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Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates

van de Lagemaat, LN; Gagnier, L; Medstrand, Patrik LU and Mager, DL (2005) In Genome Research 15(9). p.1243-1249
Abstract
Insertion of transposable elements is a major cause of genomic expansion in eukaryotes. Less is understood, however, about mechanisms underlying contraction of genomes. In this study, we show that retroelements can, in rare cases, be precisely deleted from primate genomes, most likely via recombination between 10- to 20-bp target site duplications (TSDs) flanking the retroelement. The deleted loci are indistinguishable from pre-integration sites, effectively reversing the insertion. Through human-chimpanzee-Rhesus monkey genomic comparisons, we estimate that 0.5%-1% of apparent retroelement "insertions" distinguishing humans and chimpanzees actually represent deletions. Furthermore, we demonstrate that 19% of genomic deletions of 200-500... (More)
Insertion of transposable elements is a major cause of genomic expansion in eukaryotes. Less is understood, however, about mechanisms underlying contraction of genomes. In this study, we show that retroelements can, in rare cases, be precisely deleted from primate genomes, most likely via recombination between 10- to 20-bp target site duplications (TSDs) flanking the retroelement. The deleted loci are indistinguishable from pre-integration sites, effectively reversing the insertion. Through human-chimpanzee-Rhesus monkey genomic comparisons, we estimate that 0.5%-1% of apparent retroelement "insertions" distinguishing humans and chimpanzees actually represent deletions. Furthermore, we demonstrate that 19% of genomic deletions of 200-500 bp that have occurred since the human-chimpanzee divergence are associated with flanking identical repeats of at least 10 bp. A large number of deletions internal to Alu elements were also found flanked by homologies. These results suggest that illegitimate recombination between short direct repeats has played a significant role in human genome evolution. Moreover, this study lends perspective to the view that insertions of retroelements represent unidirectional genetic events. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Genome Research
volume
15
issue
9
pages
1243 - 1249
publisher
Cold Spring Harbor Laboratory Press
external identifiers
  • wos:000231720500007
  • pmid:16140992
  • scopus:24344509193
ISSN
1549-5469
DOI
10.1101/gr.3910705
language
English
LU publication?
yes
id
2bb21e06-f58f-4891-a47b-c216be69da8c (old id 224962)
date added to LUP
2007-08-14 11:18:22
date last changed
2017-11-19 04:11:21
@article{2bb21e06-f58f-4891-a47b-c216be69da8c,
  abstract     = {Insertion of transposable elements is a major cause of genomic expansion in eukaryotes. Less is understood, however, about mechanisms underlying contraction of genomes. In this study, we show that retroelements can, in rare cases, be precisely deleted from primate genomes, most likely via recombination between 10- to 20-bp target site duplications (TSDs) flanking the retroelement. The deleted loci are indistinguishable from pre-integration sites, effectively reversing the insertion. Through human-chimpanzee-Rhesus monkey genomic comparisons, we estimate that 0.5%-1% of apparent retroelement "insertions" distinguishing humans and chimpanzees actually represent deletions. Furthermore, we demonstrate that 19% of genomic deletions of 200-500 bp that have occurred since the human-chimpanzee divergence are associated with flanking identical repeats of at least 10 bp. A large number of deletions internal to Alu elements were also found flanked by homologies. These results suggest that illegitimate recombination between short direct repeats has played a significant role in human genome evolution. Moreover, this study lends perspective to the view that insertions of retroelements represent unidirectional genetic events.},
  author       = {van de Lagemaat, LN and Gagnier, L and Medstrand, Patrik and Mager, DL},
  issn         = {1549-5469},
  language     = {eng},
  number       = {9},
  pages        = {1243--1249},
  publisher    = {Cold Spring Harbor Laboratory Press},
  series       = {Genome Research},
  title        = {Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates},
  url          = {http://dx.doi.org/10.1101/gr.3910705},
  volume       = {15},
  year         = {2005},
}