Transposable elements and genomics

Abstract

Once described as selfish DNA, transposable elements (TEs) have been revisited due to a plethora of new genomic information. TEs are considered indispensable genomic treasures during eukaryotic species evolution and supply raw materials for evolution by creating novel variation and allelic diversity (Volff 2006; Oliver et al. 2013). TEs are found ubiquitously with high copies in nearly all eukaryotic species. TEs are often present in major genomic denizens in some species by occupying more than half of the genome, contributing to the C-value paradox in eukaryotes. In this issue, six articles are published describing several aspects of transposable elements. Four review articles and two research articles are presented in this special issue. TEs are classified into class I TEs and class II TEs based on transposition mechanisms. Class I TEs are retrotransposons that retrotranspose via RNA intermediate semi-conservative manner. Class II TEs transpose via DNA intermediate conservative manner. Rajput (2015) described class I retrotransposons as the intrinsic genomic evolutionist as ‘‘Retrotransposons: the intrinsic genomic evolutionist’’. He reviewed essential information on retrotransposons. Retrotransposons are major agents in genome evolution and diversity by inducing rearrangements and restructuring genomes. Retrotransposons affect many aspects of biological organization, from gene regulation to genome obesity, which are critical in shaping current genomes. He also discusses the similarity between retrotransposons and endo-retroviruses, bringing the retrotransposons into a closer relationship to understand phylogenetics. Bae et al. contributed ‘‘Biological changes of transposable elements by radiation’’ (Bae et al. 2015). Human endogenous retroviruses (HERV) are a group of LTR (long terminal repeat) retrotransposons in the human genome. Transcriptionally-active TEs can move around in the genome and cause genome instability. HERV insertion into critical genes may lead to the progression of some diseases, including cancer. These authors reviewed cases of human disease due to HERV insertion. Radiation therapy manifests diverse, complex, and multicellular responses, including unmasking epigenetic suppression that switches silenced TEs into active ones. In the review, the authors summarized the recent understanding on radiationinduced DNA double-strand breaks (DSBs) and subsequent non-homologous end joining (NHEJ) repair. They also presented their recent results on activation of L1 elements by radiation in cancer cells, in which the methylation level of L1 was increased by relatively low radiation doses. Based on these results, the authors proposed that radiation exposure may lead directly to mutation as well as to methylation changes in TEs, which are considered important factors in cancer radiation therapy. Lee et al. contributed ‘‘Composition and evolutionary importance of transposable elements in humans and primates’’ (Lee et al. 2015). Primates, including humans, are not immune to the evolutionary impact of TEs on their genomes. Approximately half of the sequences of primate genomes are TErelated sequences. In their review, comparisons of TE constitution among primate species are extensively explained, and TE dispersions in the genome were analyzed between human and primates. These authors proposed that TE-driven structural variations are a major force in primate evolution. Roy et al. examined TEs in different aspects of molecular markers in ‘‘Marker utility of transposable elements for plant genetics, breeding, and N.-S. Kim (&) Department of Molecular Bioscience, Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea e-mail: kimnamsu@kangwon.ac.kr; nsk6472@yahoo.ca