Use of ordered deletions in genome sequencing

Ahmed, Asad; Podemski, Lynn

doi:10.1016/s0378-1119(97)00285-0

Cited by 8 publications

(13 citation statements)

References 9 publications

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“…In the course of constructing a physical map of chromosome 4, we sequenced two cosmid clones (Ahmed and Podemski 1997;Locke et al 1999) and identified 18 copies of a short, degenerate sequence. This repeat, which we have named DINE-1, for Drosophila interspersed element 1, appears to be dispersed as single elements among chromosome 4 cosmid clones (Locke et al 1999).…”

Section: Introductionmentioning

confidence: 99%

The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster

et al. 1999

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The banded portion of chromosome 4 (the "dot" chromosome) in Drosophila melanogaster displays some properties of beta-heterochromatin, which is normally found within the centric domain of the chromosomes. The nature and distribution of repetitive elements on chromosome 4 could play a role in the establishment of this unusual chromatin configuration. We describe here one such element: a short, interspersed repetitive sequence named DINE-1. Determination of a consensus sequence for the element reveals that there are two conserved regions (A and B) separated by a highly variable spacer. The conserved sequences are approximately 400 bp long but degenerate at both ends, opening the possibility that a yet-to-be-discovered mother element may be present in the genome. DINE-1 bears few of the properties of the mammalian short interspersed elements (SINEs) to which it bears a superficial resemblance in size. It does not appear to be the product of reverse transcription and lacks any polymerase III promoter consensus. The elements are not flanked by target site duplications and their termini lack direct or inverted repeats, suggesting that they themselves are not transposable. Our analysis of cosmid clones from chromosome 4, and elsewhere in the genome, revealed that the euchromatic locations of DINE-1 are almost exclusively confined to chromosome 4. In situ hybridization of a DINE-1 probe to polytene chromosomes confirmed the preferential distribution along 4, in addition to its presence in the centric heterochromatin. This unusual genomic distribution of bias toward chromosome 4 is also seen in the sibling species, D. simulans, whose dot chromosomes exhibit poorly resolved polytene bands and lack crossing over during meiosis like those of D. melanogaster. However, the dot chromosome of D. virilis, which exhibits a well-defined banded structure on polytene chromosomes and can cross over, has only a single, discrete site of DINE-1 element hybridization. The presence of DINE-1 within these regions suggests a role in the heterochromatic nature of chromosome 4 in D. melanogaster and supports the contention that repeats accumulate in regions of diminished crossing over.

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Section: Introductionmentioning

confidence: 99%

The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster

et al. 1999

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“…AF034971), who also identified a transcription start site. The complete genomic sequence of the region has also been published (Ahmed and Podemski 1997). We verified the sequences of the wild-type RpS3A transcript (van Beest et al 1998) and found that the region around the transcription start site consisted of a stretch of 13 pyrimidine nucleotides, which the published genomic sequence (Ahmed and Podemski 1997) lacked.…”

Section: Molecular Analyses Of the Rps3a Genementioning

confidence: 86%

“…PCR primers were designed from the published genomic sequence (Ahmed and Podemski 1997) at appropriate intervals around the P-element insertion site and in the RpS3A gene. Any aberrant fragments, resulting from PCR amplification of DNA from the deletion lines with matching primers, were sequenced.…”

Section: Mutation and Aberration Analysesmentioning

confidence: 99%

“…The P-element in IA5 was inserted into the first intron of pan, 2.8 kb upstream of the RpS3A gene, at the second base of the 30-kb sequence published by Ahmed and Podemski (1997). The insertion induced an 8-bp duplication of the target site (GTAACCTA).…”

Section: Molecular Analyses Of the Rps3a Genementioning

confidence: 99%

“…Thirty kilobases of genomic DNA from this region have been sequenced and published (Ahmed and Podemski 1997). This sequence covers the first exon and 467 bp of the first intron of pan, the complete ci gene, and the region intervening the two genes.…”

Section: Introductionmentioning

confidence: 99%

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Genetic organization of theci-M-panregion on chromosome IV inDrosophila melanogaster

Kronhamn

Rasmuson-Lestander²

1999

Genome

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The genes cubitus interruptus (ci), ribosomal protein S3A (RpS3A), and pangolin (pan) are localized within 73 kb in the cytological region 101F-102A on chromosome IV in Drosophila melanogaster. A region of 13 kb harbours the regulatory regions of both ci and pan, transcribed in opposite directions, and a 1.1-kb gene encoding RpS3A. This dense clustering gives rise to very complicated complementation patterns between different alleles in these loci. We investigated this region genetically and molecularly by use of an enhancer trap line (IA5), where the P-element was found to be inserted into the first intron of pan. Screens for imprecise excisions of the P-element were performed, and complementations between new and old established mutant lines were investigated. We found that when mutated or deleted the RpS3A gene gives rise to a Minute phenotype, and we conclude that M(4)101 encodes the ribosomal protein S3A.

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Expression pattern of Cubitus interruptus from the mulberry silkworm Bombyx mori in late developmental stages

Dhawan

Gopinathan

2003

Dev Genes Evol

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A partial genomic clone of Bombyx mori homologue of the segment polarity gene Cubitus interruptus (BmCi), encoding the conserved zinc finger domain and harbouring two introns, has been characterized. BmCi was expressed in the silkglands of B. mori from embryonic to the late larval stages(3rd, 4th and 5th intermoults). The expression was confined to the anterior region of the middle silkglands, overlapping with the domain of sericin-2 expression and excluding the domains of Bm invected expression, namely the middle and posterior regions of the middle silkglands. In the wing discs, the expression was restricted to the anterior compartment, which increased from 4th to 5th larval intermoults and declined later in the pupal wing buds. In gonadal tissues (both ovaries and testes) BmCi was expressed from the larval to pupal stages. The transcripts were localized to the sperm tubes containing spermatogonia in the testis of Bombyx larvae. BmCi expression, however, was not detected in any of these tissues during the moulting stages. Expression of Ci in the wing discs and gonads is evolutionarily conserved, while the silkgland represents a novel domain. Our results imply that BmCi is involved in the specification and maintenance of micro-compartment identity within the middle silkglands.

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Use of ordered deletions in genome sequencing

Cited by 8 publications

References 9 publications

The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster

The characterization of DINE-1, a short, interspersed repetitive element present on chromosome and in the centric heterochromatin of Drosophila melanogaster

Genetic organization of theci-M-panregion on chromosome IV inDrosophila melanogaster

Expression pattern of Cubitus interruptus from the mulberry silkworm Bombyx mori in late developmental stages

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