DNA bend sites in the human β-globin locus: Evidence for a basic and universal structural component of genomic DNA

Molecular Biology and Evolution

Volumn 16, Issue 7, 1999, Pages 922-930

  Wada Kiyama, Yuko ^a   Suzuki, Kiyoko ^a   Kiyama, Ryoiti ^b  

^a NIPPON MEDICAL SCHOOL   (Japan)

^b Ministry of International Trade and Industry   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBULIN; CURVED DNA; GAMMA GLOBIN;

ARTICLE; DNA FLANKING REGION; DNA STRUCTURE; GENE CONTROL; GENE EXPRESSION REGULATION; GENE INSERTION; GENE LOCATION; GENE LOCUS; GENETIC CONSERVATION; NUCLEOSOME; NUCLEOTIDE SEQUENCE;

EID: 0033010426     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026181     Document Type: Article

References (26)

1. BOLSHOY, A., P. MCNAMARA, R.E. HARRINGTON, and E. N. TRIFONOV. 1991. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. USA 88:2312-2316.
2. CALLADINE, C. R., C. M. COLLIS, H. R. DREW, and M. R. MOTT. 1991. A study of electrophoretic mobility of DNA in agarose and polyacrylamide gels. J. Mol. Biol. 221:981-1005.
3. CALLADINE, C. R., H. R. DREW, and M. J. MCCALL. 1988. The intrinsic curvature of DNA in solution. J. Mol. Biol. 201: 127-137.
4. DREW H. R., and C. R. CALLADINE. 1987. Sequence-specific positioning of core histones on an 860 base-pair DNA. J. Mol. Biol. 195:143-173.
5. FITCH, D. H., C. MAINONE, M. GOODMAN, and J. L. SLIGHTOM. 1990. Molecular history of gene conversion in the primate fetal γ-globin genes. Nucleotide sequences from the common gibbon, Hylobates lar. J. Biol. Chem. 265:781-793.
6. HARDISON, R., J. L. SLIGHTOM, D. L. GUMUCIO, M. GOODMAN, N. STOJANOVIC, and W. MILLER. 1997. Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 205:73-94.
7. IOSHIKHES, I., A. BOLSHOY, K. DERENSHTEYN, M. BORODOVSKY, and E. N. TRIFONOV. 1996. Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262:129-139.
8. KIYAMA, R. 1998. Perodicity of DNA bend sites in eukaryotic genomes. Gene. Ther. Mol. Biol. 1:641-647.
9. KOO, J.-S., H.-M. WU, and D. M. CROTHERS. 1986. DNA bending at adenine · thymine tracts. Nature 320:501-506.
10. MCPHERSON, C.E., R. HOROWITZ, C. L. WOODCOCK, C. JIANG, and K. S. ZARET. 1996. Nucleosome positioning properties of the albumin transcriptional enhancer. Nucleic Acids Res. 24:397-404.
11. NAIR, T. M. 1998. Evidence for intrinsic DNA bends within the human cdc2 promoter. FEBS Lett. 422:94-98.
12. OHKI, R., M. HIROTA, M. OISHI, and R. KIYAMA. 1998. Conservation and continuity of periodic bent DNA in genomic rearrangements between the c-myc and immunoglobulin heavy chain μ loci. Nucleic Acids Res. 26:3026-3033.
13. OLSON, W. K. 1996. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6:242-256.
14. ONISHI, Y., Y. WADA-KIYAMA, and R. KIYAMA. 1998. Expression-dependent perturbation of nucleosomal phases at HS2 of the human β-LCR: possible correlation with periodic bent DNA. J. Mol. Biol. 284:989-1004.
15. ORKIN, S. H. 1990. Globin gene regulation and switching: circa 1990. Cell 63:665-672.
16. PINA, B., D. BARETTINO, M. TRUSS, and M. BEATO. 1990. Structural features of a regulatory nucleosome. J. Mol. Biol. 216:975-990.
17. SCHURR, J. M., J. J. DELROW, B. S. FUJIMOTO, and A. S. BENIGHT. 1997. The question of long-range allosteric transitions in DNA. Biopolymers 44:283-308.
18. SHPIGELMAN, E. S., E. N. TRIFONOV, and A. BOLSHOY. 1993. CURVATURE: software for the analysis of curved DNA. Comput. Appl. Biosci. 9:435-440.
19. STAMATOYANNOPOULOS, G., and A. W. NIENHUIS. 1993. Hemoglobin switching. Pp. 107-155 in G. STAMATOYANNO-POULOS, A. W. NIENHUIS, P. MAJERUS, and H. VARMUS, eds. The molecular basis of blood diseases. W. B. Saunders, Philadelphia.
20. WADA-KIYAMA, Y., and R. KIYAMA. 1994. Periodicity of DNA bend sites in human ∈-globin gene region: possibility of sequence-directed nucleosome phasing. J. Biol. Chem. 269: 22238-22244.
21. _. 1995. Conservation and periodicity of DNA bend sites in the human β-globin gene locus. J. Biol. Chem. 270: 12439-12445.
22. _. 1996a. Conservation and periodicity of DNA bend sites in eukaryotic genomes. DNA Res. 3:25-30.
23. _. 1996b. An intrachromosomal repeating unit based on DNA bending. Mol. Cell. Biol. 16:5664-5673.
24. WIDOM, J. 1997. Chromatin: the nucleosome unwrapped. Curr. Biol. 7:R653-R655.
25. WONG, J., Q. LI, B.-Z. LEVI, Y.-B. SHI, and A. P. WOLFFE. 1997. Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J. 16:7130-7145.
26. WU, H.-M., and D. M. CROTHERS. 1984. The locus of sequence-directed and protein-induced DNA bending. Nature 308:509-513.