Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites

BMB Reports

Volumn 43, Issue 11, 2010, Pages 744-749

  Balani, Valério Américo ^a   de Lima Neto, Quirino Alves ^a   Takeda, Karen Izumi ^a   Gimenes, Fabrícia ^a   Fiorini, Adriana ^a   Debatisse, Michelle ^b   Fernandez, Maria Aparecida ^a  

^a STATE UNIVERSITY OF MARINGÁ   (Brazil)

^b INSTITUT CURIE   (France)

Author keywords

Electrophoretic mobility shift assay; In silico analysis; Intrinsically bent DNA sites; Mammalian amplified AMPD2 locus; OriGNAI3 and oriB replication origins

Indexed keywords

ADENOSINE MONOPHOSPHATE DEAMINASE; DNA;

ANIMAL; ARTICLE; CHEMISTRY; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA SEQUENCE; GEL MOBILITY SHIFT ASSAY; GENE LOCUS; GENETICS; HAMSTER;

AMP DEAMINASE; ANIMALS; CRICETINAE; DNA; DNA REPLICATION; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENETIC LOCI; REPLICATION ORIGIN; SEQUENCE ANALYSIS, DNA;

CRICETULUS GRISEUS; MAMMALIA;

EID: 78649788114     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.3858/BMBRep.2010.43.11.744     Document Type: Article

References (28)

1. Calladine, C. R., Drew, H. R., Luisi, B. F. and Travers, A. A. (2004) Understanding DNA: the molecule and how it works, 3nd ed., Elsevier Academic Press, Italy.
2. Zhang, Y., Xi, Z., Hegde, R. S., Shakked, Z. and Crothers, D. M. (2004) Predicting indirect readout effects in protein-DNA interactions. Proc. Natl. Acad. Sci. U.S.A. 101, 8337-8341.
3. Bates, A., D. and Maxwell, A. (2005) DNA Topology. Oxford University Press, Oxford.
4. Anderson, J. N. (1986) Detection, sequence patterns and function of unusual DNA structures. Nucleic. Acids. Res. 14, 8513-8533.
5. Fiorini, A., Basso, L. R. Jr., Paço-Larson, M. L. and Fernandez, M. A. (2001) Mapping of intrinsic bent DNA sites in the upstream region of DNA puff BhC4-1 amplified gene. J. Cell Biochem. 83, 1-13.
6. Fiorini, A., Gouveia, F. S., Soares, M. A. M., Stocker, A. J., Ciferri, R. R. and Fernandez, M. A. (2006) DNA bending in the replication zone of the C3 DNA puff amplicon of Rhynchosciara americana (Diptera: Sciaridae). Mol. Biol. Rep. 33, 71-82.
7. Fiorini, A., Gouveia, F. S. and Fernandez, M. A. (2006) Scaffold/Matrix Attachment Regions and Intrinsic DNA Curvature. Biochemistry Mosc. 71, 481-488.
8. Barbosa, J. F., Bravo, J. P., Takeda, K. I., Zanatta, D. B., Silva, J. L. C., Balani, V. A., Fiorini, A. and Fernandez, M. A. (2008) Intrinsic bent DNA colocalizes with the sequence involved in the Nd-sD mutation in the Bombyx mori fibroin light chain gene. BMB Rep. 41, 394-399.
9. Gouveia, F. S., Gimenes, F., Fiorini, A. and Fernandez, M. A. (2008) Intrinsic bent DNA sites in the developmentally amplified C3-22 gene promoter of Rhynchosciara americana (Diptera: Sciaridae). Biosci. Biotechnol. Biochem. 72, 1190-1198.
10. Gimenes, F., Gouveia Fde, S., Fiorini, A. and Fernandez, M. A. (2008) Intrinsic bent DNA sites in the chromosomal replication origin of Xylella fastidiosa 9a5c. Braz. J. Med.Biol. Res. 41, 295-304.
11. Gimenes, F., Takeda, K. I., Gouveia, F. S., Fiorini, A. and Fernandez, M. A. (2008) Intrinsically bent DNA in replication origins and gene promoters. Genet. Mol. Res. 7, 549-558.
12. Gimenes, F., Assis, M. A., Fiorini, A., Mareze, V. A. and Fernandez, M. A. (2009) Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain. Mol. Genet. Genomics. 281, 539-549.
13. Anglana, M., Apiou, F., Bensimon, A. and Debatisse, M. (2003) Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114, 385-394.
14. Debatisse, M., Toledo, F. and Anglana, M. (2004) Replication initiation in mammalian cells: changing preferences. Cell Cycle 3, 19-21.
15. Courbet, S., Gay, S., Arnoult, N., Wronka, G., Anglana, M., Brison, O. and Debatisse, M. (2008). Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 455, 557-560.
16. Fernandez, M. A., Baron, B., Prigent, M., Toledo, F., Buttin, G. and Debatisse, M. (1997) Matrix attachment regions and transcription units in a polygenic mammalian locus overlapping two isochores. J. Cell Biochem. 67, 541-551.
17. Ohyama, T. (2005) DNA conformation and transcription. Springer Science + Bussiness Media, New York, USA.
18. Wu, H., M. and Crothers, D. M. (1984) The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509-513.
19. Sperbeck, S. J. and Wistow, G. J. (1998) pBendBlue: modification of the pBend system for color selectability. Biotechniques 24, 66-68.
20. Gray, S. J., Liu, G., Altman A. L., Small L. E. and Fanning E. (2007) Discrete functional elements required for initiation activity of the chinese hamster dihydrofolate reductase origin beta at ectopic chromosomal sites. Exp. Cell Res. 313, 109-120.
21. Eaton, M. L., Galani, K., Kang, S., Bell, S. P. and Mac-Alpine, D. M. (2010) Conserved nucleosome positioning defines replication origins. Genes. Dev. 24, 748- 753.
22. MacAlpine, H. K., Gordan, R., Powell, S. K., Hartemink, A. J. and MacAlpine, D. M. (2010) Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome. Res. 20, 201-211.
23. Toledo, F., Baron, B., Fernandez, M. A., Lachages, A. M., Mayau, V., Buttin, G. and Debatisse, M. (1998) oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques. Nucleic. Acids. Res. 26, 2313-2321.
24. Del Sal, G., ManWoletti, G. and Schneider, C. (1989) The CTAB-DNA précipitation method: a common mini-scale preparation of template DNA from phagemids, phages or plasmids suitable for sequencing. Biotechniques 7, 514-520.
25. de Souza, O. N. and Ornstein, R. L. (1998) Inherent DNA curvature and flexibility correlate with TATA box functionality. Biopolymers 46, 403-415.
26. Kim, J., Zwieb, C., Wu, C. and Adhya, S. (1989) Bending of DNA by gene regulatory proteins: construction and use of a DNA bending vector. Gene 85, 15-23.
27. Bolshoy, A., Mcnamaera, P., Harrington, R. E. and Trifonov, E. N. (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl. Acad. Sci. U.S.A. 88, 2312-2316.
28. Eckdahl, T. T. and Anderson, J. N. (1987) Computer modelling of DNA structures involved in chromosome maintenance. Nucleic. Acids. Res. 15, 8531-8545.