Published online 20 July 2005
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Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages
Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University 202 Life Sciences Building, Baton Rouge, LA 70803, USA 1Department of Cancer Genetics, Roswell Park Cancer Institute Elm and Carlton Streets, Buffalo, NY 14263, USA
*To whom correspondence should be addressed. Tel: +1 225 578 7102; Fax: +1 225 578 7113; Email: mbatzer{at}lsu.edu
Received June 3, 2005. Revised July 1, 2005. Accepted July 1, 2005.
Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of 
18 kb of sequence from the human genome and 15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions.
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
DDBJ/EMBL/GenBank accession nos DQ017967–DQ018078
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