Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora

Abstract

Transposable elements (TEs) make up a significant portion of eukaryotic genomes and are important drivers of genome evolution. However, the extent to which TEs affect gene expression variation on a genome-wide scale in comparison with other types of variants is still unclear. We characterized TE insertion polymorphisms and their association with gene expression in 124 whole-genome sequences from a single population of Capsella grandiflora, and contrasted this with the effects of single nucleotide polymorphisms (SNPs). Population frequency of insertions was negatively correlated with distance to genes, as well as density of conserved noncoding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare SNPs contribute equally to up- and down-regulation, but have a weaker individual effect than TEs. An expression quantitative trait loci (eQTL) analysis shows that a greater proportion of common TEs are eQTLs as opposed to common SNPs, and a third of the genes with TE eQTLs do not have SNP eQTLs. In contrast with rare TE insertions, common insertions are more likely to increase expression, consistent with recent models of cis-regulatory evolution favoring enhancer alleles. Taken together, these results imply that TEs are a significant contributor to gene expression variation and are individually more likely than rare SNPs to cause extreme changes in gene expression.

Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot

“…We observed a high level of low frequency DcSto insertions, with most of them referred to as UIS if present in only one of the 31 investigated genomes, a phenomenon also reported for other species [17, 51, 52]. As proposed by Uzunović et al, localisation of TEs in genic region may be limited due to negative selection [53]. On the other hand, the prevalence of UIS may result from an ongoing TE activity.…”

Evolution and plasticity of the transcriptome under temperature fluctuations in the fungal plant pathogen Zymoseptoria tritici

“…As a first attempt towards this goal, we could observe that these regions with higher density of significant genes are also regions enriched in transposable elements. The role of transposable elements in regulating gene expression evolution has been well documented (Sudaran et al, 2014; Rech et al, 2019; Uzunovic et al, 2019; see Schrader and Schmitz, 2019 for recent review). Our results altogether suggest that new mutations –due to TE themselves or SNPS/indels– in the cis -regulatory regions of the genes could be responsible for the evolution of gene expression level.…”

The evolutionary forces shaping cis and trans regulation of gene expression within a population of outcrossing plants

“…The gene Carubv100252000m is also in the 'lightcyan' module and it has the 18th highest intramodular connectivity out of the 2,886 genes in the module, putting it in the top 1% of connected genes. Additionally, there is transposable element (TE) located near the eQTL present in three individuals (Uzunović et al 2019) . All three of these individuals carrying the TE were homozygous for the reference allele of the eQTL, but TE presence was not associated with gene expression, allele-specific expression, or flowering time (Fig.…”

“…We used a similar procedure to test for associations between trans-eQTL genotype and allele specific expression of nearby genes, which was measured for 99 individuals in (Josephs et al 2015) , except that this time we conducted a t-test for differences in quantile-normalized allele-specific-expression between heterozygous and homozygous individuals. We also used t-tests to compare expression traits and flowering time for individuals that did or did not carry a transposable element insertion (Uzunović et al 2019) . We identified orthologs between genes in the C. rubella reference genome and A. thaliana as described in (Williamson et al 2014) .…”