TGGA repeats impair nucleosome formation

Journal of Molecular Biology

Volumn 281, Issue 2, 1998, Pages 253-260

  Cao, Hui ^a   Widlund, Hans R ^a   Simonsson, Tomas ^a   Kubista, Mikael ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

Chromatin; Nucleosome; Nucleosome positioning; Selection; TGGA repeat

Indexed keywords

HISTONE; SODIUM CHLORIDE; SYNTHETIC DNA;

ANIMAL CELL; ARTICLE; CELL NUCLEUS; CHROMATIN STRUCTURE; DNA PACKAGING; DNA SEQUENCE; EUKARYOTIC CELL; MOLECULAR CLONING; MOUSE; NONHUMAN; NUCLEOSOME; NUCLEOTIDE REPEAT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; THERMODYNAMICS;

ANIMALIA; EUKARYOTA;

EID: 0032516764     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1925     Document Type: Article

References (35)

1. Albert T., Mautner J., Funk J.O., Hortnagel K., Pullner A., Eick D. Nucleosomal structures of c-myc promoters with transcriptionally engaged RNA polymerase II. Mol. Cell. Biol. 17:(8):1997;4363-4371
2. Batson S.C., Rimsky S., Sundseth R., Hansen U. Association of nucleosome-free regions and basal transcription factors with in vivo-assembled chromatin templates active in vitro. Nucl. Acids Res. 21:(15):1993;3459-3468
3. Blackburn E.H. Structure and function of telomeres. Nature. 350:(6319):1991;569-573
4. n 5′ to the human myelin basic protein gene a new form of oligonucleotide repetitive sequence showing length polymorphism. Genomics. 6:(1):1990;16-22
5. Cacchione S., Cerone M.A., Savino M. In vitro low propensity to form nucleosomes of four telomeric sequences. FEBS Letters. 400:(1):1997;37-41
6. Drew H.R., Travers A.A. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186:(4):1985;773-790
7. Felsenfeld G. Chromatin. Nature. 271:(5641):1978;115-122
8. Guschlbauer W., Chantot J.F., Thiele D. Four-stranded nucleic acid structures 25 years later from guanosine gels to telomer DNA. J. Biomol. Struct. Dynam. 8:(3):1990;491-511
9. Hammond-Kosack M.C., Kilpatrick M.W., Docherty K. The human insulin gene-linked polymorphic region adopts a G-quartet structure in chromatin assembled in vitro. J. Mol. Endocrinol. 10:(2):1993;121-126
10. Hayes J.J., Tullius T.D., Wolffe A.P. The structure of DNA in a nucleosome. Proc. Natl Acad. Sci. USA. 87:(19):1990;7405-7409
11. Kornberg R.D., Thomas J.O. Chromatin structure; oligomers of the histones. Science. 184:(139):1974;865-868
12. Lowary P.T., Widom J. Nucleosome packaging and nucleosome positioning of genomic DNA. Proc. Natl Acad. Sci. USA. 94:(4):1997;1183-1188
13. n repeats is critical for the formation of the DNase I hypersensitive sites in the Drosophila hsp26 gene. J. Mol. Biol. 225:(4):1992;985-998
14. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260
15. McGhee J.D., von Hippel P.H. Theoretical aspects of DNA-protein interactions co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86:(2):1974;469-489
16. Muyldermans S., Travers A.A. DNA sequence organization in chromatosomes. J. Mol. Biol. 235:(3):1994;855-870
17. Rhodes D., Giraldo R. Telomere structure and function. Curr. Opin. Struct. Biol. 5:(3):1995;311-322
18. Saha B.K., Shields J.J., Miller R.D., Hansen T.H., Shreffler D.C. A highly polymorphic microsatellite in the class II Eb gene allows tracing of major histocompatibility complex evolution in mouse. Proc. Natl Acad Sci. USA. 90:(11):1993;5312-5316. (Published erratum appears in Proc. Natl Acad Sci. USA, 1993 Sept. 15; 90(18), 8757).
19. Samuelson P., Jansen K., Kubista M. Long-range interactions between DNA-bound ligands. J. Mol. Recog. 7:1994;241-253
20. Satchwell S.C., Drew H.R., Travers A.A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:(4):1986;659-675
21. Schofield A.E., Martin P.G., Spillett D., Tanner M.J. The structure of the human red blood cell anion exchanger (EPB3, AE1, band 3) gene. Blood. 84:(6):1994;2000-2012
22. Sen D., Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 334:(6180):1988;364-366
23. Shimada T., Inokuchi K., Nienhuis A.W. Chromatin structure of the human dihydrofolate reductase gene promoter. Multiple protein-binding sites. J. Biol. Chem. 261:(3):1986;1445-1452
24. Shrader T.E., Crothers D.M. Artificial nucleosome positioning sequences. Proc. Natl Acad. Sci. USA. 86:(19):1989;7418-7422
25. Simpson R.T. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature. 343:(6256):1990;387-389
26. Sundquist W.I., Klug A. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 342:(6251):1989;825-829
27. Thoma F., Simpson R.T. Local protein-DNA interactions may determine nucleosome positions on yeast plasmids. Nature. 315:(6016):1985;250-252
28. van Holde K.E. Chromatin. Springer Series in Molecular Biology. 1989;Springer-Verlag, New York
29. Weller P., Jeffreys A.J., Wilson V., Blanchetot A. Organization of the human myoglobin gene. EMBO J. 3:(2):1984;439-446
30. Verdone L., Camilloni G., Di Mauro E., Caserta M. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell. Biol. 16:(5):1996;1978-1988
31. Widlund H.R., Cao H., Simonsson S., Magnusson E., Simonsson T., Nielsen P.E., Kahn J.D., Crothers D.M., Kubista M. Identification and characterization of genomic nucleosome-positioning sequences. J. Mol. Biol. 267:(4):1997;807-817
32. Williamson J.R. G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. 23:1994;703-730
33. Wolffe A.P. Trans-acting factors, DNase I sensitivity, DNase I hypersensitivity sites and chromosomal architecture. Wolffe A. Chromatin Structure and Function. 2nd edit.:1995;199-208 Academic Press, London
34. Woodford K.J., Howell R.M., Usdin K. A novel K(+)-dependent DNA synthesis arrest site in a commonly occurring sequence motif in eukaryotes. J. Biol. Chem. 269:(43):1994;27029-27035
35. Woodford K., Weitzmann M.N., Usdin K. The use of K(+)-free buffers eliminates a common cause of premature chain termination in PCR and PCR sequencing. Nucl. Acids Res. 23:(3):1995;539