Cytoplasmic organelle DNA preferentially inserts into open chromatin

Genome Biology and Evolution

Volumn 5, Issue 6, 2013, Pages 1060-1064

  Wang, Dong ^a   Timmis, Jeremy N ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

Chloroplast; Double strand break repair; Endosymbiotic gene transfer; Mitochondrion; Open chromatin

Indexed keywords

CHLOROPLAST DNA; CHROMATIN; MITOCHONDRIAL DNA; PLANT DNA;

ANIMAL; CELL LINE; CELL NUCLEUS; CHROMATIN; CYTOLOGY; DNA END JOINING REPAIR; DOUBLE STRANDED DNA BREAK; GENETICS; HUMAN; PAN TROGLODYTES; RICE; ARTICLE; CHLOROPLAST; DOUBLE-STRAND BREAK REPAIR; ENDOSYMBIOTIC GENE TRANSFER; MITOCHONDRION; OPEN CHROMATIN;

ANIMALS; CELL LINE; CELL NUCLEUS; CHROMATIN; DNA BREAKS, DOUBLE-STRANDED; DNA END-JOINING REPAIR; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; DNA, PLANT; HUMANS; ORYZA SATIVA; PAN TROGLODYTES;

CHLOROPLAST; DOUBLE-STRAND BREAK REPAIR; ENDOSYMBIOTIC GENE TRANSFER; MITOCHONDRION; OPEN CHROMATIN;

EID: 84891600269     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt070     Document Type: Article

References (31)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
2. Boyle AP, et al. 2008. High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311-322.
3. Guirouilh-Barbat J, et al. 2004. Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. Mol Cell. 14:611-623.
4. Hazkani-Covo E, Covo S. 2008. Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PLoS Genet. 4:e1000237.
5. Hogan GJ, Lee CK, Lieb JD. 2006. Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet. 2:e158.
6. Huang CY, Ayliffe MA, Timmis JN. 2003. Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422:72-76.
7. Huang X, et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497-501.
8. Karolchik D, et al. 2004. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32:D493-D496.
9. Khush GS. 1997. Origin, dispersal, cultivation and variation of rice. Plant Mol Biol. 35:25-34.
10. Kim A, Song SH, Brand M, Dean A. 2007. Nucleosome and transcription activator antagonism at human beta-globin locus control region DNase I hypersensitive sites. Nucleic Acids Res. 35:5831-5838.
11. Lin Y, Waldman AS. 2001a. Capture of DNA sequences at double-strand breaks in mammalian chromosomes. Genetics 158:1665-1674.
12. Lin Y, Waldman AS. 2001b. Promiscuous patching of broken chromosomes in mammalian cells with extrachromosomal DNA. Nucleic Acids Res. 29:3975-3981.
13. Lloyd AH, Timmis JN. 2011. The origin and characterization of new nuclear genes originating from a cytoplasmic organellar genome. Mol Biol Evol. 28:2019-2028.
14. Lloyd AH, Wang D, Timmis JN. 2012. Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis. PLoS One 7:e32255.
15. Ma J, Bennetzen JL. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 101:12404-12410.
16. Miller DG, Petek LM, Russell DW. 2004. Adeno-associated virus vectors integrate at chromosome breakage sites. Nat Genet. 36:767-773.
17. Nick McElhinny SA, et al. 2005. A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. Mol Cell. 19:357-366.
18. Pecinka A, et al. 2010. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 22:3118-3129.
19. Ricchetti M, Fairhead C, Dujon B. 1999. Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402:96-100.
20. Ricchetti M, Tekaia F, Dujon B. 2004. Continued colonization of the human genome by mitochondrial DNA. PLoS Biol. 2:E273.
21. Sheppard AE, Timmis JN. 2009. Instability of plastid DNA in the nuclear genome. PLoS Genet. 5:e1000323.
22. Sheppard AE, et al. 2008. Transfer of plastid DNA to the nucleus is elevated during male gametogenesis in tobacco. Plant Physiol. 148:328-336.
23. Song L, et al. 2011. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21:1757-1767.
24. Stegemann S, Hartmann S, Ruf S, Bock R. 2003. High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci U S A. 100:8828-8833.
25. Thorsness PE, Fox TD. 1990. Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Nature 346:376-379.
26. Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 5:123-135.
27. Tsuji J, Frith MC, Tomii K, Horton P. 2012. Mammalian NUMT insertion is non-random. Nucleic Acids Res. 40:9073-9088.
28. Wang D, Lloyd AH, Timmis JN. 2012a. Environmental stress increases the entry of cytoplasmic organellar DNA into the nucleus in plants. Proc Natl Acad Sci U S A. 109:2444-2448.
29. Wang D, Lloyd AH, Timmis JN. 2012b. Nuclear genome diversity in somatic cells is accelerated by environmental stress. Plant Signal Behav. 7:595-597.
30. Wang D, Rousseau-Gueutin M, Timmis JN. 2012. Plastid sequences contribute to some plant mitochondrial genes. Mol Biol Evol. 29:1707-1711.
31. Zhang W, et al. 2012. High-resolution mapping of open chromatin in the rice genome. Genome Res. 22:151-162.