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@ARTICLE{Wang:826680,
      author       = {Wang, Zhenxing and Schwacke, Rainer and Kunze, Reinhard},
      title        = {{DNA} {D}amage-{I}nduced {T}ranscription of {T}ransposable
                      {E}lements and {L}ong {N}on-coding {RNA}s in {A}rabidopsis
                      {I}s {R}are and {ATM}-{D}ependent},
      journal      = {Molecular plant},
      volume       = {9},
      number       = {8},
      issn         = {1674-2052},
      address      = {Oxford},
      publisher    = {Oxford Univ. Press},
      reportid     = {FZJ-2017-00898},
      pages        = {1142 - 1155},
      year         = {2016},
      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.},
      cin          = {IBG-2},
      ddc          = {580},
      cid          = {I:(DE-Juel1)IBG-2-20101118},
      pnm          = {582 - Plant Science (POF3-582)},
      pid          = {G:(DE-HGF)POF3-582},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000386584900006},
      pubmed       = {pmid:27150037},
      doi          = {10.1016/j.molp.2016.04.015},
      url          = {https://juser.fz-juelich.de/record/826680},
}