title: Replication-independent endogenous DNA double-strand breaks in Saccharomyces cerevisiae model.
abstract: Without exposure to any DNA-damaging agents, non-dividing eukaryotic cells carry endogenous DNA double-strand breaks (EDSBs), or Replication-Independent (RIND)-EDSBs. In human cells, RIND-EDSBs are enriched in the methylated heterochromatic areas of the genome and are repaired by an ATM-dependent non-homologous end-joining pathway (NHEJ). Here, we showed that Saccharomyces cerevisiae similarly possess RIND-EDSBs. Various levels of EDSBs were detected during different phases of the cell cycle, including G0. Using a collection of mutant yeast strains, we investigated various DNA metabolic and DNA repair pathways that might be involved in the maintenance of RIND-EDSB levels. We found that the RIND-EDSB levels increased significantly in yeast strains lacking proteins involved in NHEJ DNA repair and in suppression of heterochromatin formation. RIND-EDSB levels were also upregulated when genes encoding histone deacetylase, endonucleases, topoisomerase, and DNA repair regulators were deleted. In contrast, RIND-EDSB levels were downregulated in the mutants that lack chromatin-condensing proteins, such as the high-mobility group box proteins, and Sir2. Likewise, RIND-EDSB levels were also decreased in human cells lacking HMGB1. Therefore, we conclude that the genomic levels of RIND-EDSBs are evolutionally conserved, dynamically regulated, and may be influenced by genome topology, chromatin structure, and the efficiency of DNA repair systems.
authors: Inter-Department Program of BioMedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand.
authors: Jirapan
authors: J
authors: Thongsroy
authors: Oranart
authors: O
authors: Matangkasombut
authors: Araya
authors: A
authors: Thongnak
authors: Prakasit
authors: P
authors: Rattanatanyong
authors: Siwanon
authors: S
authors: Jirawatnotai
authors: Apiwat
authors: A
authors: Mutirangura
mesh_terms: D002453:Cell Cycle; D015825:Chromosomes, Fungal / Q000378:metabolism; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D004261:DNA Replication; D004271:DNA, Fungal / Q000378:metabolism; D005800:Genes, Fungal; D024243:HMGB1 Protein / Q000378:metabolism; D006367:HeLa Cells; D006570:Heterochromatin / Q000378:metabolism; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics; D008954:Models, Biological; D008970:Molecular Weight; D009154:Mutation / Q000235:genetics; D016133:Polymerase Chain Reaction; D034741:RNA, Small Interfering / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D013312:Stress, Physiological
chemical_list: D004271:DNA, Fungal; D024243:HMGB1 Protein; D006570:Heterochromatin; D034741:RNA, Small Interfering
references: DNA Repair (Amst). 2004 Aug-Sep;3(8-9):797-815
references: 15279765
references: Nucleic Acids Res. 2009 Jun;37(11):3699-713
references: 19372273
references: Gene. 2001 Nov 14;279(1):1-16
references: 11722841
references: Mol Cancer. 2010 Mar 31;9:70
references: 20356374
references: Clin Chim Acta. 2012 May 18;413(9-10):869-74
references: 22326975
references: Cytometry A. 2005 Jul;66(1):1-8
references: 15924303
references: Cell. 2003 Mar 7;112(5):725-36
references: 12628191
references: Curr Opin Genet Dev. 2013 Apr;23(2):166-73
references: 23602331
references: Nucleic Acids Res. 2008 Jun;36(11):3667-75
references: 18474527
references: J Cancer Res Clin Oncol. 2010 May;136(5):677-84
references: 19898867
references: Proc Natl Acad Sci U S A. 1979 Dec;76(12):6515-9
references: 392520
references: J Radiat Res. 2003 Mar;44(1):47-51
references: 12841599
references: Biochim Biophys Acta. 2010 Jan-Feb;1799(1-2):175-80
references: 20123079
references: Genetics. 1999 Jul;152(3):921-32
references: 10388812
references: Oncogene. 2004 Nov 18;23(54):8841-6
references: 15480421
references: Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12871-6
references: 14566050
references: Biochim Biophys Acta. 2010 Jan-Feb;1799(1-2):3-14
references: 19748605
references: Science. 2010 Dec 3;330(6009):1385-9
references: 21127252
references: Mol Biol Cell. 2006 Oct;17(10):4584-91
references: 16899507
references: Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13708-13
references: 11095743