Jackson, P.D., Clark, M.J., Brand, A.H., and Hoffmann, P.M. 1994. Specificity of bone morphogenetic protein-related factors: Cell fate and gene expression changes in Drosophila embryos induced by decapentaplegic but not 60A. Cell Growth Differ. 5: 585-593.
40. Tagami, H., Ray-Gallet, D., Almouzni, G., and Nakatani, Y. 2004. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116:51-61.
41. Thatcher, T.H., MacGaffey, J., Bowen, J., Horowitz, S., Shapiro, D.L., and Gorovsky, M.A. 1994. Independent evolutionary origin of histone H3.3-like variants of animals and Tetrahymena. Nucleic Acids Res. 22: 180-186.
42. Waterborg, J.H. 1993. Histone synthesis and turnover in alfalfa: Fast loss of highly acetylated replacement histone variant H3.2. J. Biol. Chem. 268:4912-4917.
43. -. 1998. Dynamics of histone acetylation in Chlamydomonas reinhardtii. J. Biol. Chem. 273: 27602-27609.
44. Weintraub, H. and Groudine, M. 1976. Chromosomal subunits in active genes have an altered conformation. Science 193: 848-856.
45. Wolffe, A.P. 1998. Chromatin: Structure and function, 3rd ed. Academic Press, New York.
46. Zhang, K., Tang, H., Huang, L., Blankenship, J.W., Jones, P.R., Xiang, F., Yau, P.M., and Burlingame, A.L. 2002. Identification of acetylation and methylation sites of histone H3 from chicken erythrocytes by high-accuracy matrix-assisted laser desorption ionization-time-of-flight, matrix-assisted laser desorption ionization-postsource decay, and nanoelectrospray ionization tandem mass spectrometry. Anal. Biochem. 306: 259-269.