Transposable elements and gene expression during the evolution of amniotes

Lu Zeng,David L Adelson,Stephen M Pederson,R.Daniel Kortschak

doi:10.1186/s13100-018-0124-5

Abstract

BackgroundTransposable elements (TEs) are primarily responsible for the DNA losses and gains in genome sequences that occur over time within and between species. TEs themselves evolve, with clade specific LTR/ERV, LINEs and SINEs responsible for the bulk of species-specific genomic features. Because TEs can contain regulatory motifs, they can be exapted as regulators of gene expression. While TE insertions can provide evolutionary novelty for the regulation of gene expression, their overall impact on the evolution of gene expression is unclear. Previous investigators have shown that tissue specific gene expression in amniotes is more similar across species than within species, supporting the existence of conserved developmental gene regulation. In order to understand how species-specific TE insertions might affect the evolution/conservation of gene expression, we have looked at the association of gene expression in six tissues with TE insertions in six representative amniote genomes.ResultsA novel bootstrapping approach has been used to minimise the conflation of effects of repeat types on gene expression. We compared the expression of orthologs containing recent TE insertions to orthologs that contained older TE insertions, and the expression of non-orthologs containing recent TE insertions to non-orthologs with older TE insertions. Both orthologs and non-orthologs showed significant differences in gene expression associated with TE insertions. TEs were found associated with species-specific changes in gene expression, and the magnitude and direction of expression changes were noteworthy. Overall, orthologs containing species-specific TEs were associated with lower gene expression, while in non-orthologs, non-species specific TEs were associated with higher gene expression. Exceptions were SINE elements in human and chicken, which had an opposite association with gene expression compared to other species.ConclusionsOur observed species-specific associations of TEs with gene expression support a role for TEs in speciation/response to selection by species. TEs do not exhibit consistent associations with gene expression and observed associations can vary depending on the age of TE insertions. Based on these observations, it would be prudent to refrain from extrapolating these and previously reported associations to distantly related species.

Highlights

Transposable elements (TEs) are primarily responsible for the DNA losses and gains in genome sequences that occur over time within and between species
We describe the association of clade specific TEs with gene expression in long diverged amniotes (Fig. 1a) in order to determine how much these TEs might have altered the regulation of gene expression in six tissues during the evolution of these species
Mammalian gene expression phylogenies To obtain an initial overview of gene expression patterns, we evaluated the similarity of ortholog gene expression in 6 tissues, from both males and females in our 6 species

Summary

Introduction

Transposable elements (TEs) are primarily responsible for the DNA losses and gains in genome sequences that occur over time within and between species. Zeng et al Mobile DNA (2018) 9:17 in the genomes of species from all major eukaryotic lineages and this structure is, by far, the most frequent These elements are composed of a 5’ tRNA-related region and a central region of unknown origin, followed by a stretch of homopolymeric adenosine residues or other simple repeats [10, 11]. In contrast to the very widespread phylogenetic distribution of tRNA derived SINEs, 7SLderived SINEs have been found only in mammals [9] They are composed of a 7SL-derived region followed by a poly(A) tail and can be either monomeric (B1 family) or dimeric (Alu family) [12, 13]. SINE RNAs have been shown to possess the potential to regulate gene expression at the post-transcriptional level, for example, Alu RNAs can modulate protein translation, influence on RNA editing and mRNA splicing [16]

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