Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata.
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.
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
Jesse D
JD
Hollister
Lisa M
LM
Smith
Ya-Long
YL
Guo
Felix
F
Ott
Detlef
D
Weigel
Brandon S
BS
Gaut
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation / Q000502:physiology; D004251:DNA Transposable Elements / Q000502:physiology*; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D020868:Gene Silencing / Q000502:physiology; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering; D013045:Species Specificity
D004251:DNA Transposable Elements; D018744:DNA, Plant; D018749:RNA, Plant; D034741:RNA, Small Interfering
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