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. 2011 Feb 8;108(6):2322-7.
doi: 10.1073/pnas.1018222108. Epub 2011 Jan 20.

Transposable Elements and Small RNAs Contribute to Gene Expression Divergence Between Arabidopsis Thaliana and Arabidopsis Lyrata

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Free PMC article

Transposable Elements and Small RNAs Contribute to Gene Expression Divergence Between Arabidopsis Thaliana and Arabidopsis Lyrata

Jesse D Hollister et al. Proc Natl Acad Sci U S A. .
Free PMC article

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.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Expression levels for genes in each bin of increasing distance from the nearest TE. Whiskers indicate 95% confidence intervals. Mean and confidence intervals of expression levels of all genes without a TE within 500 bp 5′ or 3′ from the gene are indicated by solid and dashed horizontal lines, respectively. Gene expression was averaged for TE distances binned in 500-bp increments, up to a maximum of 5,000 bp. A distance of zero indicates TEs within introns or UTRs.
Fig. 2.
Fig. 2.
Comparison of gene expression between A. thaliana and A. lyrata orthologs as a function of TE presence. Positive values of the log-transformed normalized expression difference indicate higher expression in A. thaliana.
Fig. 3.
Fig. 3.
Expression levels of TEs without matching 24-nt siRNAs, with multiply mapping 24-nt siRNAs only, or with multiply and uniquely mapping siRNAs.
Fig. 4.
Fig. 4.
Comparison of young and old TEs with multiply or uniquely mapping 24-nt siRNAs. These analyses are based on 914 copia and 897 gypsy retrotransposons in A. lyrata and 111 copia and 98 gypsy elements in A. thaliana.

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