What are Transposable Elements?
Mobile segments of genetic materials were first discovered by Barbara McClintock in the late 1940s. Repetitive genomic sequences that are able to move (transpose) from one chromosomal location into another are called transposable elements (TEs) (Bowen & Jordan, 2002). The eukaryotic and prokaryotic genome can be comprised of plenty of transposable elements. Recent genome sequencing studies have demonstrated that TEs inhabit approximately 50% of the primate genome and while coding DNA occupies approximately 2% of the genome(Kim, Lee, & Han, 2012).
McClintock’s observation on the continuous breakage on one arm of the chromosome in maize made to call it dissociation (Ds). Further, she proved that the breakage is simultaneously aided by other factors in a different location called the Activator (Ac) (Finnegan, 1992). Her finding has paved the route to the further discoveries of TEs movement mechanism within and out of an organism. Numerous researchers have witnessed that TEs are results of environmental stressing factors. Although they are more commonly seen in pants compared to animals Capy et al., 2000; Kim et al., 2014; Piacentini et al., 2014 and Chénais et al., 2012 demonstrated the variable results of transposition in Drosophila melanogaster due to temperature and resistance to pesticides(Canapa, Barucca, Biscotti, Forconi, & Olmo, 2016). Based on the mechanism of transposition and comparison of their genomic structures as well as their consequences, transposons are divided as RNA transposons (Class I) and DNA transposons (Class II)(Bowen & Jordan, 2002). DNA transposons use a cut-and-paste mechanism, however, the RNA transposons which can also be called retrotransposons move by copy-and-paste mechanism i.e., by duplicating the elements into a new genomic location. In this instance, conclusions show that retrotransposons enhance their number of copies more hastily than DNA transposons(Kim et al., 2012).
Once TEs were considered as selfish DNA or junk DNA in which they were understood as “genomic hitchhikers” or molecular parasites. Because, the awareness of genomic evolution and method of adaptation in the host due to TEs was limited (Piskurek & Jackson, 2012). The existence of TEs can be beneficial or deleterious to a genome. They can introduce genetic evolution as they are able to produce gene inactivation, varying gene expression and illegitimate gene recombination(Muñoz-López & García-Pérez, 2010). Such phenomenon is the consequence of altered transcriptional activity which in turn results in the production of dysfunctional or abnormal proteins(Kim et al., 2012). Their presence creates a combat between the host (to curtail their spread and the effects) and the selfish DNA (to be perpetuated).The host DNA is usually prepared for a defense mechanism against the transposable elements and is always in a process of maintaining equilibrium in order to escape from deleterious effects. For example, insertions in the heterochromatic regions (nonessential regions) or selections against during fecundation or development which were active during the embryonic or germ stage have major effects in minimizing the adverse effects (Muñoz-López & García-Pérez, 2010). The inhibition mechanism is done either through methylation or by the interference of small RNAs such as (siRNAs) in plants and PI-WI-interacting RNAs in animals (piRNAs, probably evolved as a defense mechanism against viruses) (Canapa et al., 2016).
Nowadays the progress in evolutionary–developmental biology (evo-devo) has contributed to the concepts of DNA sequencing and genomics technologies. Thus, the selfish denotation of TEs has turned in to benefit. TEs bring evolutionary changes by increasing, rearranging and diversifying the genetic makeup of an organism(Piskurek & Jackson, 2012). Over the past 6 million years from the divergence of human beings and chimpanzee a significant transmission of TEs can be illustrated i.e, 5,530 Alu, 1,835 L1, 864 SVA, and 113 HERV-K (HML-2). Still, new genomic rearrangements or de novo TEs will expectedly introduce variations in human phenotypes and diseases(Kim et al., 2012).
Classification of Transposable Elements
RNA Transposons (Class I)
Class, I transposons act by reverse transcription of an RNA intermediate, each replication cycle produces new copies of TEs. Class I elements contain long terminal repeat (LTR) elements and non-LTR elements, such as Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs) (Casacuberta & González, 2013). Until present including the Metaviridae (gypsy) and Pseudoviridae (Copia) together with the LTR and Non-LTR retrotransposons, about 30 types are known(de Lima Fávaro, de Araújo, de Azevedo, & Paccola-Meirelles, 2005). Pseudoviridae and Metaviridae in (Havecker et al., 2004) are Class I distinct groups emerged from the amino acid sequences of reverse transcriptase. They are identified by the order of the coding regions of structural (gag) and enzymatic (pol) proteins (de Lima Fávaro et al., 2005).
SINEs are usually special non-autonomous elements. They do not undergo encoding their component; but they are retrotransposed by enzymatic machinery encoded somewhere else(Bowen & Jordan, 2002). SINEs rely on LINEs form transposition which emerges from accidental retrotransposition of various polymerase III (Pol III) transcripts. Pol III promoter found in SINEs helps them for their expression unlike the absence of retro-pseudogenes. The Alu elements which make up about 10% of the human genome can be a good example. Alu consist of two CG-rich fragments, the left, and right Alu, connected by an A-rich linker and ended in a poly-A tail(Casacuberta & González, 2013).
LINEs like elements or Non –LTR elements encode the enzymes used for the propagation of the three elements during the transposition(Kim et al., 2012). LINE elements consist of the promoter Unsaturated Region at the 5′ (UTR), two ORFs and a 3′ UTR with a poly-A tail, i.e. “A” rich region(Casacuberta & González, 2013). Frequently reverse transcription of these elements is prematurely terminated producing many truncated non-autonomous copies(Bowen & Jordan, 2002).
LTR retrotransposons are mainly autonomous. Evolutionarily, their genomic structures resemble that of retroviruses(Bowen & Jordan, 2002). Structurally, they are composed of two types internal protein coding domain called ORFs (open reading frames) ranging from 5- 7kb and LTRs (long terminal repeats) of 250 – 600bp. GAG ORF encodes a structural protein which is similar to a virus-like particle. However, POL ORF encodes the enzyme responsible for reverse transcription and integration. Terminal LTRs have three functional regions, namely, U3 at 3′ is an enhancer and promoter, R is with both start and termination site for transcription and U5 exists at the 5’end (Zhang et al., 2014).
DNA Transposons (ClassII )
Although DNA transposons exist poorly in the human genome they cover elements found almost in all living organisms stretching from bacteria to mammals. Some of the popular elements can be Tc1/ mariner, hAT and piggyBac (Chénais, 2013)Class II transposon undergo a cut and paste mechanism of the transposable element from one location to another. They are comprised of transposases gene where two Terminal Inverted Repeats (TIRs) of 38–40 bp(Vizváryová & Valková, 2004) are placed on both ends. Transposase excises the segment of DNA to be transposed (Muñoz-López & García-Pérez, 2010). During insertion, every DNA transposon features a specific hallmark as the target site DNA duplicates and creates a Target Site Duplication (TSDs). Thus, DNA transposon can be categorized into different families depending on their sequence of TIRs, and/or TSDs. In the meantime classifying elements into subclasses I and II sorts out subclass II such as the Helitron and Maverick with the breaking feature they exhibit during insertion due to the lack of double-stranded DNA despite their replication.(Muñoz-López & García-Pérez, 2010)
Furthermore, according to their self-sufficiency, TEs which are found in both classes can also be categorized as autonomous and nonautonomous (Casacuberta & González, 2013). Nonautonomous elements lack the protein necessary for transposition, SINEs and MITEs can be typical examples. MITEs (Miniature Inverted-repeat Transposable Elements) are short (80-500 bp) DNA transposon-like TEs, majorly found in eukaryotes most importantly in plant species and rarely in bacteria(Muñoz-López & García-Pérez, 2010). On the other hand, Autonomous elements carry the proteins for their movement. The effectiveness of the nonautonomous elements depends on the presence of autonomous elements(Casacuberta & González, 2013).
Structural illustration of ClassI and ClassII TEs. Dark blue arrows represent direct or inverted repeats, blue boxes represent coding sequences and white boxes represent non-coding sequences(Casacuberta & González, 2013).
Horizontal Transfer of TEs (HTT) and horizontal gene transfer (HGT) mediated by TEs
Transposable elements can also be transferred horizontally from one species to another species of different ancestors (Piskurek & Jackson, 2012). During a horizontal transfer, TEs are mainly a source of mutation or otherwise they act as vectors facilitating the horizontal transfer of new genetic content (Ochman et al. 2000; Frost et al. 2005)(Casacuberta & González, 2013). Moreover, HTT can be a means of survival mechanism which may be brought about by host repression of TE activity, or by the extinction of the host lineage.(Piskurek & Jackson, 2012). According to (Gilbert et al. 2010; Kuraku et al. 2012;Wallau et al. 2012;Walsh et al. 2013),the uneven distributions of TEs in phylogenies; identification of TEs exhibiting high sequence similarity between distantly related taxa; and phylogenetic incompatibility between the host and TEs are evidences of HTT(Baidouri et al., 2014). This trend has been more studied in prokaryotes such as in bacteria rather than in eukaryotes. So far in eukaryotes despite the limited knowledge, the hurdle is required to be due to the presence of a nuclear envelope and the soma/germ division (in metazoans)(Gilbert & Cordaux, 2013). (Doak et al. 1994; Eisen et al. 1994; Kapitonov and Jurka 1999, 2007; Robertson 2002; Feschotte 2004) demonstrated that the horizontal transfer of five superfamilies of eukaryote transposase from Class II TEs namely Tc1/mariner, Mutator, Merlin, PIF-Harbinger, and ISL2EU/IS4EU, to exhibit evolutionary derivations from prokaryotic IS families IS630, IS256, IS1595, IS5, and IS4, respectively(Gilbert & Cordaux, 2013).
The importance of transposable elements in various living things
Major outcomes have been gained from TE mobilization by implementing advanced sequencing technology such as next-generation sequencing, and combined computational analyses(Kim et al., 2012). The activity of transposons can be considered as one of the contributory factors for evolution. TEs can influence the adaptive phenomena of an organism by reorganizing the genome through chromosomal rearrangements such as duplications, inversions, and translocations. Furthermore, they can signify new coding genes and regulatory elements such as enhancers as a result of molecular domestication by the host (Canapa et al., 2016).
In Antirrhinum, a Tam3 element was observed to insert into a region 5′ of the niv gene which is involved in the synthesis of anthocyanin pigments. The initial insertion was observed to down-regulate expression of the gene. However, a series of rearrangements mediated by this element resulted in a change in the level and tissue specificity of expression of niv (Fig. 1). The net effect is a new and novel distribution of anthocyanin pigment in the flower tube (20). This series of mutations exemplifies the potential for TE-mediated ”rewiring” of regulatory networks, in this case by bringing new regulatory sequences in proximity to exonic sequences via an inversion, followed by an imprecise excision event
Bacterial studies in (Sayeed et al. 2010) classified Clostridium perfringensin a pathogenic bacterium in variable livestock, into four types according to the lethal toxins they produce. The most virulent B type isolates carry three virulent genes of plasmids. The identification of IS elements (IS1151) and genes in conjugate transposition show that HGT (horizontal gene transfer) due to HTT. This, in turn, will produce adaptation and enhances the pathogenicity of the bacterium (Casacuberta & González, 2013).
Ascomycota, Basidiomycota, and Zygomycota are believed to be the old components of the fungal genome which transmitted vertically although a limited horizontal patter cannot be abandoned. Thus the sporadic dispersion of some elements produces competition, self-regulation as well as regulation by the host. On the other hand, the DNA polymorphism resulted can be implemented for identifying phylogeny, epidemiology, and pathogenicity of strains(de Lima Fávaro et al., 2005). (Hua-van et al., 1998) has recognized the host strategies against TEs during the phylogenic study of Fusarium oxysporum fungi. That is the existence of fot1 element ranging from 0-100 number of copies and an impala element existing in a fixed number of copies in the genome. The mechanisms could be eliminated by natural selection and/or genetic drift which lead to the extinction of the elements as well as rearrangements and silencing mechanisms. According to (Daboussi, 1996) insertional mutagens due to transposons that give rise to gene change can be cloned as a gene of interest. Based on this point of view (Migheli et al., 2000) illustrated the efficiency of impula transposition in recovering mutants in F.oxysporum, showing the efficiency of transposition in pathogenicity mutant generation of the fungi(de Lima Fávaro et al., 2005).
Despite the limited studies of TEs in genetic instability and disease in humans, their impact can range from silent mutation to alternative splicing resulting in various diseases, genetic disorder to cancer(Ayarpadikannan & Kim, 2014). Approaches such as “retrotransposon capture sequencing” has been found to identify somatic structural variants due to L1 and Alu elements inserted in neuronal tissues as well as in somatic mutagenesis like lung tumor (Arkhipova et al., 2012). Additionally, the principle of Tc1/mariner transposon (DNA transposon) derived from invertebrates ability to introduce germline mutagenesis and insertional mutagenesis in vertebrates, except in mammals helped for gene therapy. Therefore, a synthetic Tc1/mariner type called Sleeping Beauty (SB), Tol2 and piggyBac(PB) have been discovered. This approach has been used in children X-linked severe combined immunodeficiency (SCID-X1) and was found with minor insertional mutagenesis and lesser immunogenic features compared to the previously used retroviral vector therapy and later used naked DNA and plasmid therapy systems. Although the implementation of PBase is feared of serious insertional mutagenesis as there are PB like elements in humans it is flexible and easily engineered. On the other hand, SB elements are absent in the human genome. This makes them safer to be used for therapy purposes despite the limitations to manipulate them for greater genetically transposition efficiency. Generally, significant expectations are placed on the application of SB and PB transposons in the primary somatic or stem cells therapy(Rajabpour, Raoofian, Habibi, Akrami, & Tabrizi, 2014).
To summarize the parasitic nature of transposable elements has obviously turned in to advantage. Transposable elements do contribute mutations in the genome of living organisms. On the other hand, the applications of advanced genome sequencing techniques have shifted their presence in the studies of evolution, adaptation, therapy, and phylogenetics of an organism.
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