Biomedical subjects

Justin P Blumenstiel

Publications and source records attributed to Justin P Blumenstiel.

4 recordsLinked to original sources

PubMed2005

Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis.

Hybrid dysgenesis in Drosophila is a syndrome of gonadal atrophy, sterility, and male recombination, and it occurs in the progeny of crosses between males that harbor certain transposable elements (TEs) and females that lack them. Known examples of hybrid dysgenesis in Drosophila melanogaster result from mobilization of individual families of TEs, such as the P element, the I element, or hobo. An example of hybrid dysgenesis in Drosophila virilis is unique in that multiple, unrelated families of TEs become mobilized, but a TE designated Penelope appears to play a major role. In all known examples of hybrid dysgenesis, the paternal germ line transmits the TEs in an active state, whereas the female germ line maintains repression of the TEs. The mechanism of maternal maintenance of repression is not known. Recent evidence suggests that the molecular machinery of RNA interference may function as an important host defense against TEs. This protection is mediated by the action of endogenous small interfering RNAs (siRNAs) composed of dsRNA molecules of 21-25 nt that can target complementary transcripts for destruction. In this paper, we demonstrate that endogenous siRNA derived from the Penelope element is maternally loaded in embryos through the female germ line in D. virilis. We also present evidence that the maternal inheritance of these endogenous siRNAs may contribute to maternal repression of Penelope.

Animals↗

PubMed2004

Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies.

Comparative analysis of recently sequenced eukaryotic genomes has uncovered extensive variation in transposable element (TE) abundance, diversity, and distribution. The TE profile in the sequenced pufferfish genomes is more similar to that of Drosophila melanogaster than to human or mouse, in that pufferfish TEs exhibit low overall abundance, high family diversity, and localization in the heterochromatin. It has been suggested that selection against the deleterious effects of ectopic recombination between TEs has structured the TE profile in Drosophila and pufferfish but not in humans. We test this hypothesis by measuring the sample frequency of 48 euchromatic TE insertions in the genome of the green spotted pufferfish (Tetraodon nigroviridis). We estimate the strength of selection acting on recent insertions by analyzing the site frequency spectrum using a maximum-likelihood approach. We show that in contrast to Drosophila, euchromatic TE insertions in Tetraodon are selectively neutral and that the low copy number and compartmentalized distribution of TEs in the Tetraodon genome must be caused by regulation by means other than purifying selection acting on recent insertions. Inference of regulatory processes governing TE profiles should take into account factors such as effective population size, incidence of inbreeding/outcrossing, and other species-specific traits.

Animals↗

PubMed2002

Genome complexity reduction for SNP genotyping analysis.

Efficient single nucleotide polymorphism (SNP) genotyping methods are necessary to accomplish many current gene discovery goals. A crucial element in large-scale SNP genotyping is the number of individual biochemical reactions that must be performed. An efficient method that can be used to simultaneously amplify a set of genetic loci across a genome with high reliability can provide a valuable tool for large-scale SNP genotyping studies. In this paper we describe and characterize a method that addresses this goal. We have developed a strategy for reducing genome complexity by using degenerate oligonucleotide primer (DOP)-PCR and applied this strategy to SNP genotyping in three complex eukaryotic genomes; human, mouse, and Arabidopsis thaliana. Using a single DOP-PCR primer, SNP loci spread throughout a genome can be amplified and accurately genotyped directly from a DOP-PCR product mixture. DOP-PCRs are extremely reproducible. The DOP-PCR method is transferable to many species of interest. Finally, we describe an in silico approach that can effectively predict the SNP loci amplified in a given DOP-PCR, permitting the design of an efficient set of reactions for large-scale, genome-wide SNP studies.

Animals↗

PubMed2002

Patterns of insertion and deletion in contrasting chromatin domains.

Transposable elements (TEs) play a fundamental role in the evolution of genomes. In Drosophila they are disproportionately represented in regions of low recombination, such as in heterochromatin. This pattern has been attributed to selection against repeated elements in regions of normal recombination, owing to either (1) the slightly deleterious position effects of TE insertions near or into genes, or (2) strong selection against chromosomal abnormalities arising from ectopic exchange between TE repeats. We have used defective non-long-terminal repeat (LTR) TEs that are "dead-on-arrival" (DOA) and unable to transpose in order to estimate spontaneous deletion rates in different constituents of chromatin. These elements have previously provided evidence for an extremely high rate of spontaneous deletion in Drosophila as compared with mammals, potentially explaining at least part of the differences in the genome sizes in these organisms. However, rates of deletion could be overestimated due to positive selection for a smaller likelihood of ectopic exchange. In this article, we show that rates of spontaneous deletion in DOA repeats are as high in heterochromatin and regions of euchromatin with low recombination as they are in regions of euchromatin with normal recombination. We have also examined the age distribution of five non-LTR families throughout the genome. We show that there is substantial variation in the historical pattern of transposition of these TEs. The overrepresentation of TEs in the heterochromatin is primarily due to their longer retention time in heterochromatin, as evidenced by the average time since insertion. Fragments inserted recently are much more evenly distributed in the genome. This contrast demonstrates that the accumulation of TEs in heterochromatin and in euchromatic regions of low recombination is not due to biased transposition but by greater probabilities of fixation in these regions relative to regions of normal recombination.

Animals↗