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      Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution.

      Proceedings of the National Academy of Sciences of the United States of America
      Animals, Evolution, Molecular, Genetic Variation, genetics, Mice, Multigene Family, RNA, Small Interfering, Rats, Recombination, Genetic, Time Factors

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          Abstract

          Piwi-interacting RNAs (piRNAs) are approximately 30 nucleotide noncoding RNAs that may be involved in transposon silencing in mammalian germline cells. Most piRNA sequences are found in a small number of genomic regions referred to as clusters, which range from 1 to hundreds of kilobases. We studied the evolution of 140 rodent piRNA clusters, 103 of which do not overlap protein-coding genes. Phylogenetic analysis revealed that 14 clusters were acquired after rat-mouse divergence and another 44 after rodent-primate divergence. Most clusters originated in a process analogous to the duplication of protein-coding genes by ectopic recombination, via insertions of long sequences that were mediated by flanking chromosome-specific repetitive elements (REs). Source sequences for such insertions are often located on the same chromosomes and also harbor clusters. The rate of piRNA cluster expansion is higher than that of any known gene family and, in contrast to other large gene families, there was not a single cluster loss. These observations suggest that piRNA cluster expansion is driven by positive selection, perhaps caused by the need to silence the ever-expanding repertoire of mammalian transposons.

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          Author and article information

          Journal
          19357307
          2667148
          10.1073/pnas.0900523106

          Chemistry
          Animals,Evolution, Molecular,Genetic Variation,genetics,Mice,Multigene Family,RNA, Small Interfering,Rats,Recombination, Genetic,Time Factors

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