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Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain

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Abstract

Bent DNA sites promote the curvature of DNA in both eukaryotic and prokaryotic chromosomes. Here, we investigate the localization and structure of intrinsically bent DNA sites in the extensively characterized Drosophila melanogaster third chromosome DAFC-66D segment (Drosophila amplicon in the follicle cells). This region contains the amplification control element ACE3, which is a replication enhancer that acts in cis to activate the major replication origin ori-β. Through both electrophoretic and in silico analysis, we have identified three major bent DNA sites in DAFC-66D. The bent DNA site (b1) is localized in the ACE3 element, whereas the other two bent DNA sites (b2 and b3) are localized in the ori-β region. Four additional bent DNA sites were identified in the intron of the S18 gene and near the TATA box of the S15, S19, and S16 genes. The identification of DNA bent sites in genomic regions previously characterized as functionally relevant for DNA amplification further supports a function for DNA bent sites in DNA replication in eukaryotes.

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Acknowledgments

We thank Valmir Peron and Marli Licero Schuete Silva for their dedicated technical assistance. FSG received a fellowship from CAPES. This work was supported by grants from CNPq and The Academy of Sciences for the Developing World—TWAS and Universidade Estadual de Maringá facilites (COMCAP laboratories).

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Authors and Affiliations

  1. Departamento de Biologia Celular e Genética, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, PR, 87020-900, Brazil

    Fabrícia Gimenes, Mariana Aprígio Assis, Vânia Aparecida Mareze & Maria Aparecida Fernandez

  2. Centro Universitário de Maringá, CESUMAR, Av. Guedner, 1610, Maringá, PR, 87050-390, Brazil

    Adriana Fiorini

  3. Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo (USP), Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil

    Nadia Monesi

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  1. Fabrícia Gimenes
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  2. Mariana Aprígio Assis
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  3. Adriana Fiorini
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  4. Vânia Aparecida Mareze
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  5. Nadia Monesi
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  6. Maria Aparecida Fernandez
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Corresponding author

Correspondence to Maria Aparecida Fernandez.

Additional information

Communicated by G. Reuter.

Electronic supplementary material

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438_2009_430_MOESM1_ESM.doc

Supplementary Fig. 1. Location of primers employed in permutation analysis of the615 ori-β 840 bp sequence. The 129 nucleotides before the ori-β sequence are shown in 616 italics. The six pairs of primers that flank the intrinsically bent DNA sites b2 and b3 and 617 that were employed to amplify the 195 bp permuted fragments are shown in color. (DOC 24 kb)

438_2009_430_MOESM2_ESM.tif

Supplementary Fig. 2. 2D projection of the 3D DNA path of the 2348 bp fragment620 containing the ACE3 element, the S18 gene and the ori-β region. The four intrinsically621 bent DNA sites at the 180 (b1), 757 (iS18), 1558 (b2) and 1910 (b3) positions are622 shown. In the figure, rings of different sizes and colors represent the free energy623 variation (ΔG), which predicts the stability of the double helix in the AT rich regions.624 The larger blue rings represent greater ΔG, and the small gray rings represent lower625 values (TIFF 62 kb)

438_2009_430_MOESM3_ESM.pdf

Supplementary Fig. 3. The 600 bp fragments containing the 627 promoter regions of the628 S18, S15, S19 and S16 genes that were employed in the analyses described in Fig. 8 are629 shown. The TATA box region is highlighted in yellow, the ATG in green and the630 intrinsically bent DNA sites in red. The lowercase letters indicate intron sequences. ThedA⋅dT tracts with two or more nucleotides are shown in bold. The CAn631 T motif is632 highlighted in gray. (PDF 16 kb)

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Gimenes, F., Assis, M.A., Fiorini, A. et al. Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain. Mol Genet Genomics 281, 539–549 (2009). https://doi.org/10.1007/s00438-009-0430-1

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  • DOI: https://doi.org/10.1007/s00438-009-0430-1

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