Transposon variants and their effects on gene expression in Arabidopsis

PLoS Genet. 2013;9(2):e1003255. doi: 10.1371/journal.pgen.1003255. Epub 2013 Feb 7.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis* / genetics
  • Arabidopsis* / metabolism
  • DNA Methylation
  • DNA Transposable Elements / genetics*
  • Epigenesis, Genetic
  • Evolution, Molecular*
  • Gene Expression Regulation, Plant*
  • Gene Silencing
  • Genome, Plant
  • Polymorphism, Genetic
  • RNA, Small Interfering


  • DNA Transposable Elements
  • RNA, Small Interfering

Associated data

  • GEO/GSE24569
  • GEO/GSE24669

Grant support

LMS was supported by a European Community FP7 Marie Curie Fellowship (PIEF-GA-2008-221553) and an EMBO long-term fellowship. Small RNA studies in the DW laboratory were supported by European Community FP6 IP SIROCCO contract LSHG-CT-2006-037900, FP7 Collaborative Project AENEAS contract KBBE-2009-226477, and the Max Planck Society. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.