Analysis of miRNA duplication in the human genome and the role of transposon evolution in this process

Abstract

Duplication of miRNAs is one of the modes of their evolution. This study demonstrates that human miRNAs arranged mostly in 5000-nt clusters and their copies are scattered randomly throughout the genome at an average distance of 4.3 × 106 bp. We compared the neighborhood of miRNAs copies with the transposable elements (TEs) and found that most miRNAs homologues (96%) propagate by DNA transposons and retroelements. Copies of primate-specific made1 elements containing the has-mir-548 miRNAs family contributed the most to this process. An analysis of made1’s evolution supports the earlier observation that these TEs emerged and multiplied explosively over the genome of a common ancestor and diverged later at average genomic rates. At that time, the modern copies of the has-mir-548 family appeared due to adaptive mutagenesis of some of the transposons copies; they were recruited into the silencing system. Nucleotide changes leading to transposon transformation into miRNAs genes and numerous miRNA copies may be helpful in predicting new miRNAs.