Front Bioeng Biotechnol. 2015 Jun 9;3:71. doi: 10.3389/fbioe.2015.00071. eCollection 2015.

Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes.

Kannan S¹, Chernikova D², Rogozin IB¹, Poliakov E³, Managadze D¹, Koonin EV¹, Milanesi L⁴.

Author information

1: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, MD , USA.
2: Department of Genetics, Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College , Hanover, NH , USA.
3: Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health , Bethesda, MD , USA.
4: Institute for Biomedical Technologies, National Research Council , Segrate , Italy.

Abstract

Transposable elements (TEs) are abundant in mammalian genomes and appear to have contributed to the evolution of their hosts by providing novel regulatory or coding sequences. We analyzed different regions of long intergenic non-coding RNA (lincRNA) genes in human and mouse genomes to systematically assess the potential contribution of TEs to the evolution of the structure and regulation of expression of lincRNA genes. Introns of lincRNA genes contain the highest percentage of TE-derived sequences (TES), followed by exons and then promoter regions although the density of TEs is not significantly different between exons and promoters. Higher frequencies of ancient TEs in promoters and exons compared to introns implies that many lincRNA genes emerged before the split of primates and rodents. The content of TES in lincRNA genes is substantially higher than that in protein-coding genes, especially in exons and promoter regions. A significant positive correlation was detected between the content of TEs and evolutionary rate of lincRNAs indicating that inserted TEs are preferentially fixed in fast-evolving lincRNA genes. These results are consistent with the repeat insertion domains of LncRNAs hypothesis under which TEs have substantially contributed to the origin, evolution, and, in particular, fast functional diversification, of lincRNA genes.