The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs

Biophysical Chemistry

Volumn 83, Issue 3, 2000, Pages 223-237

  Filesi, Ilaria ^a   Cacchione, Stefano ^a   De Santis, Pasquale ^b   Rossetti, Luigi ^a   Savino, Maria ^a  

^a Pasteur Institute   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Competitive reconstitution; Nucleosome; Sequence dependent DNA elasticity; Telomeres; Theoretical prediction

Indexed keywords

EXONUCLEASE;

ARABIDOPSIS; ARTICLE; CALCULATION; DNA SEQUENCE; ELASTICITY; ENERGY; HUMAN; MODEL; NONHUMAN; NUCLEOSOME; PREDICTION; PRIORITY JOURNAL; RIGIDITY; TELOMERE; TEMPERATURE;

ANIMALS; ARABIDOPSIS; BASE SEQUENCE; BOMBYX; CHLAMYDOMONAS REINHARDTII; DNA; DNA, FUNGAL; DNA, PLANT; DNA, PROTOZOAN; ELASTICITY; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEOSOMES; PROTEIN BIOSYNTHESIS; SACCHAROMYCES CEREVISIAE; TELOMERE; TETRAHYMENA THERMOPHILA; THERMODYNAMICS;

EID: 0033988692     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(99)00143-X     Document Type: Article

References (43)

1. Zakian V.A. Telomeres: beginning to understand the end. Science. 270:1995;1601-1607.
2. Greider C.W. Telomere length regulation. Annu. Rev. Biochem. 65:1996;337-365.
3. Williamson J.R. G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomol. Struct. 23:1994;703-730.
4. Acevedo O.L., Dickinson L.A., Macke T.J., Thomas C.A. Jr. The coherence of synthetic telomeres. Nucleic Acids Res. 19:1991;3409-3419.
5. Rhodes D., Giraldo R. Telomere structure and function. Curr. Opin. Struct. Biol. 5:1995;311-322.
6. Ahmed S., Kintanar A., Henderson E. Human telomeric C-strand tetraplexes. Nature Struct. Biol. 1:1994;83-88.
7. Cacchione S., Cerone M.A., Savino M. In vitro low propensity to form nucleosomes of four telomeric sequences. FEBS Lett. 400:1997;37-41.
8. Rossetti L., Cacchione S., Fuà M., Savino M. Nucleosome assembly on telomeric sequences. Biochemistry. 37:1998;6727-6737.
9. Godde J.S., Wolffe A.P. Nucleosome assembly on CTG triplet repeats. J. Biol. Chem. 271:1996;15222-15229.
10. Godde J.S., Kass S.U., Hirst M.C., Wolffe A.P. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J. Biol. Chem. 271:1996;24325-24328.
11. Chastain P.D. II, Eichler E.E., Kang S., Nelson D.L., Levene S.D., Sinden R.R. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry. 34:1995;16125-16131.
12. Hagerman P. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:1988;265-286.
13. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. X-ray structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-259.
14. Anselmi C., Bocchinfuso G., De Santis P., Fuà M., Savino M., Scipioni A. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J. Mol. Biol. 286:1999;1293-1301.
15. De Santis P., Palleschi A., Savino M., Scipioni A. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry. 29:1990;9269-9273.
16. Sanger W. Principles of Nucleic Acids Structure. 1984;148-149 Springer Verlag.
17. Shrader T.E., Crothers D.M. Artificial nucleosome positioning sequences. Proc. Natl. Acad. Sci. U.S.A. 86:1989;7418-7422.
18. Shrader T.E., Crothers D.M. Effects of DNA sequence and histone-histone interactions on nucleosome placement. J. Mol. Biol. 216:1990;69-84.
19. Cacchione S., Cerone M.A., De Santis P., Savino M. Superstructural features of the upstream regulatory regions of two pea rbcS genes and nucleosomes positioning: theoretical prediction and experimental evaluation. Biophys. Chem. 53:1995;267-281.
20. Cohen P., Blackburn E. Two types of telomeric chromatin in Tetrahymena thermophila. J. Mol. Biol. 280:1998;327-344.
21. Satchwell S., Drew H., Travers A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:1986;659-675.
22. Lowary P.T., Widom J. Nucleosome packaging and nucleosome positioning of genomic DNA. Proc. Natl. Acad. Sci. U.S.A. 94:1997;1183-1188.
23. Linxweiler W., Horz W. Reconstitution experiments show that sequence-specific histone-DNA interactions are the basis for nucleosome phasing on mouse satellite DNA. Cell. 42:1985;281-290.
24. Pennings S., Meersseman G., Bradbury E.M. Mobility of positioned nucleosomes on 5 S rDNA. J. Mol. Biol. 220:1991;101-110.
25. Alessi R., Cacchione S., De Santis P., Fuà M., Savino M. Multiple nucleosome positioning with unique rotational phasing on multimers of the light responsive elements of pea rbcS-3A and rbcS-3.6 genes: comparison between experimental and theoretical mapping. Biophys. Chem. 67:1997;151-158.
26. De Santis P., Fuà M., Savino M., Anselmi C., Bocchinfuso G. Sequence dependent circularization of DNAs: a physical model to predict the DNA sequence propensity to circularization and its changes in the presence of protein induced bending. J. Phys. Chem. 100:1996;9968-9976.
27. Kotlarz D., Fritsch A., Buc H. Variations of intramolecular ligation rates allow the detection of protein-induced bends in DNA. EMBO J. 5:1986;799-803.
28. Cacchione S., De Santis P., Foti D., Palleschi A., Savino M. Periodical polydeoxynucleotides and DNA curvature. Biochemistry. 28:1989;8706-8713.
29. Boffelli D., De Santis P., Palleschi A., Risuleo G., Savino M. A theoretical method to predict DNA permutation gel electrophoresis from the sequence. FEBS Lett. 300:1992;175-178.
30. Anselmi C., Bocchinfuso G., De Santis P., Fuà M., Scipioni A., Savino M. Statistical thermodynamic approach for evaluating the writhe transformations in circular DNA. J. Phys. Chem. 102:1998;5704-5714.
31. Gotoh O., Takashira Y. Stabilities of nearest neighbour doublets in double helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers. 20:1981;1033-1042.
32. Thomas K.R., Olivera B.M. Processivity of DNA exonucleases. J. Biol. Chem. 253:1978;424-429.
33. Camier S., Gabrielsen O., Baker R., Sentenac A. A split binding site for transcription factor tau on the tRNA3Glu gene. EMBO J. 4:1985;491-500.
34. Kovall R., Matthews B.W. Toroidal structure of lambda-exonuclease. Science. 277:1997;1824-1827.
35. Cao H., Widlund H.R., Simonsson T., Kubista M. TGGA repeats impair nucleosome formation. J. Mol. Biol. 281:1998;253-260.
36. Widlund H.R., Cao H., Simonsson S. et al. Identification and characterization of genomic nucleosome positioning sequences. J. Mol. Biol. 267:1997;807-817.
37. Lowary P.T., Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:1998;19-42.
38. Drew H., Travers A. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186:1985;773-790.
39. Makarov V.L., Lejnine S., Bedoyan J., Langmore J.P. Nucleosomal organization of telomere-specific chromatin in rat. Cell. 73:1993;775-787.
40. Tommerup H., Dousmanis A., De Lange T. Unusual chromatin in human telomeres. Mol. Cell. Biol. 14:1994;5777-5785.
41. Wright J.H., Gottschling D.E., Zakian V.A. Saccharomyces telomeres assume a non-nucleosomal chromatin structure. Genes Dev. 6:1992;197-210.
42. Larson D.D., Spangler E.A., Blackburn E.H. Dynamics of telomere length variation in Tetrahymena thermophila. Cell. 50:1987;477-483.
43. Harley C.B. Blackburn E.H., Greider C.W. Telomeres. 1995;247 Cold Spring Harbor Lab. Press, New York.