title: Cytoplasmic organelle DNA preferentially inserts into open chromatin.
abstract: DNA transfer from chloroplasts and mitochondria to the nucleus is ongoing in eukaryotes but the mechanisms involved are poorly understood. Mitochondrial DNA was observed to integrate into the nuclear genome through DNA double-strand break repair in Nicotiana tabacum. Here, 14 nuclear insertions of chloroplast DNA (nupts) that are unique to Oryza sativa subsp. indica were identified. Comparisons with the preinsertion nuclear loci identified in the related subspecies, O. sativa subsp. japonica, which lacked these nupts, indicated that chloroplast DNA had integrated by nonhomologous end joining. Analyzing public DNase-seq data revealed that nupts were significantly more frequent in open chromatin regions of the nucleus. This preference was tested further in the chimpanzee genome by comparing nuclear loci containing integrants of mitochondrial DNA (numts) with their corresponding numt-lacking preinsertion sites in the human genome. Mitochondrial DNAs also tended to insert more frequently into regions of open chromatin revealed by human DNase-seq and Formaldehyde-Assisted Isolation of Regulatory Elements-seq databases.
authors: School of Molecular and Biomedical Science, The University of Adelaide, South Australia, Australia.
authors: Dong
authors: D
authors: Wang
authors: Jeremy N
authors: JN
authors: Timmis
mesh_terms: D000818:Animals; D002460:Cell Line; D002467:Cell Nucleus / Q000235:genetics*; D002843:Chromatin / Q000235:genetics*; D053903:DNA Breaks, Double-Stranded; D059766:DNA End-Joining Repair; D018742:DNA, Chloroplast / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D006801:Humans; D012275:Oryza / Q000166:cytology / Q000235:genetics; D002679:Pan troglodytes / Q000235:genetics
chemical_list: D002843:Chromatin; D018742:DNA, Chloroplast; D004272:DNA, Mitochondrial; D018744:DNA, Plant
keywords: chloroplast; double-strand break repair; endosymbiotic gene transfer; mitochondrion; open chromatin
references: Genome Res. 2012 Jan;22(1):151-62
references: 22110044
references: Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10
references: 15240870
references: Mol Biol Evol. 2012 Jul;29(7):1707-11
references: 22319165
references: Nature. 2003 Mar 6;422(6927):72-6
references: 12594458
references: Mol Cell. 2004 Jun 4;14(5):611-23
references: 15175156
references: Nat Genet. 2004 Jul;36(7):767-73
references: 15208627
references: Nucleic Acids Res. 2007;35(17):5831-8
references: 17720709
references: Mol Biol Evol. 2011 Jul;28(7):2019-28
references: 21252282
references: Nucleic Acids Res. 2012 Oct;40(18):9073-88
references: 22761406
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Cell. 2008 Jan 25;132(2):311-22
references: 18243105
references: PLoS One. 2012;7(2):e32255
references: 22389691
references: Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2444-8
references: 22308419
references: Nat Rev Genet. 2004 Feb;5(2):123-35
references: 14735123
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
references: 14681465
references: Mol Cell. 2005 Aug 5;19(3):357-66
references: 16061182
references: Genome Res. 2011 Oct;21(10):1757-67
references: 21750106
references: Plant Mol Biol. 1997 Sep;35(1-2):25-34
references: 9291957
references: Plant Cell. 2010 Sep;22(9):3118-29
references: 20876829
references: Nucleic Acids Res. 2001 Oct 1;29(19):3975-81
references: 11574679
references: PLoS Genet. 2006 Sep 22;2(9):e158
references: 17002501
references: Nature. 2012 Oct 25;490(7421):497-501
references: 23034647
references: Plant Physiol. 2008 Sep;148(1):328-36
references: 18660434
references: Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8828-33
references: 12817081
references: Genetics. 2001 Aug;158(4):1665-74
references: 11514454
references: Plant Signal Behav. 2012 May;7(5):595-7
references: 22516813
references: Nature. 1990 Jul 26;346(6282):376-9
references: 2165219
references: PLoS Biol. 2004 Sep;2(9):E273
references: 15361937
references: PLoS Genet. 2008 Oct;4(10):e1000237
references: 18949041
references: PLoS Genet. 2009 Jan;5(1):e1000323
references: 19119415
references: Nature. 1999 Nov 4;402(6757):96-100
references: 10573425