Ten things you should know about transposable elements

Abstract

Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.

TERAD: Extraction of transposable element composition from RADseq data

“…Finally, the limitation of low‐coverage sampling of the genome is not unique to ddRADseq and would similarly affect LC‐WGS (Rasmussen & Noor, ). Furthermore, older and inactive TEs tend to accumulate more mutations (Bourque et al, ), which could create new restriction sites. Thus, TEs that are sampled from RADseq may be more sensitive towards older elements than newly active elements.…”

“…Transposable elements (TEs) are selfish genetic elements that can move within a genome via a copy‐and‐paste or cut‐and‐paste mechanism (Feschotte, Jiang, & Wessler, ). Ubiquitous among all organisms, TEs are the main contributor of genome size differences across eukaryotes (Gregory, ), and they play a critical role in evolution by introducing mutation and facilitating genomic rearrangement (Bourque et al, ). Cross‐species comparative studies have been instrumental in understanding how ecology affects TE abundance (Kalendar, Tanskanen, Immonen, Nevo, & Schulman, ) and how TEs drive evolution (Feiner, ; Staton & Burke, ).…”

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

“…Thus, LINE1 is a much more versatile mutagen than previously thought, and is then subject to the powerful forces of natural selection during evolution, to potentially lead to its enrichment at heterochromatin. Bourque and colleagues recently stated that “on average, any two human haploid genomes differ by approximately a thousand TE insertions, primarily from the LINE1 or Alu families.” The full spectrum of mutagenesis induced by LINE1 deserves further investigation.…”

“…The mutagenic activity of TEs has made them potent drivers of genomic change and evolution (reviewed in ref. [52–55]). It is striking to note that the genomic content of TEs but not genes has steadily increased with species biological complexity .…”

“…Most TE‐related mutations are lost to genetic drift, and the cases where they have an irreparably detrimental impact tend to be lost to natural selection. It is therefore misplaced to ask whether TE‐induced variation overall has an adaptive value, much in the same way that we would not ask that question of other sources of variation, such as point mutations—the answer would naturally be: “it depends.” What is clear is that TE‐induced variation carries a very high information content, given the numerous ways in which it can modulate gene activity, and the profound impact that it has had in the evolution of genomes.…”