Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
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DOI：
10.1073/pnas.1018222108
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发表时间：
2011-02-08
影响因子：
11.1
通讯作者：
Gaut, Brandon S.
中科院分区：
文献类型：
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作者：
Hollister, Jesse D.;Smith, Lisa M.;Gaut, Brandon S.
转座因子（TE）通常是真核生物基因组大小差异的主要决定因素。在植物中，TE的增殖通过防止移动性的表观遗传沉默机制来对抗。最近使用模式植物拟南芥的研究表明，甲基化的TE插入通常与附近基因的表达减少有关，并且由于这种效应，这些插入可能会受到纯化选择。对其他植物物种中TEs表观遗传沉默的全基因组模式知之甚少。在这里，我们比较了来自A. thaliana和一个密切相关的同源物，TE拷贝数高出两到三倍，拟南芥lyrata。我们发现，TEs，特别是siRNA靶向的TEs，与两个物种内的基因表达减少，也与直系同源物之间的基因表达差异。此外，A. lyrata TE被较低比例的独特匹配siRNA靶向，这与TE表达的更有效沉默相关。我们的研究结果表明，RNA介导的DNA甲基化沉默在A. lyrata，这一发现可能揭示了物种间TE增殖差异的原因。
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.