Dataset Information

Characterization of the flamenco region of the Drosophila melanogaster genome.

ABSTRACT: The flamenco gene, located at 20A1-3 in the beta-heterochromatin of the Drosophila X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. As a first step to characterize this gene, approximately 100 kb of genomic DNA flanking a P-element-induced mutation of flamenco was isolated. This DNA is located in a sequencing gap of the Celera Genomics project, i.e., one of those parts of the genome in which the "shotgun" sequence could not be assembled, probably because it contains long stretches of repetitive DNA, especially on the proximal side of the P insertion point. Deficiency mapping indicated that sequences required for the normal flamenco function are located >130 kb proximal to the insertion site. The distal part of the cloned DNA does, nevertheless, contain several unique sequences, including at least four different transcription units. Dip1, the closest one to the P-element insertion point, might be a good candidate for a gypsy regulator, since it putatively encodes a nuclear protein containing two double-stranded RNA-binding domains. However, transgenes containing dip1 genomic DNA were not able to rescue flamenco mutant flies. The possible nature of the missing flamenco sequences is discussed.

SUBMITTER: Robert V

PROVIDER: S-EPMC1461675 | biostudies-other | 2001 Jun

REPOSITORIES: biostudies-other

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Characterization of the flamenco region of the Drosophila melanogaster genome.

Robert V V Prud'homme N N Kim A A Bucheton A A Pélisson A A

Genetics 20010601 2

The flamenco gene, located at 20A1-3 in the beta-heterochromatin of the Drosophila X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. As a first step to characterize this gene, approximately 100 kb of genomic DNA flanking a P-element-induced mutation of flamenco was isolated. This DNA is located in a sequencing gap of the Celera Genomics project, i.e., one of those parts of the genome in which the "shotgun" sequence could not be assembled, probably because it contains lo ...[more]

PMID: 11404334

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Project description:Pseudogenes are copies of genes that cannot produce a protein. They can be detected from disruptions to their apparent coding sequence, caused by frameshifts and premature stop codons. They are classed as either processed pseudogenes (made by reverse transcription from an mRNA) or duplicated pseudogenes, arising from duplication in the genomic DNA and subsequent disablement. Historically, there is anecdotal evidence that the fruit fly (Drosophila melanogaster) has few pseudogenes. Investigators have linked this to a high deletion rate of genomic DNA, for which there is evidence from genetic experiments on genome size. Here, we apply a homology-based pipeline that was developed previously to identify pseudogenes in other eukaryotic genomes, to the fruit fly, so as to derive the first complete survey of its pseudogene population. We find approximately 100 pseudogenes, with at least a sixth of these as candidate processed pseudogenes. This gives a much lower proportion of pseudogenes (compared with the size of the proteome) than in the genomes of other eukaryotes for which data are available (human, nematode and budding yeast). Closest matching proteins to Drosophila pseudogenes are significantly longer than the average protein in its proteome (up to approximately 60% more than the average protein's length), in contrast to the situation in the three other eukaryotic genomes. This may be due to the persistence of fragments of longer genes. In the fly pseudogene population, we found most pseudogenes for serine proteases (which are more abundant in the Drosophila lineage compared with the other eukaryotes), immunoglobulin-motif-containing proteins and cytochromes P450. Data on the sequences and positions of the putative pseudogenes are available at: http://www.pseudogene.org/fly. The detection of a small number of pseudogenes in the Drosophila genome and the higher mean length for the closest matching proteins to pseudogenes (possibly because remnants of genes encoding longer proteins are more likely to persist) are further evidence for a high deletion rate of genomic DNA in the fruit fly. The data are useful for molecular evolution study in Drosophila.

Dataset Information

Characterization of the flamenco region of the Drosophila melanogaster genome.

Publications

Characterization of the flamenco region of the Drosophila melanogaster genome.

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