Retroelements and their impact on genome evolution and functioning

Abstract

Retroelements comprise a considerable fraction of eukaryotic genomes. Since their initial discovery by Barbara McClintock in maize DNA, retroelements have been found in genomes of almost all organisms. First considered as a "junk DNA" or genomic parasites, they were shown to influence genome functioning and to promote genetic innovations. For this reason, they were suggested as an important creative force in the genome evolution and adaptation of an organism to altered environmental conditions. In this review, we summarize the up-to-date knowledge of different ways of retroelement involvement in structural and functional evolution of genes and genomes, as well as the mechanisms generated by cells to control their retrotransposition.

Fig. 1

Schematic representation of different retroelements. White triangles short direct repeats (target site duplications), UTR untranslated region, ORF open reading frame, LTR long terminal repeat, PR protease, RT reverse transcriptase, RH ribonuclease H, IN integrase, Env envelope, YR tyrosine recombinase, EN endonuclease

Fig. 2

a Formation of tRNA-like SINEs as an example of a role of REs in generation of new genetic elements; b retroelements as substrates for recombination events; c transduction of 3′-flanking sequences; d formation of processed pseudogenes by LINE enzymatic machinery; e generation of chimeric elements by template switches during LINE retrotransposition

Fig. 3

Different mechanisms of RE influence on gene transcription. Red boxes retroelements, green boxes gene exons, green arrow gene transcriptional start site, purple oval enhancer element