Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin
| Autor: | Pierre Fontanillas, Max Reuter, Daniel L. Hartl |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2007 |
| Předmět: |
Transposable element
Cancer Research Genome evolution Transcription Genetic Euchromatin lcsh:QH426-470 Eukaryotes Pseudogene Genome Insect Biology Genome 03 medical and health sciences 0302 clinical medicine Genes X-Linked Untranslated Regions Gene density Genetics Animals Arthropods Molecular Biology Gene Conserved Sequence Genetics (clinical) Ecology Evolution Behavior and Systematics 030304 developmental biology Genomic organization Evolutionary Biology 0303 health sciences Base Sequence food and beverages Genetics and Genomics Introns Insects lcsh:Genetics Drosophila melanogaster Germ Cells Gene Expression Regulation Multigene Family DNA Transposable Elements Drosophila DNA Intergenic 030217 neurology & neurosurgery Research Article DNA Transposable Elements/genetics DNA Intergenic/genetics Drosophila melanogaster/genetics Euchromatin/genetics Gene Expression Regulation/genetics Genome Insect/genetics Germ Cells/metabolism Introns/genetics Untranslated Regions/genetics |
| Zdroj: | PLoS Genetics, Vol 3, Iss 11, p e210 (2007) PLoS Genetics, vol. 3, no. 11, pp. e210 PLoS Genetics |
| ISSN: | 1553-7404 1553-7390 |
| Popis: | The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection against new insertions. Understanding the distribution of TEs therefore provides insights into the forces shaping the organization of genomes. Past research has shown that TEs tend to accumulate in genomic regions with low gene density and low recombination rate. However, little is known about the factors modulating insertion rates across the genome and their evolutionary significance. One candidate factor is gene expression, which has been suggested to increase local insertion rate by rendering DNA more accessible. We test this hypothesis by comparing the TE density around germline- and soma-expressed genes in the euchromatin of Drosophila melanogaster. Because only insertions that occur in the germline are transmitted to the next generation, we predicted a higher density of TEs around germline-expressed genes than soma-expressed genes. We show that the rate of TE insertions is greater near germline- than soma-expressed genes. However, this effect is partly offset by stronger selection for genome compactness (against excess noncoding DNA) on germline-expressed genes. We also demonstrate that the local genome organization in clusters of coexpressed genes plays a fundamental role in the genomic distribution of TEs. Our analysis shows that—in addition to recombination rate—the distribution of TEs is shaped by the interaction of gene expression and genome organization. The important role of selection for compactness sheds a new light on the role of TEs in genome evolution. Instead of making genomes grow passively, TEs are controlled by the forces shaping genome compactness, most likely linked to the efficiency of gene expression or its complexity and possibly their interaction with mechanisms of TE silencing. Author Summary Transposable elements (TEs) are parasitic DNA segments that can move within a host genome. These selfish mobile elements are present in virtually all eukaryote species and can contribute significantly to their DNA. TEs multiply by copying themselves within the genome. Depending on where they land, new copies can alter the organism's phenotype, often negatively but sometimes positively. Although TEs have some preferences, they have few opportunities to choose their landing places. It has been proposed that new copies arise in places that are easily accessible to their insertion. Increased accessibility can occur close to genes that are actively transcribed, because the DNA is uncoiled and laid bare. We have tested whether this effect has a detectable influence on the distribution of TEs in the genome of the fruitfly, D. melanogaster. Our analysis shows that this is indeed the case. Thus, TE insertions are denser around genes expressed in the cells that give rise to sperm and eggs (the germline). This is expected because only those new copies arising in these cells are transmitted to future generations. In addition, we found that genomic regions vary in their tolerance to insertions. Thus, TEs are rare wherever a considerable increase in noncoding DNA is deleterious. |
| Databáze: | OpenAIRE |
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