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Vol. 10, Issue 10, 1496-1508, October 2000

LETTER
Reading between the LINEs: Human Genomic Variation Induced by LINE-1 Retrotransposition

Fang-miin Sheen,1,5 Stephen T. Sherry,2,5,6 Gregory M. Risch,2 Myles Robichaux,2 Ivane Nasidze,3 Mark Stoneking,3 Mark A. Batzer,2 and Gary D. Swergold4,7

1 Promega Corporation, Madison, Wisconsin 53711, USA; 2 Departments of Pathology, Biometry and Genetics, Biochemistry, and Molecular Biology, Stanley S. Scott Cancer Center, Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA; 3 Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; 4 Division of Molecular Medicine, Department of Medicine, Columbia University, New York, New York 10032, USA

The insertion of mobile elements into the genome represents a new class of genetic markers for the study of human evolution. Long interspersed elements (LINEs) have amplified to a copy number of about 100,000 over the last 100 million years of mammalian evolution and comprise ~15% of the human genome. The majority of LINE-1 (L1) elements within the human genome are 5' truncated copies of a few active L1 elements that are capable of retrotransposition. Some of the young L1 elements have inserted into the human genome so recently that populations are polymorphic for the presence of an L1 element at a particular chromosomal location. L1 insertion polymorphisms offer several advantages over other types of polymorphisms for human evolution studies. First, they are typed by rapid, simple, polymerase chain reaction (PCR)-based assays. Second, they are stable polymorphisms that rarely undergo deletion. Third, the presence of an L1 element represents identity by descent, because the probability is negligible that two different young L1 repeats would integrate independently between the exact same two nucleotides. Fourth, the ancestral state of L1 insertion polymorphisms is known to be the absence of the L1 element, which can be used to root plots/trees of population relationships. Here we report the development of a PCR-based display for the direct identification of dimorphic L1 elements from the human genome. We have also developed PCR-based assays for the characterization of six polymorphic L1 elements within the human genome. PCR analysis of human/rodent hybrid cell line DNA samples showed that the polymorphic L1 elements were located on several different chromosomes. Phylogenetic analysis of nonhuman primate DNA samples showed that all of the recently integrated "young" L1 elements were restricted to the human genome and absent from the genomes of nonhuman primates. Analysis of a diverse array of human populations showed that the allele frequencies and level of heterozygosity for each of the L1 elements was variable. Polymorphic L1 elements represent a new source of identical-by-descent variation for the study of human evolution.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF242435-AF242451.]

5 These authors contributed equally to this work.

6 Present address: National Center for Biotechnology Information, 2600 Rockville Pike, Bethesda, MD 20892, USA.

7 Corresponding author.

10:1496-1508 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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