Mammalian transposable elements and their impacts on genome evolution

Abstract

Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.

TERAD: Extraction of transposable element composition from RADseq data

“…The distribution of TEs varies in different lineages such that some lineages (e.g. mammals) have genomes where LINEs and SINE non-LTR retrotransposons dominate (Platt, Vandewege, & Ray, 2018), whereas other lineages (e.g. teleost fishes) have highly diverse TE superfamilies (Chalopin, Naville, Plard, Galiana, & Volff, 2015).…”

What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation

“…Approximately one third to half of the typical mammalian genome is derived from transposable elements (TEs) . TEs are DNA sequences that are capable of inserting into new locations in the genome, giving rise to repeated copies of the elements and to genome expansion.…”

“…Mammalian genomes contain low amounts of DNA transposons (<3%) and limited LTR elements (4–10%) but are dominated by the accumulation and activity of the non‐LTR elements (about 75% in most mammals) (reviewed in ref. [2]). Genomic distribution of a TE family often follows a pattern originating from a two‐step process: first, intrinsic features of transposition direct the initial location of the insertions, and second, selective pressures shape the evolving distribution of TEs (reviewed in ref.…”

The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements

“…Because of their ability to mobilize, TEs are powerful mutagens as novel TE insertions can disrupt exons, regulatory elements, and splice junctions, and also facilitate non-homologous recombination. As a result, TE insertions have been linked to genomic deletions, duplications, inversions, translocations, and chromosome breaks in a variety of genomes (Cheng et al 2005;Franke et al 2017;Platt et al 2018). Although some TE insertions have proven to be adaptive, TEs are generally considered a serious challenge to genome integrity.…”