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要旨:
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 examine the interplay of siRNA targeting and TE evolution, and how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs and gene expression among three Arabidopsis thaliana accessions. Both polymorphism levels and TE presence contribute to intraspecific variation in gene expression. We find that the expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variable TEs. Polymorphism levels of TEs and adjacent genes are positively correlated, when TEs are less than 2 kb away. We also investigated the distribution of 24 nt long siRNAs, which are known to 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 the location of deletions and hence evolution of gene expression and plant genomes.
