Transposable elements: genome innovation, chromosome diversity, and centromere conflict

Abstract

Although it was nearly 70 years ago when transposable elements (TEs) were first discovered "jumping" from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive. Finally, we focus on the role of TEs in the establishment, maintenance, and stabilization of critical, yet rapidly evolving, chromosome features: eukaryotic centromeres. Across centromeres, specific types of TEs participate in genomic conflict, a balancing act wherein they are actively inserting into centromeric domains yet are harnessed for the recruitment of centromeric histones and potentially new centromere formation.

Keywords: Centromeric retroelement; Chromosome evolution; Conflict; Genome defense; Satellite; TE; Transposable element.

Fig. 1

The impact of TEs on the genome. a From left: insertion of a TE (red) into an exon and incorporation into the final mRNA; insertion of a TE (red) into an intron and contribution of splice donor and acceptor sites that lead to splicing of the TE into the mRNA; insertion of a TE (red) into a 3′ UTR with concomitant use of an alternative splice donor (asterisk) within the last exon and use of a splice acceptor within the TE, resulting in an alternative 3′ UTR including the TE. b Insertion of a TE (red) into a target site (arrowhead) results in various insertional mutations, right. From top: insertion of TE and TSDs; insertion of TE and TSDs with a small deletion in the right TSD; insertion of the TE, TSDs, and a local mRNA transcript (blue) as a retroduplication. c Insertion of a TE upstream of a coding region can result in, from left: establishment of a new promoter; enhanced transcription; localized silencing due to methylation of the TE (red lollipops). d (Top) NAHR events between two related TEs (red and orange) in tandem on either the same strand or different strands of DNA can result in duplications or deletions. (Bottom) NAHR events between inverted TEs results in an inversion

Fig. 2

a (Top) The structure of a centromere following homogenization of a stable satellite (gradient arrowheads) results in arrays of satellites, each sharing 70–80% identity, which are then organized in a tandem higher order array, with each block of satellites (dotted arrowheads), known as a HOR, sharing 97–99% identity. Random insertions of TEs (colored bars) are found interspersed among the HORs. (Bottom) Illustration of the graphical map of the same centromere shown in A, with bubbles on the inner circle representing each monomer satellite and how it is arranged in relation to other monomers in the array. Gradient bubbles correspond to gradient arrowheads. Lines indicate respective satellite or TE neighbor for each satellite. TE insertions and their relative location with respect to specific monomers are indicated by solid bubbles linked to the inner circle. b The structure of a complex centromere, exemplified by maize, rice, and potato, is characterized by diverse TEs (colored bars) and variable satellites (gradient arrowheads). c The structure of a neocentromere in which a single transcriptionally active mobile element (pink) inserted into non-centromeric DNA (gray). Arrowhead indicates promoter activity

Fig. 3

TEs and the evolution of centromeres. An initial destabilization event leads to the formation of a neocentromere (black dot indicates new centromere location, open circle indicates former centromere location on an ideogram representation of a chromosome), linked to the transcription of a TE (purple) in the absence of satellite DNA (gray). Following recruitment of CENP-A nucleosomes (yellow), more TEs insertions occur and incorporation of CENP-A nucleosomes (yellow, other H3-containing nucleosomes are indicated by blue) spread to form a complex centromere. As the complex centromere establishes an equilibrium state, TEs accumulate and satellites (arrowheads) begin to emerge. While individual variation in the placement of CENP-A nucleosomes (CENP-A containing nucleosomes are yellow, other centromeric H3-nucleosomes are blue, non-centromeric nucleosomes are brown) can exist within a population, the average centromere domain is relatively stable. At this stage of centromere evolution, interchromosomal movement of TEs can influence homogenization of arrays across non-homologous chromosomes. Finally, a dominant satellite emerges that subsequently forms higher order arrays with only intermittent TE insertions. Following a chromosome destabilization event, the HOR is either inactivated by unknown mechanisms, or lost due to chromosome damage, and a new centromere emerges in a different location