Genomic and phylogenetic footprinting at the epsilon-globin silencer region in intact human cells

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1678, Issue 2-3, 2004, Pages 126-134

  Temple, Mark D ^a   Freebody, John ^a   Murray, Vincent ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

amsacrine attached nitrogen mustard; C5O AMSA; DNA damaging agent; HS 2; hypersensitive site 2; LCR; ligation mediated polymerase chain reaction; LMPCR; locus control region; Nitrogen mustard analogue; Positioned nucleosome; Protein DNA interaction

Indexed keywords

CHLORMETHINE DERIVATIVE; EPSILON GLOBIN; PROTEIN SUBUNIT; TRANSCRIPTION FACTOR GATA 1; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL PROTECTION; CELL STRAIN K 562; CHROMATIN STRUCTURE; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA FOOTPRINTING; DNA SEQUENCE; GENE SILENCING; GENETIC CONSERVATION; GENOME IMPRINTING; HELA CELL; HUMAN; HUMAN CELL; MAMMALIAN GENETICS; MOLECULAR PHYLOGENY; MOLECULAR PROBE; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; PROTEIN MOTIF; SILENCER GENE;

AMINO ACID MOTIFS; ANIMALS; BASE SEQUENCE; BINDING SITES; CHROMATIN; DNA; DNA DAMAGE; GLOBINS; HELA CELLS; HUMANS; K562 CELLS; MECHLORETHAMINE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEOSOMES; PHYLOGENY; POLYMERASE CHAIN REACTION; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

BRASSICACEAE; MAMMALIA;

EID: 2442598203     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbaexp.2004.03.003     Document Type: Article

References (35)

1. Bulger M., Bender M.A., van Doorninck J.H., Wertman B., Farrell Catherine M., Felsenfeld G., Groudine M., Hardison R. Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters. Proc. Natl. Acad. Sci. U. S. A. 97:2000;14560-14565
2. Stamatoyannopoulos G., Nienhuis A.W. Stamatoyannopoulos G., Nienhuis A.W., Majerus P.J., Varmus H. The Molecular Basis of Blood Diseases. 2nd ed. 1994;107-156 W.B. Saunders, Philadelphia
3. Grosveld F., van Assendelft G.B., Greaves D.R., Kollias G. Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell. 51:1987;975-985
4. Ptashne M., Gann A.A. Activators and targets. Nature. 346:1990;329-331
5. Grosveld F., Antoniou M., Berry M., De Boer E., Dillon N., Ellis J., Fraser P., Hanscombe O., Hurst J., Imam A. The regulation of human globin gene switching. Philos. Trans. R. Soc. Lond., B Biol. Sci. 339:1993;183-191
6. Wijgerde M., Grosveld F., Fraser P. Transcription complex stability and chromatin dynamics in vivo. Nature. 377:1995;209-213
7. Grosveld F., de Boer E., Dillon N., Fraser P., Gribnau J., Milot E., Trimborn T., Wijgerde M. The dynamics of globin gene expression and gene therapy vectors. Semin. Hematol. 35:1998;105-111
8. Gong Q., Dean A. Enhancer-dependent transcription of the epsilon-globin promoter requires promoter-bound GATA-1 and enhancer-bound AP-1/NF-E2. Mol. Cell. Biol. 13:1993;911-917
9. Gong Q.H., McDowell J.C., Dean A. Essential role of NF-E2 in remodeling of chromatin structure and transcriptional activation of the epsilon-globin gene in vivo by 5′ hypersensitive site 2 of the beta-globin locus control region. Mol. Cell. Biol. 16:1996;6055-6064
10. Crossley M., Merika M., Orkin S.H. Self-association of the erythroid transcription factor GATA-1 mediated by its zinc finger domains. Mol. Cell. Biol. 15:1995;2448-2456
11. Gui C.-Y., Dean A. Acetylation of a specific promoter nucleosome accompanies activation of the epsilon-globin gene by beta-globin locus control region HS2. Mol. Cell. Biol. 21:2001;1155-1163
12. Motamed K., Bastiani C., Zhang Q., Bailey A., Shen C.K. CACC box and enhancer response of the human embryonic epsilon globin promoter. Gene. 123:1993;235-240
13. Merika M., Orkin S.H. Functional synergy and physical interactions of the erythroid transcription factor GATA-1 with the Kruppel family proteins Sp1 and EKLF. Mol. Cell. Biol. 15:1995;2437-2447
14. Asano H., Li Xi S., Stamatoyannopoulos G. FKLF, a novel Kruppel-like factor that activates human embryonic and fetal beta-like globin genes. Mol. Cell. Biol. 19:1999;3571-3579
15. Tanimoto K., Liu Q., Grosveld F., Bungert J., Engel James D. Context-dependent EKLF responsiveness defines the developmental specificity of the human epsilon-globin gene in erythroid cells of YAC transgenic mice. Genes Dev. 14:2000;2778-2794
16. Gong Q.H., Stern J., Dean A. Transcriptional role of a conserved GATA-1 site in the human epsilon-globin gene promoter. Mol. Cell. Biol. 11:1991;2558-2566
17. Ikonomi P., Noguchi Constance T., Miller W., Kassahun H., Hardison R., Schechter Alan N. Levels of GATA-1/GATA-2 transcription factors modulate expression of embryonic and fetal hemoglobins. Gene. 261:2000;277-287
18. Cao S.X., Gutman P.D., Dave H.P., Schechter A.N. Identification of a transcriptional silencer in the 5′-flanking region of the human epsilon-globin gene. Proc. Natl. Acad. Sci. U. S. A. 86:1989;5306-5309
19. Raich N., Papayannopoulou T., Stamatoyannopoulos G., Enver T. Demonstration of a human epsilon-globin gene silencer with studies in transgenic mice. Blood. 79:1992;861-864
20. Peters B., Merezhinskaya N., Diffley J.F., Noguchi C.T. Protein-DNA interactions in the epsilon-globin gene silencer. J. Biol. Chem. 268:1993;3430-3437
21. Raich N., Clegg C.H., Grofti J., Romeo P.H., Stamatoyannopoulos G. GATA1 and YY1 are developmental repressors of the human epsilon-globin gene. EMBO J. 14:1995;801-809
22. Temple M.D., Cairns M.J., Denny W.A., Murray V. Protein-DNA interactions in the human beta-globin locus control region hypersensitive site-2 as revealed by four nitrogen mustards. Nucleic Acids Res. 25:1997;3255-3260
23. Temple M.D., Cairns M.J., Kim A., Murray V. Protein-DNA footprinting of the human epsilon-globin promoter in human intact cells using nitrogen mustard analogues and other DNA-damaging agents. Biochim. Biophys. Acta. 1445:1999;245-256
24. Kim A., Murray V. Chromatin structure at the 3′-boundary of the human beta-globin locus control region hypersensitive site-2. Int. J. Biochem. Cell Biol. 33:2001;1183-1192
25. Murray V. A survey of the sequence specific interaction of damaging agents with DNA: emphasis on anti-tumour agents. Prog. Nucleic Acid Res. Mol. Biol. 63:2000;367-415
26. Fan J.Y., Valu K.K., Woodgate P.D., Baguley B.C., Denny W.A. Aniline mustard analogues of the DNA-intercalating agent amsacrine: DNA interaction and biological activity. Anti-Cancer Drug Des. 12:1997;181-203
27. Murray V., Martin R.F. The sequence specificity of bleomycin-induced DNA damage in intact cells. J. Biol. Chem. 260:1985;10389-10391
28. Maxam A.M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65:1980;499-560
29. Murray V. Improved double-stranded DNA sequencing using the linear polymerase chain reaction. Nucleic Acids Res. 17:1989;8889
30. Cairns M.J., Murray V. Influence of chromatin structure on bleomycin-DNA interactions at base pair resolution in the human beta-globin gene cluster. Biochemistry. 35:1996;8753-8760
31. Garrity P.A., Wold B.J. Effects of different DNA polymerases in ligation-mediated PCR: enhanced genomic sequencing and in vivo footprinting. Proc. Natl. Acad. Sci. U. S. A. 89:1992;1021-1025
32. Charnay P., Maniatis T. Transcriptional regulation of globin gene expression in the human erythroid cell line K562. Science. 220:1983;1281-1283
33. Yang W.M., Inouye C., Zeng Y., Bearss D., Seto E. Transcriptional repression by YY1 is mediated by interaction with a mammalian homolog of the yeast global regulator RPD3. Proc. Natl. Acad. Sci. U. S. A. 93:1996;12845-12850
34. Gumucio D.L., Shelton D.A., Bailey W.J., Slightom J.L., Goodman M. Phylogenetic footprinting reveals unexpected complexity in trans factor binding upstream from the epsilon-globin gene. Proc. Natl. Acad. Sci. U. S. A. 90:1993;6018-6022
35. Porter C.A., Sampaio I., Schneider H., Schneider M.P., Czelusniak J., Goodman M. Evidence on primate phylogeny from epsilon-globin gene sequences and flanking regions. J. Mol. Evol. 40:1995;30-55