title: eQTL mapping of transposon silencing reveals a position-dependent stable escape from epigenetic silencing and transposition of AtMu1 in the Arabidopsis lineage.
abstract: Transposons are massively abundant in all eukaryotic genomes and are suppressed by epigenetic silencing. Transposon activity contributes to the evolution of species; however, it is unclear how much transposition-induced variation exists at a smaller scale and how transposons are targeted for silencing. Here, we exploited differential silencing of the AtMu1c transposon in the Arabidopsis thaliana accessions Columbia (Col) and Landsberg erecta (Ler). The difference persisted in hybrids and recombinant inbred lines and was mapped to a single expression quantitative trait locus within a 20-kb interval. In Ler only, this interval contained a previously unidentified copy of AtMu1c, which was inserted at the 3' end of a protein-coding gene and showed features of expressed genes. By contrast, AtMu1c(Col) was intergenic and associated with heterochromatic features. Furthermore, we identified widespread natural AtMu1c transposition from the analysis of over 200 accessions, which was not evident from alignments to the reference genome. AtMu1c expression was highest for insertions within 3' untranslated regions, suggesting that this location provides protection from silencing. Taken together, our results provide a species-wide view of the activity of one transposable element at unprecedented resolution, showing that AtMu1c transposed in the Arabidopsis lineage and that transposons can escape epigenetic silencing by inserting into specific genomic locations, such as the 3' end of genes.
authors.affiliation: Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
authors.forename: Tina
authors.initials: T
authors.lastname: Kabelitz
authors.affiliation: Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Kappel
authors.affiliation: Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
authors.forename: Kirstin
authors.initials: K
authors.lastname: Henneberger
authors.affiliation: Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
authors.forename: Eileen
authors.initials: E
authors.lastname: Benke
authors.affiliation: Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, 18190 Sanitz, Germany.
authors.forename: Christiane
authors.initials: C
authors.lastname: Nöh
authors.affiliation: Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany isabel.baeurle@uni-potsdam.de.
authors.forename: Isabel
authors.identifier: http://orcid.org/0000-0001-5633-8068
authors.initials: I
authors.lastname: Bäurle
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping; D004251:DNA Transposable Elements / Q000502:physiology*; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D040641:Quantitative Trait Loci
chemical_list: D004251:DNA Transposable Elements
references.citation: Nature. 2009 Sep 17;461(7262):423-6
references.pmid: 19734880
references.citation: Nat Rev Genet. 2010 Mar;11(3):204-20
references.pmid: 20142834
references.citation: Nat Rev Genet. 2011 Aug 18;12(9):615-27
references.pmid: 21850042
references.citation: Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3535-43
references.pmid: 23940361
references.citation: Biochim Biophys Acta. 2011 Aug;1809(8):452-8
references.pmid: 21514406
references.citation: Nat Rev Genet. 2013 Jan;14(1):49-61
references.pmid: 23247435
references.citation: Plant J. 1996 Oct;10(4):733-6
references.pmid: 8893548
references.citation: Science. 2007 Oct 5;318(5847):109-12
references.pmid: 17916737
references.citation: PLoS One. 2012;7(10):e47043
references.pmid: 23118865
references.citation: Nature. 2009 Oct 22;461(7267):1135-8
references.pmid: 19847267
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Nature. 2006 Oct 5;443(7111):521-4
references.pmid: 17024082
references.citation: Nat Rev Genet. 2013 Feb;14(2):100-12
references.pmid: 23329111
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: Methods Mol Biol. 2013;1057:123-42
references.pmid: 23918425
references.citation: Genes Dev. 2001 Mar 1;15(5):591-602
references.pmid: 11238379
references.citation: Genome Res. 2010 Sep;20(9):1297-303
references.pmid: 20644199
references.citation: Bioinformatics. 2014 Aug 1;30(15):2114-20
references.pmid: 24695404
references.citation: Nature. 2001 May 10;411(6834):212-4
references.pmid: 11346800
references.citation: Plant Physiol. 2013 May;162(1):116-31
references.pmid: 23542151
references.citation: PLoS Biol. 2003 Dec;1(3):E67
references.pmid: 14691539
references.citation: Genome Res. 2009 Aug;19(8):1419-28
references.pmid: 19478138
references.citation: EMBO J. 2011 May 18;30(10):1928-38
references.pmid: 21487388
references.citation: Trends Plant Sci. 2010 Aug;15(8):471-8
references.pmid: 20541961
references.citation: Nat Struct Mol Biol. 2014 Jan;21(1):64-72
references.pmid: 24336224
references.citation: Nature. 2013 Mar 14;495(7440):193-8
references.pmid: 23467092
references.citation: Nat Protoc. 2010 Mar;5(3):457-72
references.pmid: 20203663
references.citation: Plant J. 2001 Jan;25(1):79-91
references.pmid: 11169184
references.citation: Plant Signal Behav. 2013 Aug;8(8):
references.pmid: 23759554
references.citation: Bioinformatics. 2011 Nov 1;27(21):2957-63
references.pmid: 21903629
references.citation: Genome Res. 2009 Sep;19(9):1639-45
references.pmid: 19541911
references.citation: PLoS Genet. 2005 Jul;1(1):109-18
references.pmid: 16103920
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2322-7
references.pmid: 21252301
references.citation: Nat Genet. 2013 Sep;45(9):1029-39
references.pmid: 23852169
references.citation: Nature. 2009 Sep 17;461(7262):427-30
references.pmid: 19734882
references.citation: Plant J. 2007 Jan;49(1):38-45
references.pmid: 17144899
references.citation: Cell. 2009 Feb 6;136(3):461-72
references.pmid: 19203581
references.citation: Nature. 2004 Jan 8;427(6970):164-7
references.pmid: 14712277
references.citation: Science. 1993 Jun 25;260(5116):1926-8
references.pmid: 8316832
references.citation: Methods Mol Biol. 2010;631:1-11
references.pmid: 20204863
references.citation: Science. 2012 Nov 9;338(6108):758-67
references.pmid: 23145453
references.citation: Plant Cell. 2012 Sep;24(9):3603-12
references.pmid: 23001035
references.citation: Curr Opin Plant Biol. 2012 Nov;15(5):511-6
references.pmid: 22824142
references.citation: Science. 1984 Nov 16;226(4676):792-801
references.pmid: 15739260
references.citation: Plant J. 2007 Aug;51(3):526-36
references.pmid: 17559516
references.citation: Plant Cell. 2014 Apr 25;26(4):1792-1807
references.pmid: 24769482
references.citation: Genes Dev. 2007 Feb 1;21(3):267-77
references.pmid: 17242155
references.citation: PLoS Genet. 2009 Nov;5(11):e1000733
references.pmid: 19936291
references.citation: Bioinformatics. 2004 Jan 22;20(2):289-90
references.pmid: 14734327
references.citation: Curr Opin Plant Biol. 2012 Nov;15(5):503-10
references.pmid: 22940592
references.citation: Annu Rev Biochem. 2012;81:65-95
references.pmid: 22663077
references.citation: Brief Bioinform. 2013 Mar;14(2):178-92
references.pmid: 22517427
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147