title: DNA Damage-Induced Transcription of Transposable Elements and Long Non-coding RNAs in Arabidopsis Is Rare and ATM-Dependent.
abstract: Induction and mobilization of transposable elements (TEs) following DNA damage or other stresses has been reported in prokaryotes and eukaryotes. Recently it was discovered that eukaryotic TEs are frequently associated with long non-coding RNAs (lncRNAs), many of which are also upregulated by stress. Yet, it is unknown whether DNA damage-induced transcriptional activation of TEs and lncRNAs occurs sporadically or is a synchronized, genome-wide response. Here we investigated the transcriptome of Arabidopsis wild-type (WT) and ataxia telangiectasia mutated (atm) mutant plants 3 h after induction of DNA damage. In WT, expression of 5.2% of the protein-coding genes is ≥2-fold changed, whereas in atm plants, only 2.6% of these genes are regulated, and the response of genes associated with DNA repair, replication, and cell cycle is largely lost. In contrast, only less than 0.6% of TEs and lncRNAs respond to DNA damage in WT plants, and the regulation of ≥95% of them is ATM-dependent. The ATM-downstream factors BRCA1, DRM1, JMJ30, AGO2, and the ATM-independent AGO4 participate in the regulation of individual TEs and lncRNAs. Remarkably, protein-coding genes located adjacent to DNA damage-responsive TEs and lncRNAs are frequently coexpressed, which is consistent with the hypothesis that TEs and lncRNAs located close to genes commonly function as controlling elements.
authors.affiliation: Institute of Biology - Applied Genetics, Dahlem Centre of Plant Sciences - DCPS, Freie Universität Berlin, Albrecht-Thaler-Weg 6, 14195 Berlin, Germany.
authors.forename: Zhenxing
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425 Jülich, Germany.
authors.forename: Rainer
authors.initials: R
authors.lastname: Schwacke
authors.affiliation: Institute of Biology - Applied Genetics, Dahlem Centre of Plant Sciences - DCPS, Freie Universität Berlin, Albrecht-Thaler-Weg 6, 14195 Berlin, Germany. Electronic address: reinhard.kunze@fu-berlin.de.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Kunze
mesh_terms: D000249:Adenosine Monophosphate / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics*; D004249:DNA Damage / Q000235:genetics / Q000502:physiology*; D004251:DNA Transposable Elements / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D015533:Transcriptional Activation / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D062085:RNA, Long Noncoding; D018749:RNA, Plant; D000249:Adenosine Monophosphate
keywords: Arabidopsis thaliana; DNA damage response; ataxia telangiectasia mutated; long non-coding RNA; transposable element