Author
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Peterson Burch, Brooke |
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NETTLETON, DAN - IA STATE UNIV |
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VOYTAS, DANIEL - IA STATE UNIV |
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Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 9/2/2004 Publication Date: 9/29/2004 Citation: Peterson Burch, B.D., Nettleton, D., Voytas, D.F. 2004. Genomic neighborhoods for arabidopsis retrotansposons: genome sequence analysis reveals a role for targeted integration in the distribution of the metaviridae. Genome Biology. Interpretive Summary: Much (often most) of the genome in organisms we see around us, such as plants or people, has nothing to do with making sure they grow properly and remain alive. Genomes are filled with copies of retrotransposons, similar to their sinister cousins the retroviruses, like HIV, but unable to infect other cells. Their miniature 'genomes' of a few genes exist only to spread new copies throughout the host's genome. The completed genome sequence of Arabidopsis thaliana, a highly studied weed, made it possible to look at why retrotransposons are tolerated by the host organism and examine why they are much more abundant in some chromosome locations. We identified all members of the Arabidopsis retrotransposon populations and used that information to test models predicting retrotransposon distribution along the plant's chromosomes. The Pseudoviridae and Metaviridae retrotransposon families we focused on employ a number of strategies to survive in the host. Populations of the Athila and Tat sub-lineages of the Metaviridae family target their insertion into regions of the chromosomes where there are few active genes so insertion may be less likely to cause harmful mutations. The distribution of the other lineages supports models where retrotransposons insert randomly and only accumulate in the locations where they do not mutate host genes and that are less susceptible to elimination through recombination. This information is useful to geneticists, suggesting ways to identify retrotransposon lineages which may cause harmful mutations while others appear to be carried by the host without repercussion. Technical Abstract: Background Retroelements are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution. Results We identified the full complement of A. thaliana LTR retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. In total, 3.36% of the A. thaliana genome is comprised of retroelements of the Pseudoviridae and Metaviridae families. Relative-age distributions were assessed by comparing sequence divergence between LTRs of full-length elements; the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-random. Although both Pseudoviridae and Metaviridae tend to cluster within centromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages (Metavirus, Tat, Athila). Among these, Tat and Athila are strictly associated with centromeric heterochromatin. Conclusions The non-random genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target site bias, selection against euchromatin integration, and centromeric accumulation of elements due to suppression of recombination. However, comparisons based on age of elements and their chromosomal distribution indicates that integration site specificity is likely the primary factor determining genomic organization of the Athila and Tat sublineages of the Metaviridae. We predict that like retroelements in yeast, the Athila and Tat elements target integration to centromeres by recognizing a specific feature of centromeric heterochromatin. |
