title: Migrating bubble during break-induced replication drives conservative DNA synthesis.
abstract: The repair of chromosomal double strand breaks (DSBs) is crucial for the maintenance of genomic integrity. However, the repair of DSBs can also destabilize the genome by causing mutations and chromosomal rearrangements, the driving forces for carcinogenesis and hereditary diseases. Break-induced replication (BIR) is one of the DSB repair pathways that is highly prone to genetic instability. BIR proceeds by invasion of one broken end into a homologous DNA sequence followed by replication that can copy hundreds of kilobases of DNA from a donor molecule all the way through its telomere. The resulting repaired chromosome comes at a great cost to the cell, as BIR promotes mutagenesis, loss of heterozygosity, translocations, and copy number variations, all hallmarks of carcinogenesis. BIR uses most known replication proteins to copy large portions of DNA, similar to S-phase replication. It has therefore been suggested that BIR proceeds by semiconservative replication; however, the model of a bona fide, stable replication fork contradicts the known instabilities associated with BIR such as a 1,000-fold increase in mutation rate compared to normal replication. Here we demonstrate that in budding yeast the mechanism of replication during BIR is significantly different from S-phase replication, as it proceeds via an unusual bubble-like replication fork that results in conservative inheritance of the new genetic material. We provide evidence that this atypical mode of DNA replication, dependent on Pif1 helicase, is responsible for the marked increase in BIR-associated mutations. We propose that the BIR mode of synthesis presents a powerful mechanism that can initiate bursts of genetic instability in eukaryotes, including humans.
authors.affiliation: School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Natalie
authors.initials: N
authors.lastname: Saini
authors.forename: Sreejith
authors.initials: S
authors.lastname: Ramakrishnan
authors.forename: Rajula
authors.initials: R
authors.lastname: Elango
authors.forename: Sandeep
authors.initials: S
authors.lastname: Ayyar
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.forename: Angela
authors.initials: A
authors.lastname: Deem
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Ira
authors.forename: James E
authors.initials: JE
authors.lastname: Haber
authors.forename: Kirill S
authors.initials: KS
authors.lastname: Lobachev
authors.forename: Anna
authors.initials: A
authors.lastname: Malkova
mesh_terms: D019457:Chromosome Breakage; D053903:DNA Breaks, Double-Stranded; D004265:DNA Helicases / Q000378:metabolism; D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics*; D004271:DNA, Fungal / Q000096:biosynthesis* / Q000235:genetics; D042822:Genomic Instability / Q000235:genetics; D016296:Mutagenesis / Q000235:genetics; D016196:S Phase / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; C085463:PIF1 protein, S cerevisiae; D004265:DNA Helicases
references.citation: J Bacteriol. 1995 Dec;177(23):6844-53
references.pmid: 7592477
references.citation: Yeast. 1994 Dec;10(13):1793-808
references.pmid: 7747518
references.citation: Proc Natl Acad Sci U S A. 1996 May 28;93(11):5419-24
references.pmid: 8643590
references.citation: Genetics. 1999 May;152(1):143-52
references.pmid: 10224249
references.citation: Cell Cycle. 2008 Apr 1;7(7):859-64
references.pmid: 18414031
references.citation: Mol Cell. 2012 May 25;46(4):424-35
references.pmid: 22607975
references.citation: Curr Opin Genet Dev. 2013 Jun;23(3):271-9
references.pmid: 23790415
references.citation: DNA Repair (Amst). 2010 Aug 5;9(8):914-21
references.pmid: 20663718
references.citation: Mol Microbiol. 1995 May;16(3):373-84
references.pmid: 7565099
references.citation: PLoS Genet. 2010 May 13;6(5):e1000948
references.pmid: 20485519
references.citation: Annu Rev Cell Biol. 1991;7:375-402
references.pmid: 1809350
references.citation: Genetics. 1998 Nov;150(3):1037-47
references.pmid: 9799256
references.citation: Annu Rev Genet. 2012;46:455-73
references.pmid: 23146099
references.citation: Science. 2008 Mar 7;319(5868):1352-5
references.pmid: 18323444
references.citation: Mol Cell Biol. 2004 Mar;24(6):2344-51
references.pmid: 14993274
references.citation: Mol Cell Biol. 2009 Mar;29(6):1432-41
references.pmid: 19139272
references.citation: Yeast. 1999 Oct;15(14):1541-53
references.pmid: 10514571
references.citation: PLoS Genet. 2008 Nov;4(11):e1000264
references.pmid: 19023402
references.citation: Curr Protoc Cytom. 2001 May;Chapter 8:Unit 8.10
references.pmid: 18770738
references.citation: Methods Mol Biol. 2009;557:209-34
references.pmid: 19799185
references.citation: Genetics. 2008 Aug;179(4):1845-60
references.pmid: 18689895
references.citation: PLoS Genet. 2009 Jan;5(1):e1000327
references.pmid: 19180184
references.citation: Genes Dev. 2010 Jun 1;24(11):1133-44
references.pmid: 20516198
references.citation: Bioessays. 2011 Apr;33(4):290-9
references.pmid: 21290399
references.citation: Methods Mol Biol. 2011;745:437-45
references.pmid: 21660709
references.citation: PLoS Genet. 2008 Sep 05;4(9):e1000175
references.pmid: 18773114
references.citation: PLoS Biol. 2011 Feb 15;9(2):e1000594
references.pmid: 21347245
references.citation: Cell. 1986 Dec 5;47(5):793-806
references.pmid: 3022939
references.citation: Yeast. 2006 Oct-Nov;23(14-15):1045-51
references.pmid: 17083135
references.citation: Nature. 2007 Aug 16;448(7155):820-3
references.pmid: 17671506
references.citation: Genetics. 1996 Mar;142(3):717-26
references.pmid: 8849882
references.citation: Nature. 2007 May 3;447(7140):102-5
references.pmid: 17410126
references.citation: Methods Enzymol. 1995;262:613-27
references.pmid: 8594382
references.citation: Mol Cell Biol. 2007 Apr;27(7):2601-14
references.pmid: 17242181
references.citation: Mol Cell Biol. 2005 Feb;25(3):933-44
references.pmid: 15657422