The insertional history of an active family of L1 retrotransposons in humans.
As humans contain a currently active L1 (LINE-1) non-LTR retrotransposon family (Ta-1), the human genome database likely provides only a partial picture of Ta-1-generated diversity. We used a non-biased method to clone Ta-1 retrotransposon-containing loci from representatives of four ethnic populations. We obtained 277 distinct Ta-1 loci and identified an additional 67 loci in the human genome database. This collection represents approximately 90% of the Ta-1 population in the individuals examined and is thus more representative of the insertional history of Ta-1 than the human genome database, which lacked approximately 40% of our cloned Ta-1 elements. As both polymorphic and fixed Ta-1 elements are as abundant in the GC-poor genomic regions as in ancestral L1 elements, the enrichment of L1 elements in GC-poor areas is likely due to insertional bias rather than selection. Although the chromosomal distribution of Ta-1 inserts is generally a function of chromosomal length and gene density, chromosome 4 significantly deviates from this pattern and has been much more hospitable to Ta-1 insertions than any other chromosome. Also, the intra-chromosomal distribution of Ta-1 elements is not uniform. Ta-1 elements tend to cluster, and the maximal gaps between Ta-1 inserts are larger than would be expected from a model of uniform random insertion.
Boissinot
Stéphane
S
Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA.
Entezam
Ali
A
Young
Lynn
L
Munson
Peter J
PJ
Furano
Anthony V
AV
D002874:Chromosome Mapping / Q000706:statistics & numerical data; D002877:Chromosomes, Human / Q000235:genetics; D016384:Consensus Sequence / Q000235:genetics; D030541:Databases, Genetic; D005006:Ethnicity / Q000235:genetics; D019143:Evolution, Molecular; D020862:GC Rich Sequence / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008297:Male; D016254:Mutagenesis, Insertional / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D016008:Statistical Distributions
D018626:Retroelements