Intrinsic bent DNA colocalizes with the sequence involved in the Nd-s<sup>D</sup> mutation in the Bombyx mori fibroin light chain gene

Barbosa, Joice F; Bravo, Juliana Pereira; Takeda, Karen Izumi; Zanatta, Daniela B; Silva, Jose Luis Da Conceicao; Balani, Valério Américo; Fiorini, Adriana; Fernandez, Maria Aparecida

doi:10.5483/bmbrep.2008.41.5.394

Cited by 7 publications

(6 citation statements)

References 25 publications

(28 reference statements)

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“…Sequence analysis showed that this intron has several conserved regions, mainly in the segment involved in the Nd-s D mutation in the fib-L gene. Recently, our research group demonstrated that this segment has an alternative DNA structure that could be involved in DNA duplication and breakage for the establishment of this mutation (Barbosa et al, 2008).…”

Section: Resultsmentioning

confidence: 99%

Allelic variability in the third intron of the fibroin light chain gene in Bombyx mori (Lepidoptera: Bombycidae)

Barbosa¹,

Bravo²,

Zanatta³

et al. 2009

Genet. Mol. Res.

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ABSTRACT. Conformation-sensitive gel electrophoresis is a useful method for identifying allele polymorphism; it provides co-dominant molecular markers. Using this method, we identified genetic variability in the third intron of the fibroin light chain gene, fib-L, in six Bombyx mori strains. Only Chinese C21A strain did not demonstrate allelic alterations, showing only homoduplex DNA molecules. We found distinct heteroduplex profiles in the Japanese HAA, M12B and M19-2 and the Chinese C25B and C24-2 strains. Analysis with restriction endonuclease fingerprinting conformation-sensitive gel electrophoresis demonstrated the potential of this method for the identification of allelic variability in B. mori; this was confirmed by cloning and sequencing the different alleles. The main alteration was a 12-bp deletion in two alleles of the C24-2 strain and one allele of the HAA strain; this deletion results in specific heteroduplex DNA molecule profiles.

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Section: Resultsmentioning

confidence: 99%

Allelic variability in the third intron of the fibroin light chain gene in Bombyx mori (Lepidoptera: Bombycidae)

Barbosa¹,

Bravo²,

Zanatta³

et al. 2009

Genet. Mol. Res.

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“…Genomic DNA from the C24A and M11A strains was extracted from the silk glands of 5-day-old fifth-instar larvae using the protocol previously described by Mills and Goldsmith (2000) with modifications detailed in Barbosa et al (2008). The A3 actin first intron from both strains was amplified with primers that anneal to sequences in exon 1 and exon 2 (forward 5ꞌAGG TGG TGC TCG AAC AGT GC3ꞌ; reverse 5ꞌAAT TTG CCG CGT GGG TCA GT3ꞌ) of the B. mori actin gene sequence (GenBank U49854).…”

Section: Dna Samplementioning

confidence: 99%

“…A pool of first-instar larvae from both strains (M11A and C24A) were macerated with liquid nitrogen, and DNA was extracted as previously described (Barbosa et al, 2008(Barbosa et al, , 2009. DNA fragments were amplified using the primers described in the DNA sample section.…”

Section: Conformation-sensitive Gel Electrophoresis -Csgementioning

confidence: 99%

Differential structure of the intronic promoter of the Bombyx mori A3 actin gene correlated with silkworm sensitivity/resistance to nucleopolyhedrovirus

Tavares

Bravo²,

Gimenes³

et al. 2011

Genet. Mol. Res.

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ABSTRACT. Previous reports demonstrated that actin is necessary for nucleocapsid transport and viral gene expression during nucleopolyhedrovirus infection of Bombyx mori. The first intron of B. mori A3 actin contains a cryptic promoter that drives expression of a rare isoform. We detected differences in the size and nucleotide composition of the first intron of the A3 actin gene from B. mori strain C24A, which is more resistant to nucleopolyhedrovirus than the M11A strain (22 and 95% lethality, respectively). We sought to determine if resistance to BmMNPV infection and the A3 actin promoter structure are correlated. Intrinsically bent DNA sites in these sequences, which determine curved structures, were analyzed by electrophoretic mobility assays and the helical parameters ENDS ratio, roll and twist. We found both fragments to have non-centralized bent DNA sites with distinct ENDS ratio values, nucleotide positions and two-dimensional structures. Additionally, a conformational-sensitive gel electrophoresis assay identified an allelic variation found in strain M11A that is absent in strain C24A. These data suggest that A3 actin intronic sequence variations impair virus propagation and are markers of BmMNPV-resistant populations.

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“…Flanking sequences around the phased AT tracts and in CA n T motifs may also contribute to DNA conformation (Calladine et al 2004). These structures have been proposed to play a role in segments involved in the initiation of replication (Biamonti et al 2003;Altman and Fanning 2004;Fiorini et al 2006a), and they also seem to be structurally relevant for transcription (Fiorini et al 2001;Ohyama 2005;Gouveia et al 2008), nucleosome formation (Virstedt et al 2004), recombination events (Iarovaia et al 2004; Barbosa et al 2008), and fragile sites (Palin et al 1998). Furthermore, these structures have been found in Matrix Associated Regions (MARs) and replication origins (Anderson 1986;Krajewski and Razin 1992;reviewed in Fiorini et al 2006b).…”

Section: Introductionmentioning

confidence: 97%

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

et al. 2009

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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-beta. 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-beta 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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Intrinsic bent DNA colocalizes with the sequence involved in the Nd-s^D mutation in the Bombyx mori fibroin light chain gene

Abstract: Multiple sequence alignments of the

Cited by 7 publications

References 25 publications

Allelic variability in the third intron of the fibroin light chain gene in Bombyx mori (Lepidoptera: Bombycidae)

Allelic variability in the third intron of the fibroin light chain gene in Bombyx mori (Lepidoptera: Bombycidae)

Differential structure of the intronic promoter of the Bombyx mori A3 actin gene correlated with silkworm sensitivity/resistance to nucleopolyhedrovirus

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

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Intrinsic bent DNA colocalizes with the sequence involved in the Nd-sD mutation in the Bombyx mori fibroin light chain gene

Abstract: Multiple sequence alignments of the

Cited by 7 publications

References 25 publications

Allelic variability in the third intron of the fibroin light chain gene in Bombyx mori (Lepidoptera: Bombycidae)

Allelic variability in the third intron of the fibroin light chain gene in Bombyx mori (Lepidoptera: Bombycidae)

Differential structure of the intronic promoter of the Bombyx mori A3 actin gene correlated with silkworm sensitivity/resistance to nucleopolyhedrovirus

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

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Intrinsic bent DNA colocalizes with the sequence involved in the Nd-s^D mutation in the Bombyx mori fibroin light chain gene