Fitness Cost of LINE-1 (L1) Activity in Humans

The self-replicating LINE-1 (L1) retrotransposon family is the dominant retrotransposon family in mammals and has generated 30-40% of their genomes. Active L1 families are present in modern mammals but the important question of whether these currently active families affect the genetic fitness of th...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 103; no. 25; pp. 9590 - 9594
Main Authors Boissinot, Stephane, Davis, Jerel, Entezam, Ali, Petrov, Dimitri, Furano, Anthony V.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 20.06.2006
National Acad Sciences
Subjects
Adaptation, Physiological - genetics
Alleles
Biological Sciences
DNA
Ecological competition
Genes
Genetic loci
Genetic research
Genome, Human - genetics
Genomes
Genomics
Human populations
Human subjects
Humans
Long Interspersed Nucleotide Elements - genetics
Mammals
Maximum likelihood estimation
Models, Genetic
Negative selection
Parametric models
Polymorphism, Genetic
Selection, Genetic
Short Interspersed Nucleotide Elements - genetics
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Summary:The self-replicating LINE-1 (L1) retrotransposon family is the dominant retrotransposon family in mammals and has generated 30-40% of their genomes. Active L1 families are present in modern mammals but the important question of whether these currently active families affect the genetic fitness of their hosts has not been addressed. This issue is of particular relevance to humans as Homo sapiens contains the active L1 Ta1 subfamily of the human specific Ta (L1Pa1) L1 family. Although DNA insertions generated by the Ta1 subfamily can cause genetic defects in current humans, these are relatively rare, and it is not known whether Ta1-generated inserts or any other property of Ta1 elements have been sufficiently deleterious to reduce the fitness of humans. Here we show that full-length (FL) Ta1 elements, but not the truncated Ta1 elements or SINE (Alu) insertions generated by Ta1 activity, were subject to negative selection. Thus, one or more properties unique to FL L1 elements constitute a genetic burden for modern humans. We also found that the FL Ta1 elements became more deleterious as the expansion of Ta1 has proceeded. Because this expansion is ongoing, the Ta1 subfamily almost certainly continues to decrease the fitness of modern humans.
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Communicated by Maxine F. Singer, Carnegie Institution of Washington, Washington, DC, April 26, 2006
S.B., J.D., and A.E. contributed equally to this work.
Author contributions: S.B. and A.V.F. designed research; S.B. and A.E. performed research; J.D. and D.P. analyzed data; and D.P. and A.V.F. wrote the paper.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0603334103