Human piRNAs Are Under Selection in Africans and Repress Transposable Elements

Piwi-interacting RNAs (piRNAs) are a recently discovered class of 24- to 30-nt noncoding RNAs whose best-understood function is to repress transposable elements (TEs) in animal germ lines. In humans, TE-derived sequences comprise ∼45% of the genome and there are several active TE families, including...

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Bibliographic Details
Published in:Molecular biology and evolution 2011-11, Vol.28 (11), p.3061-3067
Main Authors: Lukic, Sergio, Chen, Kevin
Format: Article
Language:English
Subjects:
African Continental Ancestry Group - genetics
Animals
Computational Biology
DNA Transposable Elements - genetics
Evolution
Evolution, Molecular
Gene Expression Regulation - genetics
Gene Frequency
Genetics, Population
Genomics
Humans
Mice
Models, Genetic
Mutation
Pan troglodytes - genetics
Polymorphism, Single Nucleotide - genetics
Ribonucleic acid
RNA
RNA, Small Interfering - genetics
Selection, Genetic
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Summary:Piwi-interacting RNAs (piRNAs) are a recently discovered class of 24- to 30-nt noncoding RNAs whose best-understood function is to repress transposable elements (TEs) in animal germ lines. In humans, TE-derived sequences comprise ∼45% of the genome and there are several active TE families, including LINE-1 and Alu elements, which are a significant source of de novo mutations and intrapopulation variability. In the "ping-pong model," piRNAs are thought to alternatively cleave sense and antisense TE transcripts in a positive feedback loop. Because piRNAs are poorly conserved between closely related species, including human and chimpanzee, we took a population genomics approach to study piRNA function and evolution. We found strong statistical evidence that piRNA sequences are under selective constraint in African populations. We then mapped the piRNA sequences to human TE sequences and found strong correlations between the age of each LINE-1 and Alu subfamily and the number of piRNAs mapping to the subfamily. This result supports the idea that piRNAs function as repressors of TEs in humans. Finally, we observed a significant depletion of piRNA matches in the reverse transcriptase region of the consensus human LINE-1 element but not of the consensus mouse LINE-1 element. This result suggests that reverse transcriptase might have an endogenous role specific to humans. Overall, our results elucidate the function and evolution of piRNAs in humans and highlight the utility of population genomics analysis for studying this rapidly evolving genetic system.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msr141