Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

Abstract

Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent mobility. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to this effect. Less is known about the genome-wide patterns of epigenetic silencing of TEs in other plant species. Here, we compare the 24-nt siRNA complement from A. thaliana and a closely related congener with a two-to threefold higher TE copy number, Arabidopsis lyrata. We show that TEs-particularly siRNA-targeted TEs -are associated with reduced gene expression within both species and also with gene expression differences between orthologs. In addition, A. lyrata TEs are targeted by a lower fraction of uniquely matching siRNAs, which are associated with more effective silencing of TE expression. Our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species.gene silencing | transposons

Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice

“…However, the gain of methylation at the D1 locus in Epi-d1 is associated with the upstream repeat sequences (Miura et al, 2009), similar to fwa and Epi-rav6. Therefore, these repeat elements around the causal genes in Epi-d1, fwa, and Epi-rav6 might function as epigenetic mediators to influence nearby gene expression, further confirming previous findings (Hollister et al, 2011;Wei et al, 2014).…”

“…S3A). TEs, especially those proximal to genes, can act as epigenetic mediators to influence nearby gene expression (Hollister and Gaut, 2009;Hollister et al, 2011;Wei et al, 2014). So, we performed bisulfite sequencing to analyze methylation in a 2,358-bp genomic region consisting of 573 bp of gene body, 1,321 bp of upstream region, and 464 bp of 59 distal retrotransposon sequence (Supplemental Fig.…”

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

“…These biological processes are congruent with the presumed defence function of siRNAs in plants against the proliferation of endogenous TEs or invading viruses through transcriptional or post‐transcriptional gene silencing (Carrington & Ambros, 2003). However, siRNAs could also indirectly affect gene expression of adjacent genes in the proximity of TEs (Hollister et al., 2011). Thus, changes in expression in sRNAs could ultimately be adaptive and evolve quickly under natural selection (Chapman & Carrington, 2007).…”

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

“…Given that species divergence is low relative to the coalescent history of C. grandiflora (that is, most of the C. rubella alleles are shared with C. grandiflora), it is probable that npg l e t t e r s longer timescales are required for transposable element copy number to diverge noticeably. Thus, our analyses suggest little evidence for large-scale changes in transposable element abundance, as the evolution of selfing in Capsella occurred about 100,000 years ago, and imply that transposable element activity may be specifically elevated in A. lyrata 20 . C. rubella is a young species with an origin that is probably associated with a severe founder event and a shift to a highly selfing mating system.…”