Transposons Continue the Amaze

Gozukirmizi, N. International Journal of Science Letters. 2019. 1(1): 1-13. Review Transposons continue the amaze Nermin Gozukirmizi 1 Department of Molecular Biology and Genetics, Faculty of Art and Science, Istinye University, Istanbul/Turkey Abstract Article History Transposable elements (TEs) were first discovered in maize plants. However, they exist almost in all species with a few exceptions (Plasmodium falciparum, Ashbya gossypii and Kluveromuyces lactis). They are the most important contributors to genome plasticity and evolution and even epigenetic genome regulation. Organisms with large genomes have high transposon percentages. For example, Arabidopsis thaliana has a genome size of 125 Mb which comprises 14% transposons, Homo sapiens (3000 Mb) 45-48.5%, and Hordeum vulgare genome (5300 Mb) has 80%. TEs are classified into two major groups based on their transposition mechanisms: Class I (RNA transposons – retrotransposons) and Class II (DNA transposons). Recent progress in whole-genome sequencing and long-read assembly have resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. All TEs in a cell are named as transposome (mobilome), and transposomics is a new area to work with transposome. Although a number of bioinformatics softwares have recently been developed for the annotation of TEs in sequenced genomes, there are very few computational tools strictly dedicated to the identification of active TEs using genome-wide approaches. In this review article, after a brief introduction and review of the transposable elements, I discussed their effects in gene expression, evolution, recent applications and also share our research on retrotransposons with different organisms. Received 01.06.2019 Accepted 02.08.2019 Keywords Evolution, Genome dynamics, Mobile elements, Over-sized transposable elements, Transposon based genome editing 1. Introduction Transposon, a segment of DNA that moves to a new location in a chromosome, to another chromosome or cell, even different organism and alters existing genetic structure, causes significant changes and play an important role during evolution. Transposons were first described by Barbara McClintock (1950), a maize cytogeneticist who was rewarded with 1 Correspondence: 1 Nobel prize almost 30 years later than her exploration of the relationship between chromosome breaks and maize grain colour alterations. Today, we are aware that gene and genome plasticity caused by transposons exist in somatic tissues almost all living organisms. Different terms, such as jumping genes, mobile elements, controlling elements, transposable elements are used in synonymous ways. Altough there are a vast amount of knowledge on structure, types and life cycles of these genomic sequences everyday with the recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in new informations for their origin, functions, roles in gene expression, and evolutionary processes. TEs in the genomes of living organisms, are either defective, fossilized copies or potentially active copies that are restrained by host silencing systems. However, active transposition evidenced by instances of mutagenic (yet potentially evolutionarily significant) insertions has been demonstrated. For example, TEs have been shown to silence or alter expression of genes adjacent to insertion sites, contribute to chromosomal rearrangements via recombination, epigenetically alter regional methylation patterns, and provide template sequences for RNA interference (Feschotte et al., 2002; Bennetzen, 2005; Morgante et al., 2007; Weil and Martienssen, 2008; Slotkin et al., 2012; Lerat et al., 2019). This diverse functional impacts of TEs, and their intrinsic contribution to genomic plasticity suggest that these elements play a major role in molecular diversification, and ultimately, species divergence (Schrader and Schmitz, 2019; Dupeyron et al., 2019; Boissinot et al., 2019). This review article covers a short overview of TEs classification, transposition mechanisms, their effects on gene expression and evolutionary processesand even importance and usage of transposons for different purposes such as transposon markers, transposomics, and . Particularly their impact on protein coding and those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, number of long non-coding RNAs (lncRNAs) are originated from TEs in plants (Cho et al., 2018). 2. Structure of Transposons According to the traditional simplistic representation transposons are classified into two class as Class I and Class II (retrotransposons and DNA transposons, respectively). However, there are many subtypes under this classification (Piégua et al., 2015) (Figure 1). Nowadays over-sized transposons come into consideration with some of the proposed models for gene 2 capture by eukaryotic TEs (Arkhipova et al., 2019). Before we mention about types and classification of transposons, general explanation of their structures will be helpful to understand the following parts of this review. Transposons use many different enzymes for their transposition. While some transposons can encode these enzymes (autonomous), others can not (non-autonomous) and use enzymes of autonomous transposons. Figure 1 indicated comparison and content from two proposals for the classification and annotation of eukaryotic TEs. The Repbase proposal is shown on the right (Jurka et al., 2005; Kapitonov and Jurka, 2008) and the Wicker proposal on the left (Wicker et al., 2007). Both proposals are based on DNA and amino acid sequence features. Both proposals divide all TEs into two groups, the retrotransposons and the DNA transposons (Piégua et al., 2015). Figure 1. New classification of transposons. 3 Retrotransposons have more complex structure than DNA transposons. They have LTR (Long Terminal Repeat), R (Repeated region), U3 (Unique for 3’end of RNA), U5 (Unique for 5’ end of RNA), PBS (Primer Binding Site), GAG (Group-specific antigen), POL (Polyprotein), AP (Aspartic Peptidase), RT (Reverse Transcriptase), RH (Ribonuclease H), INT (Integrase), ENV (Envelope), PPT (PolyPurine Tract) and TSD (Target Site Duplication) (Figure 2). Figure 2. Schematic demonstration of a retrotransposon having LTR regions. Despite the complex structure of retrotransposons, DNA transposons have more simple structure (Figure 3). DNA transposons encode a transposase (Tase) enzyme. This enzyme cuts DNA transposon and integrates it to a new location. Figure 3. Schematic demonstration of a DNA transposon. (TIR, Terminal Inverted Repeat; Tase, Transposase; TSD, Target Site Duplication). DNA t (...truncated)