Campus Units
Genetics, Development and Cell Biology, Statistics
Document Type
Article
Publication Version
Published Version
Publication Date
2004
Journal or Book Title
Genome Biology
Volume
5
First Page
R78
DOI
10.1186/gb-2004-5-10-r78
Abstract
Background: Retrotransposons 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 long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-uniform. Although both Pseudoviridae and Metaviridae tend to cluster within pericentromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages (Metavirus, Tat and Athila). Among these, Tat and Athila are strictly associated with pericentromeric heterochromatin.
Conclusions: The non-uniform genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target-site bias, selection against integration into euchromatin and pericentromeric accumulation of elements as a result of suppression of recombination. However, comparisons based on the age of elements and their chromosomal location indicate that integration-site specificity is likely to be the primary factor determining distribution of the Athila and Tat sublineages of the Metaviridae. We predict that, like retroelements in yeast, the Athila and Tat elements target integration to pericentromeric regions by recognizing a specific feature of pericentromeric heterochromatin.
Rights
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.
Language
en
File Format
application/pdf
Recommended Citation
Peterson-Burch, Brooke D.; Nettleton, Dan; and Voytas, Daniel F., "Genomic neighborhoods for Arabidopsisretrotransposons: a role for targeted integration in the distribution of the Metaviridae" (2004). Statistics Publications. 228.
https://lib.dr.iastate.edu/stat_las_pubs/228
Included in
Applied Statistics Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, Statistical Models Commons
Comments
This article is published as Peterson-Burch, Brooke D., Dan Nettleton, and Daniel F. Voytas. "Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae." Genome biology 5, no. 10 (2004): R78. doi: 10.1186/gb-2004-5-10-r78.