Constitutive Promoter Occupancy by the MBF-1 Activator and Chromatin Modification of the Developmental Regulated Sea Urchin α-H2A Histone Gene

Journal of Molecular Biology

Volumn 365, Issue 5, 2007, Pages 1285-1297

  Di Caro, Valentina ^a   Cavalieri, Vincenzo ^a   Melfi, Raffaella ^a   Spinelli, Giovanni ^a  

^a UNIVERSITY OF PALERMO   (Italy)

Author keywords

chromatin immunoprecipitation; histone modifications; MBF 1 activator; nucleosome phasing; sea urchin histone genes

Indexed keywords

HISTONE; HISTONE DEACETYLASE; HISTONE H2A; HISTONE H2A ALPHA; HISTONE H3; OLIGONUCLEOTIDE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MBF 1; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALPHA H2A GENE; ARTICLE; BINDING SITE; BLASTULA; CHROMATIN STRUCTURE; DEACETYLATION; DEVELOPMENTAL STAGE; DOWN REGULATION; EMBRYO; ENHANCER REGION; GASTRULATION; GENE; GENE CONTROL; GENE INSERTION; GENE LOCATION; GENE MAPPING; GENE REPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; IMMUNOPRECIPITATION; MORULA; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN METHYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; SEA URCHIN; TATA BOX; TRANSACTIVATION;

ECHINOIDEA;

EID: 33845976630     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.10.098     Document Type: Article

References (67)

1. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 (1997) 251-260
2. Luger K. Structure and dynamic behavior of nucleosomes. Curr. Opin. Genet. Dev. 13 (2003) 127-135
3. Khorasanizadeh S. The nucleosome: from genomic organization to genomic regulation. Cell 116 (2004) 259-272
4. Luger K. Dynamic nucleosomes. Chromosome Res. 14 (2006) 5-16
5. Workman J.L., and Kingston R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67 (1998) 545-579
6. Luger K., and Hansen J.C. Nucleosome and chromatin fiber dynamics. Curr. Opin. Struct. Biol. 15 (2005) 188-196
7. Narlikar G.J., Fan H.Y., and Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108 (2002) 475-487
8. Langst G., and Becker P.B. Nucleosome remodeling: one mechanism, many phenomena?. Biochim. Biophys. Acta 1677 (2004) 58-63
9. Flaus A., and Owen-Hughes T. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer?. Curr. Opin. Genet. Dev. 14 (2004) 165-173
10. Berger S.L. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12 (2002) 142-148
11. Zhang L., Eugeni E.E., Parthun M.R., and Freitas M.A. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma 112 (2003) 77-86
12. Xu F., Zhang K., and Grunstein M. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell 121 (2005) 375-385
13. Freitas M.A., Sklenar A.R., and Parthun M.R. Application of mass spectrometry to the identification and quantification of histone post-translational modifications. J. Cell Biochem. 92 (2004) 691-700
14. Allfrey V.G., Faulkner R., and Mirsky A.E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51 (1964) 786-794
15. Roth S.Y., Denu J.M., and Allis C.D. Histone acetyltransferases. Annu. Rev. Biochem. 70 (2001) 81-120
16. Jenuwein T., and Allis C.D. Translating the histone code. Science 293 (2001) 1074-1080
17. Turner B.M. Cellular memory and the histone code. Cell 111 (2002) 285-291
18. Spinelli G., Gianguzza F., Casano C., Acierno P., and Burckhardt J. Evidences of two different sets of histone genes active during embryogenesis of the sea urchin Paracentrotus lividus. Nucl. Acids Res. 6 (1979) 545-560
19. Spinelli G., and Birnstiel M.L. The modulator is a constitutive enhancer of a developmentally regulated sea urchin histone H2A gene. Bioessays 24 (2002) 850-857
20. Childs G., Nocente-McGrath C., Lieber T., Holt C., and Knowles J.A. Sea urchin (lytechinus pictus) late-stage histone H3 and H4 genes: characterization and mapping of a clustered but nontandemly linked multigene family. Cell 31 (1982) 383-393
21. Weinberg E.S., Overton G.C., Hendricks M.B., Newrock K.M., and Cohen L.H. Histone gene heterogeneity in the sea urchin Strongylocentrotus purpuratus. Cold Spring Harbor Symp. Quant. Biol. 42 (1978) 1093-1100
22. Spinelli G., Albanese I., Anello L., Ciaccio M., and Di Liegro I. Chromatin structure of histone genes in sea urchin sperms and embryos. Nucl. Acids Res. 10 (1982) 7977-7991
23. Bryan P.N., Olah J., and Birnstiel M.L. Major changes in the 5′ and 3′ chromatin structure of sea urchin histone genes accompany their activation and inactivation in development. Cell 33 (1983) 843-848
24. Fronk J., Tank G.A., and Langmore J.P. Chromatin structure of the developmentally regulated early histone genes of the sea urchin Strongylocentrotus purpuratus. Nucl. Acids Res. 18 (1990) 5255-5263
25. Palla F., Casano C., Albanese I., Anello L., Gianguzza F., Di Bernardo M.G., et al. Cis-acting elements of the sea urchin histone H2A modulator bind transcriptional factors. Proc. Natl Acad. Sci. USA 86 (1989) 6033-6037
26. Palla F., Bonura C., Anello L., Casano C., Ciaccio M., and Spinelli G. Sea urchin early histone H2A modulator binding factor 1 is a positive transcription factor also for the early histone H3 gene. Proc. Natl Acad. Sci. USA 90 (1993) 6854-6858
27. Palla F., Bonura C., Anello L., Di Gaetano L., and Spinelli G. Modulator factor-binding sequence of the sea urchin early histone H2A promoter acts as an enhancer element. Proc. Natl Acad. Sci. USA 91 (1994) 12322-12326
28. Palla F., Melfi R., Di Gaetano L., Bonura C., Anello L., Alessandro C., and Spinelli G. Regulation of the sea urchin early H2A histone gene expression depends on the modulator element and on sequences located near the 3′ end. Biol. Chem. 380 (1999) 159-165
29. Alessandro C., Di Simone P., Buscaino A., Anello L., Palla F., and Spinelli G. Identification of the enhancer binding protein MBF-1 of the sea urchin modulator alpha-H2A histone gene. Biochem. Biophys. Res. Commun. 295 (2002) 519-525
30. Grosschedl R., and Birnstiel M.L. Delimitation of far upstream sequences required for maximal in vitro transcription of an H2A histone gene. Proc. Natl Acad. Sci. USA 79 (1982) 297-301
31. Grosschedl R., Machler M., Rohrer U., and Birnstiel M.L. A functional component of the sea urchin H2A gene modulator contains an extended sequence homology to a viral enhancer. Nucl. Acids Res. 11 (1983) 8123-8136
32. Palla F., Melfi R., Anello L., Di Bernardo M., and Spinelli G. Enhancer blocking activity located near the 3′ end of the sea urchin early H2A histone gene. Proc. Natl Acad. Sci. USA 94 (1997) 2272-2277
33. Di Caro D., Melfi R., Alessandro C., Serio G., Di Caro V., Cavalieri V., et al. Down-regulation of early sea urchin histone H2A gene relies on cis regulative sequences located in the 5′ and 3′ regions and including the enhancer blocker sns. J. Mol. Biol. 342 (2004) 1367-1377
34. Anello L., Albanese I., Casano C., Palla F., Gianguzza F., Di Bernardo M.G., et al. Different micrococcal nuclease cleavage patterns characterize transcriptionally active and inactive sea-urchin histone genes. Eur. J. Biochem. 156 (1986) 367-374
35. Melfi R., Palla F., Di Simone P., Alessandro C., Cali L., Anello L., and Spinelli G. Functional characterization of the enhancer blocking element of the sea urchin early histone gene cluster reveals insulator properties and three essential cis-acting sequences. J. Mol. Biol. 304 (2000) 753-763
36. Di Simone P., Di Leonardo A., Costanzo G., Melfi R., and Spinelli G. The sea urchin sns insulator blocks CMV enhancer following integration in human cells. Biochem. Biophys. Res. Commun. 284 (2001) 987-992
37. Acuto S., Di Marzo R., Calzolari R., Baiamonte E., Maggio A., and Spinelli G. Functional characterization of the sea urchin sns chromatin insulator in erythroid cells. Blood Cells Mol. Dis. 35 (2005) 339-344
38. Polach K.J., and Widom J. Restriction enzymes as probes of nucleosome stability and dynamics. Methods Enzymol. 304 (1999) 278-298
39. Verdin E., Paras Jr. P., and Van Lint C. Chromatin disruption in the promoter of human immunodeficiency virus type 1 during transcriptional activation. EMBO J. 12 (1993) 3249-3259
40. Polach K.J., and Widom J. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254 (1995) 130-149
41. DiLiberto M., Lai Z.C., Fei H., and Childs G. Developmental control of promoter-specific factors responsible for the embryonic activation and inactivation of the sea urchin early histone H3 gene. Genes Dev. 3 (1989) 973-985
42. Nemer M. Histone deacetylase mRNA temporally and spatially regulated in its expression in sea urchin embryos. Dev. Growth Differ. 40 (1998) 583-590
43. Turner B.M. Reading signals on the nucleosome with a new nomenclature for modified histones. Nature Struct. Mol. Biol. 12 (2005) 110-112
44. Kedes L.H., Chang A.C., Houseman D., and Cohen S.N. Isolation of histone genes from unfractionated sea urchin DNA by subculture cloning in E. coli. Nature 255 (1975) 533-538
45. Clarkson S.G., Smith H.O., Schaffner W., Gross K.W., and Birnstiel M.L. Integration of eukaryotic genes for 5S RNA and histone proteins into a phage lambda receptor. Nucl. Acids Res. 3 (1976) 2617-2632
46. Grosschedl R., and Birnstiel M.L. Identification of regulatory sequences in the prelude sequences of an H2A histone gene by the study of specific deletion mutants in vivo. Proc. Natl Acad. Sci. USA 77 (1980) 1432-1436
47. Grosschedl R., and Birnstiel M.L. Spacer DNA sequences upstream of the T-A-T-A-A-A-T-A sequence are essential for promotion of H2A histone gene transcription in vivo. Proc. Natl Acad. Sci. USA 77 (1980) 7102-7106
48. Levine M., and Manley J.L. Transcriptional repression of eukaryotic promoters. Cell 59 (1989) 405-408
49. Herschbach B.M., and Johnson A.D. Transcriptional repression in eukaryotes. Annu. Rev. Cell Biol. 9 (1993) 479-509
50. Maldonado E., Hampsey M., and Reinberg D. Repression: targeting the heart of the matter. Cell 99 (1999) 455-458
51. Redd M.J., Stark M.R., and Johnson A.D. Accessibility of alpha 2-repressed promoters to the activator Gal4. Mol. Cell. Biol. 16 (1996) 2865-2869
52. Dellino G.I., Schwartz Y.B., Farkas G., McCabe D., Elgin S.C., and Pirrotta V. Polycomb silencing blocks transcription initiation. Mol. Cell 13 (2004) 887-893
53. Chen L., and Widom J. Mechanism of transcriptional silencing in yeast. Cell 120 (2005) 37-48
54. Weinberg E.S., Hendricks M.B., Hemminki K., Kuwabara P.E., and Farrelly L.A. Timing and rates of synthesis of early histone mRNA in the embryo of Strongylocentrotus purpuratus. Dev. Biol. 98 (1983) 117-129
55. Aronson A.I., and Chen K. Rates of RNA chain growth in developing sea urchin embryos. Dev. Biol. 59 (1977) 39-48
56. Lynn D.A., Angerer L.M., Bruskin A.M., Klein W.H., and Angerer R.C. Localization of a family of MRNAS in a single cell type and its precursors in sea urchin embryos. Proc. Natl Acad. Sci. USA 80 (1983) 2656-2660
57. Conconi A., Widmer R.M., Koller T., and Sogo J.M. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell 57 (1989) 753-761
58. Jasinskas A., Jasinskiene N., and Langmore J.P. Psoralen crosslinking of active and inactive sea urchin histone and rRNA genes. Biochim. Biophys. Acta 1397 (1998) 285-294
59. Beato M., and Eisfeld K. Transcription factor access to chromatin. Nucl. Acids Res. 25 (1997) 3559-3563
60. Imbalzano A.N., Kwon H., Green M.R., and Kingston R.E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370 (1994) 481-485
61. Martinez-Campa C., Politis P., Moreau J.L., Kent N., Goodall J., Mellor J., and Goding C.R. Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1. Mol. Cell 15 (2004) 69-81
62. Zhang Y., and Reinberg D. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 15 (2001) 2343-2360
63. West A.G., Gaszner M., and Felsenfeld G. Insulators: many functions, many mechanisms. Genes Dev. 16 (2002) 271-288
64. Felsenfeld G., and Groudine M. Controlling the double helix. Nature 421 (2003) 448-453
65. West A.G., Huang S., Gaszner M., Litt M.D., and Felsenfeld G. Recruitment of histone modifications by USF proteins at a vertebrate barrier element. Mol. Cell 16 (2004) 453-463
66. Mutskov V.J., Farrell C.M., Wade P.A., Wolffe A.P., and Felsenfeld G. The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation. Genes Dev. 16 (2002) 1540-1554
67. von Holt C., Brandt W.F., Greyling H.J., Lindsey G.G., Retief J.D., Rodrigues J.D., et al. Isolation and characterization of histones. Methods Enzymol. 170 (1989) 431-523