Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

Ikhlak Ahmed, Alexis Sarazin, Chris Bowler, Vincent Colot, Hadi Quesneville

Research output: Contribution to journalArticle

84 Citations (Scopus)

Abstract

Transposable elements (TEs) and their relics play major roles in genome evolution. However, mobilization of TEs is usually deleterious and strongly repressed. In plants and mammals, this repression is typically associated with DNA methylation, but the relationship between this epigenetic mark and TE sequences has not been investigated systematically. Here, we present an improved annotation of TE sequences and use it to analyze genome-wide DNA methylation maps obtained at single-nucleotide resolution in Arabidopsis. We show that although the majority of TE sequences are methylated, ∼26 are not. Moreover, a significant fraction of TE sequences densely methylated at CG, CHG and CHH sites (where H=A, T or C) have no or few matching small interfering RNA (siRNAs) and are therefore unlikely to be targeted by the RNA-directed DNA methylation (RdDM) machinery. We provide evidence that these TE sequences acquire DNA methylation through spreading from adjacent siRNA-targeted regions. Further, we show that although both methylated and unmethylated TE sequences located in euchromatin tend to be more abundant closer to genes, this trend is least pronounced for methylated, siRNA-targeted TE sequences located 5′ to genes. Based on these and other findings, we propose that spreading of DNA methylation through promoter regions explains at least in part the negative impact of siRNA-targeted TE sequences on neighboring gene expression.

Original languageEnglish
Pages (from-to)6919-6931
Number of pages13
JournalNucleic Acids Research
Volume39
Issue number16
DOIs
Publication statusPublished - 1 Sep 2011
Externally publishedYes

Fingerprint

DNA Transposable Elements
DNA Methylation
Arabidopsis
Genome
Small Interfering RNA
Euchromatin
Genetic Promoter Regions
Epigenomics
Genes
Mammals
Nucleotides
RNA
Gene Expression

ASJC Scopus subject areas

  • Genetics

Cite this

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. / Ahmed, Ikhlak; Sarazin, Alexis; Bowler, Chris; Colot, Vincent; Quesneville, Hadi.

In: Nucleic Acids Research, Vol. 39, No. 16, 01.09.2011, p. 6919-6931.

Research output: Contribution to journalArticle

Ahmed, Ikhlak ; Sarazin, Alexis ; Bowler, Chris ; Colot, Vincent ; Quesneville, Hadi. / Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. In: Nucleic Acids Research. 2011 ; Vol. 39, No. 16. pp. 6919-6931.
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