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Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin

Fontanillas, P; Hartl, DL; Reuter, M; (2007) Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLOS GENET , 3 (11) , Article e210. 10.1371/journal.pgen.0030210. Green open access

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Abstract

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.

Type: Article
Title: Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pgen.0030210
Publisher version: http://dx.doi.org/10.1371/journal.pgen.0030210
Language: English
Additional information: © 2007 Fontanillas et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: PF was supported by a Marie Curie Outgoing Fellowship from the European Commission and postdoctoral fellowships from the Swiss National Science Foundation. MR was supported by a Marie Curie Intra-European fellowship from the European Commission and a postdoctoral fellowship (NE/D009189/1) from the Natural Environment Research Council.
Keywords: RECOMBINATION RATE, CAENORHABDITIS-ELEGANS, ECTOPIC RECOMBINATION, ARABIDOPSIS-THALIANA, CHROMOSOMAL DOMAINS, LOCAL TRANSPOSITION, GERM-LINE, DNA LOSS, EVOLUTION, PATTERNS
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/152685
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