Advertisement

Biochemistry (Moscow)

, Volume 79, Issue 1, pp 37–43 | Cite as

Straight core structure of DNA replication origins in the mammalian AMPD2 locus

  • Q. A. Lima Neto
  • F. S. Rando
  • D. V. B. Freitas
  • L. F. Rodrigues
  • F. R. Rosado
  • A. Fiorini
  • F. Gimenes
  • J. Tavares
  • M. A. FernandezEmail author
Article

Abstract

Identification of the nucleotide consensus sequence in mammalian replication origins is a difficult and controversial problem. The hypothesis that local DNA topology could be involved in recognition by replication proteins is an exciting possibility. Secondary DNA structures, including intrinsically bent DNA, can be easily detected, and they may indicate a specific pattern in or near mammalian replication origins. This work presents the entire mapping of the intrinsically bent DNA sites (IBDSs), using in silico analysis and a circular permutation assay, of the DNA replication origins oriGNAI3, oriC, oriB, and oriA in the mammalian amplified AMPD2 gene domain. The results show that each origin presents an IBDS that flanks the straight core of these DNA replication sites. In addition, the in silico prediction of the nucleosome positioning reveals a strong indication that the center of an IBDS is localized in a nucleosome-free region (NFR). The structure of each of these curved sites is presented together with their helical parameters and topology. Together, the data that we present here indicate that the oriGNAI3 origin where preferential firing to the replication initiation events in the amplified AMPD2 domain occurs is the only origin that presents a straight, narrow region that is flanked on both sides by two intrinsically bent DNA sites within a short distance (∼300 bp); however, all of the origins present at least one IBDS, which is localized in the NFR region. These results indicate that structural features could be implicated in the mammalian DNA replication origin and support the possibility of detecting and characterizing these segments.

Key words

intrinsically bent DNA sites DNA replication origins AMPD2 mammalian amplified domain 

Abbreviations

IBDSs

intrinsically bent DNA sites

NFRs

nucleosome-free regions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

10541_2014_9870_MOESM1_ESM.pdf (457 kb)
Supplementary material, approximately 456 KB.

References

  1. 1.
    Robinson, N. P., and Bell, S. D. (2005) FEBS J., 272, 3757–3766.PubMedCrossRefGoogle Scholar
  2. 2.
    Bell, S. P., and Stillman, B. (1992) Nature, 357, 128–134.PubMedCrossRefGoogle Scholar
  3. 3.
    Bell, S. P., and Dutta, A. (2002) Annu. Rev. Biochem., 71, 333–374.PubMedCrossRefGoogle Scholar
  4. 4.
    Masai, H., Matsumoto, S., You, Z., Yoshizawa-Sugata, N., and Oda, M. (2010) Annu. Rev. Biochem., 79, 89–130.PubMedCrossRefGoogle Scholar
  5. 5.
    Cadoret, J. C., and Prioleau, M. N. (2010) Chromosome Res., 18, 79–89.PubMedCrossRefGoogle Scholar
  6. 6.
    Cayrou, C., Coulombe, P., and Mechali, M. (2010) Chromosome Res., 18, 137–145.PubMedCrossRefGoogle Scholar
  7. 7.
    Meisch, F., and Prioleau, M. N. (2011) Brief Funct. Genom., 10, 30–36.CrossRefGoogle Scholar
  8. 8.
    Ohyama, T. (2005) DNA Conformation and Transcription, Springer Science and Business Media, New York.Google Scholar
  9. 9.
    Milot, E., Belmaaza, A., Wallenburg, J. C., Gusew, N., Bradley, W. E., and Chartrand, P. (1992) EMBO J., 11, 5063–5070.PubMedGoogle Scholar
  10. 10.
    Barbosa, J. F., Bravo, J. P., Takeda, K. I., Zanatta, D. B., Silva, J. L., Balani, V. A., Fiorini, A., and Fernandez, M. A. (2008) BMB Rep., 41, 394–399.PubMedCrossRefGoogle Scholar
  11. 11.
    Fiorini, A., Basso, L. R., Paco-Larson, M. L., and Fernandez, M. A. (2001) J. Cell Biochem., 83, 1–13.PubMedCrossRefGoogle Scholar
  12. 12.
    Altman, A. L., and Fanning, E. (2004) Mol. Cell Biol., 24, 4138–4150.PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Fiorini, A., de Gouveia, F. S., de Soares, M. A., Stocker, A. J., Ciferri, R. R., and Fernandez, M. A. (2006) Mol. Biol. Rep., 33, 71–82.PubMedCrossRefGoogle Scholar
  14. 14.
    Marilley, M., Milani, P., Thimonier, J., Rocca-Serra, J., and Baldacci, G. (2007) Nucleic Acids Res., 35, 6832–6845.PubMedCentralPubMedCrossRefGoogle Scholar
  15. 15.
    Gimenes, F., Assis, M. A., Fiorini, A., Mareze, V. A., Monesi, N., and Fernandez, M. A. (2009) Mol. Genet. Genom., 281, 539–549.CrossRefGoogle Scholar
  16. 16.
    Balani, V. A., de Lima Neto, Q. A., Takeda, K. I., Gimenes, F., Fiorini, A., Debatisse, M., and Fernandez, M. A. (2010) BMB Rep., 43, 744–749.PubMedCrossRefGoogle Scholar
  17. 17.
    Rampakakis, E., Arvanitis, D. N., Di Paola, D., and Zannis-Hadjopoulos, M. (2009) J. Cell Biochem., 106, 512–520.PubMedCrossRefGoogle Scholar
  18. 18.
    Rampakakis, E., Gkogkas, C., Di Paola, D., and Zannis-Hadjopoulos, M. (2010) J. Cell Biochem., 110, 45–53.Google Scholar
  19. 19.
    Mechali, M. (2010) Nat. Rev. Cell Mol. Biol., 11, 728–738.CrossRefGoogle Scholar
  20. 20.
    Fernandez, M. A., Baron, B., Prigent, M., Toledo, F., Buttin, G., and Debatisse, M. (1997) J. Cell Biochem., 67, 541–551.PubMedCrossRefGoogle Scholar
  21. 21.
    Anachkova, B., Djeliova, V., and Russev, G. (2005) J. Cell Biochem., 96, 951–961.PubMedCrossRefGoogle Scholar
  22. 22.
    Fiorini, A., Gouveia, F. e S., and Fernandez, M. A. (2006) Biochemistry (Moscow), 71, 481–488.CrossRefGoogle Scholar
  23. 23.
    Courbet, S., Gay, S., Arnoult, N., Wronka, G., Anglana, M., Brison, O., and Debatisse, M. (2008) Nature, 455, 557–560.PubMedCrossRefGoogle Scholar
  24. 24.
    Rivera-Mulia, J. C., Hernandez-Munoz, R., Martinez, F., and Aranda-Anzaldo, A. (2011) BMC Cell Biol., 12, 3.PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Fiorini, A., Gimenes, F., Lima Neto, Q. A., Rosado, F. R., and Fernandez, M. A. (2011) in Fundamental Aspects of DNA Replication, InTech — Open Access Publisher, Rijeka, Croatia, pp. 145–160.Google Scholar
  26. 26.
    MacAlpine, H. K., Gordan, R., Powell, S. K., Hartemink, A. J., and MacAlpine, D. M. (2010) Genome Res., 20, 201–211.PubMedCrossRefGoogle Scholar
  27. 27.
    Eaton, M. L., Galani, K., Kang, S., Bell, S. P., and MacAlpine, D. M. (2010) Genes Dev., 24, 748–753.PubMedCrossRefGoogle Scholar
  28. 28.
    Gouveia, F. e. S., Gimenes, F., Fiorini, A., and Fernandez, M. A. (2008) Biosci. Biotechnol. Biochem., 72, 1190–1198.CrossRefGoogle Scholar
  29. 29.
    Bolshoy, A., McNamara, P., Harrington, R. E., and Trifonov, E. N. (1991) Proc. Natl. Acad. Sci. USA, 88, 2312–2316.PubMedCrossRefGoogle Scholar
  30. 30.
    Eckdahl, T. T., and Anderson, J. N. (1987) Nucleic Acids Res., 15, 8531–8545.PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Xi, L., Fondufe-Mittendorf, Y., Xia, L., Flatow, J., Widom, J., and Wang, J. P. (2010) BMC Bioinformatics, 11, 346.PubMedCentralPubMedCrossRefGoogle Scholar
  32. 32.
    Anglana, M., Apiou, F., Bensimon, A., and Debatisse, M. (2003) Cell, 114, 385–394.PubMedCrossRefGoogle Scholar
  33. 33.
    Debatisse, M., Toledo, F., and Anglana, M. (2004) Cell Cycle, 3, 19–21.PubMedCrossRefGoogle Scholar
  34. 34.
    Sambrook, J., and Russel, D. W. (2001) in Molecular Cloning, a Laboratory Manual, 3rd Edn., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.Google Scholar
  35. 35.
    Del Sal, G., Manfioletti, G., and Schneider, C. (1989) Biotechniques, 7, 514–520.PubMedGoogle Scholar
  36. 36.
    Kalendar, R., Lee, D., and Schulman, A. H. (2011) Genomics, 98, 137–144.PubMedCrossRefGoogle Scholar
  37. 37.
    Silva, W. A., Costa, M. C., Valente, V., Sousa, J. F., Paco-Larson, M. L., Espreafico, E. M., Camargo, S. S., Monteiro, E., Holanda, A. J., Zago, M. A., Simpson, A. J., and Dias Neto, E. (2001) Biotechniques, 30,537, 540–542.Google Scholar
  38. 38.
    Sperbeck, S. J., and Wistow, G. J. (1998) Biotechniques, 24, 66–68.PubMedGoogle Scholar
  39. 39.
    Caddle, M. S., Lussier, R. H., and Heintz, N. H. (1990) J. Mol. Biol., 211, 19–33.PubMedCrossRefGoogle Scholar
  40. 40.
    Cayrou, C., Coulombe, P., Puy, A., Rialle, S., Kaplan, N., Segal, E., and Mechali, M. (2012) Cell Cycle, 11, 658–667.PubMedCrossRefGoogle Scholar
  41. 41.
    Lubelsky, Y., Sasaki, T., Kuipers, M. A., Lucas, I., Le Beau, M. M., Carignon, S., Debatisse, M., Prinz, J. A., Dennis, J. H., and Gilbert, D. M. (2011) Nucleic Acids Res., 39, 3141–3155.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2014

Authors and Affiliations

  • Q. A. Lima Neto
    • 1
  • F. S. Rando
    • 1
  • D. V. B. Freitas
    • 1
  • L. F. Rodrigues
    • 1
  • F. R. Rosado
    • 1
  • A. Fiorini
    • 1
  • F. Gimenes
    • 1
  • J. Tavares
    • 1
  • M. A. Fernandez
    • 1
    Email author
  1. 1.Departamento de Biotecnologia, Genética e Biologia CelularUniversidade Estadual de Maringá, UEMMaringá, ParanáBrasil

Personalised recommendations