Sequence-Directed DNA Curvature in Replication Origins Segments

Fiorini, Adriana; Gimenes, Fernanda Raphael Escobar; Neto, Quirino Alves de Lima; Rosado, Fábio Rogério; Fernandez, Maria Aparecida

doi:10.5772/18263

Cited by 2 publications

(2 citation statements)

References 80 publications

(101 reference statements)

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“…Intrinsic curvature of DNA can be found in promoter regions of prokaryotes and eukaryotes replication origins and transcription regions (reviewed in [22]). Bramhill and Kornberg [23] proposed a model involving both discrete sites of intrinsically DNA bent in replication origins of prokaryotes, which can act at the opening of double-stranded DNA mediated by protein DnaA.…”

Section: Discussionmentioning

confidence: 99%

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from <i>Drosophila melanogaster</i>

Freitas¹,

Gimenes²,

Fiorini³

et al. 2014

OJGen

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DNA replication is a crucial process for species survival, nevertheless it is not clear which factors define origin selection in multicellular eukaryotes. Developmental gene amplification systems, such as the one described during ovarian follicles development in Drosophila melanogaster, are useful tools for studying of DNA replication process in these organisms. We previously described that the well characterized third chromosome amplified domain of D. melanogater displays three intrinsically bent DNA sites: b1, localized at an amplification control element (ACE3), b2 and b3, both localized at the preferential origin ori-β. This proposal aimed to construct a Drosophila transformation vector, which contains a short deletion at the ACE3, in order to reduce the intrinsically bent DNA site b1, and analyze the functional role of this site in the gene amplification process. Through a series of cloning steps, we obtained a Big Parent vector derivative, containing a deletion at the positions 176-180 bp, inside the ACE3. The generation of a Drosophila transformation vector displays a reduced intrinsically bent DNA site in the third chromosome amplified domain, it will allow the analysis of the functional role of this curvature in developmental gene amplification, providing new insights on replication initiation in D. melanogaster and the function of intrinsically bent DNA sites.

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Section: Discussionmentioning

confidence: 99%

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from <i>Drosophila melanogaster</i>

Freitas¹,

Gimenes²,

Fiorini³

et al. 2014

OJGen

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show abstract

“…SGD and oriDB databases were used for collation of information. Also, an effort was made to identify the presence and location of known replication enhancer (RE) sequences and matrix attachment regions (MAR) within these APS [ 24 ]. A 189 bp region has crucial role for ARS activity and scaffold binding being reported earlier by Amati et al, 1990 [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences

Sehgal

Kaul

Dhar

2015

The Scientific World Journal

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The present investigation was aimed at understanding the molecular mechanism of gene amplification. Interplay of fragile sites in promoting gene amplification was also elucidated. The amplification promoting sequences were chosen from the Saccharomyces cerevisiae ARS, 5S rRNA regions of Plantago ovata and P. lagopus, proposed sites of replication pausing at Ste20 gene locus of S. cerevisiae, and the bend DNA sequences within fragile site FRA11A in humans. The gene amplification assays showed that plasmid bearing APS from yeast and human beings led to enhanced protein concentration as compared to the wild type. Both the in silico and in vitro analyses were pointed out at the strong bending potential of these APS. In addition, high mitotic stability and presence of TTTT repeats and SAR amongst these sequences encourage gene amplification. Phylogenetic analysis of S. cerevisiae ARS was also conducted. The combinatorial power of different aspects of APS analyzed in the present investigation was harnessed to reach a consensus about the factors which stimulate gene expression, in presence of these sequences. It was concluded that the mechanism of gene amplification was that AT rich tracts present in fragile sites of yeast serve as binding sites for MAR/SAR and DNA unwinding elements. The DNA protein interactions necessary for ORC activation are facilitated by DNA bending. These specific bindings at ORC promote repeated rounds of DNA replication leading to gene amplification.

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Sequence-Directed DNA Curvature in Replication Origins Segments

Cited by 2 publications

References 80 publications

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from <i>Drosophila melanogaster</i>

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from <i>Drosophila melanogaster</i>

Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences

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Sequence-Directed DNA Curvature in Replication Origins Segments

Cited by 2 publications

References 80 publications

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from &lt;i&gt;Drosophila melanogaster&lt;/i&gt;

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from &lt;i&gt;Drosophila melanogaster&lt;/i&gt;

Mechanism of Gene Amplification via Yeast Autonomously Replicating Sequences

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Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from <i>Drosophila melanogaster</i>

Construction of Vector for Functional Analysis of the Intrinsically Bent DNA in the ACE3 Replicator from <i>Drosophila melanogaster</i>