These are often guided by opposite selective forces, a balancing act of facilitating future propagation while mitigating deleterious effects on host cell function. TEs exhibit various levels of preference for insertion within certain features or compartments of the genome (Fig. Thus, it is perhaps not surprising that TEs are rarely, if ever, randomly distributed in the genome. These interactions encompass processes familiar to ecologists, such as parasitism, cooperation, and competition. The genome may be viewed as an ecosystem inhabited by diverse communities of TEs, which seek to propagate and multiply through sophisticated interactions with each other and with other components of the cell. However, much like the taxonomy of species, the classification of TEs is in constant flux, perpetually subject to revision due to the discovery of completely novel TE types, the introduction of new levels of granularity in the classification, and ongoing development of methods and criteria to detect and classify TEs. Thus, in principle, every TE sequence in a genome can be affiliated to a (sub)family, superfamily, subclass, and class (Fig. This ancestral copy can be inferred as a consensus sequence, which is representative of the entire (sub)family.
At the most detailed level of TE classification, elements are grouped into families or subfamilies, which can be defined as a closely related group of elements that can be traced as descendants of a single ancestral unit. Similarly, Tc1/ mariner, hAT (hobo-Ac-Tam3), and MULEs (Mutator-like elements) are three superfamilies of DNA transposons that are widespread across the eukaryotic tree. For example, T圓/ gypsy and Ty1/ copia elements are two major superfamilies of LTR retrotransposons that occur in virtually all major groups of eukaryotes. For detailed reviews on individual TE types and transposition mechanisms, we refer the reader to the monograph edited by Craig et al.Įach TE subclass is further divided into subgroups (or superfamilies) that are typically found across a wide range of organisms, but share a common genetic organization and a monophyletic origin. Class 2 elements, also known as DNA transposons, are mobilized via a DNA intermediate, either directly through a ‘cut-and-paste’ mechanism or, in the case of Helitrons, a ‘peel-and-paste’ replicative mechanism involving a circular DNA intermediate. For non-LTR retrotransposons, which include both long and short interspersed nuclear elements (LINEs and SINEs), chromosomal integration is coupled to the reverse transcription through a process referred to as target-primed reverse transcription. For long terminal repeat (LTR) retrotransposons, integration occurs by means of a cleavage and strand-transfer reaction catalyzed by an integrase much like retroviruses. Class 1 elements, also known as retrotransposons, mobilize through a ‘copy-and-paste’ mechanism whereby a RNA intermediate is reverse-transcribed into a cDNA copy that is integrated elsewhere in the genome. TEs can be divided into two major classes based on their mechanism of transposition, and each class can be subdivided into subclasses based on the mechanism of chromosomal integration. As a result of their deep evolutionary origins and continuous diversification, TEs come in a bewildering variety of forms and shapes (Fig. Transposable elements (TEs) are DNA sequences that have the ability to change their position within a genome.
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