Data from: Transposon variants and their effects on gene expression in Arabidopsis

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA-mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24 nt long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA-targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.

转座因子（Transposable elements, TEs）构成了多数植物基因组的主要组成部分。其转录与转座过程受到小干扰RNA（small interfering RNAs, siRNAs）以及包括DNA甲基化在内的表观遗传标记的调控。为解析siRNA介导的调控与TE演化之间的相互作用，并探究TE差异如何影响邻近基因的表达，我们对3个拟南芥（Arabidopsis thaliana）生态型的全基因组范围内TE、siRNA与基因表达的差异展开了研究。TE序列多态性以及连锁TE的存在，均与基因表达的种内变异呈正相关。位于保守TE 2 kb范围内的基因，其表达稳定性要高于毗邻携带序列多态性的变异TE的基因。TE的多态性水平与紧密相邻的基因同样呈正相关。我们还对介导TE沉默的24 nt长siRNA的分布情况进行了研究。被唯一比对siRNA靶向的TE，平均而言距离编码基因更远，这显然是因为它们对邻近基因的表达抑制作用更强。此外，siRNA（尤其是唯一比对siRNA）在其他生态型中缺失的TE区域中富集。由此可见，被唯一比对siRNA靶向似乎会促进TE的序列缺失。总体而言，本研究表明，对TE的siRNA靶向可能会影响基因组序列的清除，进而影响植物的基因表达演化。