Home LiteratureArticle Details
PMID: 21406975 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't

Damage-induced localized hypermutability.

Cell cycle (Georgetown, Tex.) ·Vol. 10 ·No. 7 ·2011-04-01 ·Pages 1073-85

Burch LH, Yang Y, Sterling JF, Roberts SA, Chao FG, Xu H, Zhang L, Walsh J, Resnick MA, Mieczkowski PA, Gordenin DA

Abstract

Genome instability continuously presents perils of cancer, genetic disease and death of a cell or an organism. At the same time, it provides for genome plasticity that is essential for development and evolution. We address here the genome instability confined to a small fraction of DNA adjacent to free DNA ends at uncapped telomeres and double-strand breaks. We found that budding yeast cells can tolerate nearly 20 kilobase regions of subtelomeric single-strand DNA that contain multiple UV-damaged nucleotides. During restoration to the double-strand state, multiple mutations are generated by error-prone translesion synthesis. Genome-wide sequencing demonstrated that multiple regions of damage-induced localized hypermutability can be tolerated, which leads to the simultaneous appearance of multiple mutation clusters in the genomes of UV- irradiated cells. High multiplicity and density of mutations suggest that this novel form of genome instability may play significant roles in generating new alleles for evolutionary selection as well as in the incidence of cancer and genetic disease.

MeSH Terms
DNA Breaks, Double-Stranded/radiation effects DNA Damage/genetics,radiation effects Genetic Variation Genomic Instability/genetics Mutation/radiation effects Saccharomyces cerevisiae Proteins/genetics Saccharomycetales Sequence Analysis, DNA Telomere/genetics,radiation effects Telomere-Binding Proteins/genetics Ultraviolet Rays
Chemicals
Cdc13 protein, S cerevisiae Saccharomyces cerevisiae Proteins Telomere-Binding Proteins
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Burch Lauranell H
National Institute of Environmental Health Sciences, Research Triangle Park, NC USA.
Yang Yong
Sterling Joan F
Roberts Steven A
Chao Frank G
Xu Hong
Zhang Leilei
Walsh Jesse
Resnick Michael A
Mieczkowski Piotr A
Gordenin Dmitry A
References (82)
82 references, click to expand
  1. Long regions of single-stranded DNA in human cells.
    Nature. 1979 Aug 2;280(5721):420-3 PMID: 223063
  2. Adaptive mutation by deletions in small mononucleotide repeats.
    Science. 1994 Jul 15;265(5170):405-7 PMID: 8023163
  3. The chromosome ends of Saccharomyces cerevisiae.
    Yeast. 1995 Dec;11(16):1553-73 PMID: 8720065
  4. Break-induced replication is highly inaccurate.
    PLoS Biol. 2011 Feb 15;9(2):e1000594 PMID: 21347245
  5. Avoiding dangerous missense: thermophiles display especially low mutation rates.
    PLoS Genet. 2009 Jun;5(6):e1000520 PMID: 19543367
  6. Yeast ARMs (DNA at-risk motifs) can reveal sources of genome instability.
    Mutat Res. 1998 May 25;400(1-2):45-58 PMID: 9685581
  7. Regulation of DNA double-strand break repair pathway choice.
    Cell Res. 2008 Jan;18(1):134-47 PMID: 18157161
  8. DNA repair: Decision at the break point.
    Nature. 2010 May 20;465(7296):301-2 PMID: 20485424
  9. Cells deficient in PARP-1 show an accelerated accumulation of DNA single strand breaks, but not AP sites, over the PARP-1-proficient cells exposed to MMS.
    Mutat Res. 2009 Dec 1;671(1-2):93-9 PMID: 19778542
  10. Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance.
    Microbiol Mol Biol Rev. 2009 Mar;73(1):134-54 PMID: 19258535
  11. The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes.
    Ann N Y Acad Sci. 1999 May 18;870:100-7 PMID: 10415476
  12. EGFR somatic doublets in lung cancer are frequent and generally arise from a pair of driver mutations uncommonly seen as singlet mutations: one-third of doublets occur at five pairs of amino acids.
    Oncogene. 2008 Jul 17;27(31):4336-43 PMID: 18372921
  13. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae.
    Genetics. 2008 Jan;178(1):67-82 PMID: 18202359
  14. T4 DNA polymerase (3'-5') exonuclease, an enzyme for the detection and quantitation of stable DNA lesions: the ultraviolet light example.
    Nucleic Acids Res. 1985 May 10;13(9):3285-304 PMID: 2987881
  15. Cyclobutane pyrimidine dimers and (6-4) photoproducts block polymerization by DNA polymerase I.
    Biochemistry. 1985 Oct 8;24(21):5723-8 PMID: 4084488
  16. Primer3 on the WWW for general users and for biologist programmers.
    Methods Mol Biol. 2000;132:365-86 PMID: 10547847
  17. The roles of REV3 and RAD57 in double-strand-break-repair-induced mutagenesis of Saccharomyces cerevisiae.
    Genetics. 2002 Nov;162(3):1063-77 PMID: 12454056
  18. Balancing AID and DNA repair during somatic hypermutation.
    Trends Immunol. 2009 Apr;30(4):173-81 PMID: 19303358
  19. Quantitative amplification of single-stranded DNA (QAOS) demonstrates that cdc13-1 mutants generate ssDNA in a telomere to centromere direction.
    Nucleic Acids Res. 2001 Nov 1;29(21):4414-22 PMID: 11691929
  20. Exploring protein fitness landscapes by directed evolution.
    Nat Rev Mol Cell Biol. 2009 Dec;10(12):866-76 PMID: 19935669
  21. Apn1 and Apn2 endonucleases prevent accumulation of repair-associated DNA breaks in budding yeast as revealed by direct chromosomal analysis.
    Nucleic Acids Res. 2008 Apr;36(6):1836-46 PMID: 18267974
  22. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis.
    PLoS Genet. 2010 Sep 09;6(9):e1001109 PMID: 20838597
  23. Missense meanderings in sequence space: a biophysical view of protein evolution.
    Nat Rev Genet. 2005 Sep;6(9):678-87 PMID: 16074985
  24. Human CtIP promotes DNA end resection.
    Nature. 2007 Nov 22;450(7169):509-14 PMID: 17965729
  25. Suffering in silence: the tolerance of DNA damage.
    Nat Rev Mol Cell Biol. 2005 Dec;6(12):943-53 PMID: 16341080
  26. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation.
    Mol Cell. 2005 Sep 16;19(6):791-804 PMID: 16168374
  27. Formation and processing of UV photoproducts: effects of DNA sequence and chromatin environment.
    Photochem Photobiol. 1997 Feb;65(2):270-83 PMID: 9066304
  28. A genome-wide view of the spectrum of spontaneous mutations in yeast.
    Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9272-7 PMID: 18583475
  29. Genomic mutation rates: what high-throughput methods can tell us.
    Bioessays. 2009 Sep;31(9):912-20 PMID: 19644920
  30. Targeting of somatic hypermutation.
    Nat Rev Immunol. 2006 Aug;6(8):573-83 PMID: 16868548
  31. Human mutation rate associated with DNA replication timing.
    Nat Genet. 2009 Apr;41(4):393-5 PMID: 19287383
  32. Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions.
    Mol Cell. 2006 Jan 6;21(1):15-27 PMID: 16387650
  33. Genome-wide model for the normal eukaryotic DNA replication fork.
    Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17674-9 PMID: 20876092
  34. Whole-genome profiling of mutagenesis in Caenorhabditis elegans.
    Genetics. 2010 Jun;185(2):431-41 PMID: 20439774
  35. Repair of endogenous DNA damage.
    Cold Spring Harb Symp Quant Biol. 2000;65:127-33 PMID: 12760027
  36. Blunt-ended DNA double-strand breaks induced by endonucleases PvuII and EcoRV are poor substrates for repair in Saccharomyces cerevisiae.
    DNA Repair (Amst). 2010 Jun 4;9(6):617-26 PMID: 20356803
  37. DNA replication fidelity.
    Annu Rev Biochem. 2000;69:497-529 PMID: 10966467
  38. Repair of UV-induced DNA damage and survival in yeast. I. Dimer excision.
    Mutat Res. 1975 Nov;30(2):209-18 PMID: 1107831
  39. Use of high throughput sequencing to observe genome dynamics at a single cell level.
    Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20830-5 PMID: 19934054
  40. Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.
    PLoS One. 2008;3(11):e3714 PMID: 19005564
  41. Regulation of ultraviolet light-induced gene expression by gene size.
    Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6582-6 PMID: 15087501
  42. Interchangeable parts of the Escherichia coli recombination machinery.
    Cell. 2003 Mar 21;112(6):741-4 PMID: 12654241
  43. A single-strand specific lesion drives MMS-induced hyper-mutability at a double-strand break in yeast.
    DNA Repair (Amst). 2010 Aug 5;9(8):914-21 PMID: 20663718
  44. Timing, coordination, and rhythm: acrobatics at the DNA replication fork.
    J Biol Chem. 2010 Jun 18;285(25):18979-83 PMID: 20382733
  45. Evidence for mutation showers.
    Proc Natl Acad Sci U S A. 2007 May 15;104(20):8403-8 PMID: 17485671
  46. An epigenetic code for DNA damage repair pathways?
    Biochem Cell Biol. 2005 Jun;83(3):270-85 PMID: 15959555
  47. Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach.
    Genetics. 2010 Oct;186(2):493-503 PMID: 20660644
  48. The genomic complexity of primary human prostate cancer.
    Nature. 2011 Feb 10;470(7333):214-20 PMID: 21307934
  49. Repair of pyrimidine dimer damage induced in yeast by ultraviolet light.
    J Bacteriol. 1972 Mar;109(3):979-86 PMID: 4551759
  50. The sequence of the human genome.
    Science. 2001 Feb 16;291(5507):1304-51 PMID: 11181995
  51. Genetic constraints on protein evolution.
    Crit Rev Biochem Mol Biol. 2007 Sep-Oct;42(5):313-26 PMID: 17917869
  52. Non-B DNA structure-induced genetic instability and evolution.
    Cell Mol Life Sci. 2010 Jan;67(1):43-62 PMID: 19727556
  53. Analysis of genetic inheritance in a family quartet by whole-genome sequencing.
    Science. 2010 Apr 30;328(5978):636-9 PMID: 20220176
  54. Measurements of spontaneous rates of mutations in the recent past and the near future.
    Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1169-76 PMID: 20308091
  55. DNA synthesis errors associated with double-strand-break repair.
    Genetics. 1995 Jul;140(3):965-72 PMID: 7672595
  56. Hotspots of biased nucleotide substitutions in human genes.
    PLoS Biol. 2009 Jan 27;7(1):e26 PMID: 19175294
  57. The transition of closely opposed lesions to double-strand breaks during long-patch base excision repair is prevented by the coordinated action of DNA polymerase delta and Rad27/Fen1.
    Mol Cell Biol. 2009 Mar;29(5):1212-21 PMID: 19075004
  58. Rates of spontaneous mutation.
    Genetics. 1998 Apr;148(4):1667-86 PMID: 9560386
  59. Forces shaping the fastest evolving regions in the human genome.
    PLoS Genet. 2006 Oct 13;2(10):e168 PMID: 17040131
  60. Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells.
    Methods Mol Biol. 2006;314:183-99 PMID: 16673882
  61. Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases.
    Curr Opin Genet Dev. 2004 Apr;14(2):113-9 PMID: 15196456
  62. Two levels of protection for the B cell genome during somatic hypermutation.
    Nature. 2008 Feb 14;451(7180):841-5 PMID: 18273020
  63. The impact of recombination on nucleotide substitutions in the human genome.
    PLoS Genet. 2008 May 09;4(5):e1000071 PMID: 18464896
  64. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing.
    Nucleic Acids Res. 1997 Jul 15;25(14):2745-51 PMID: 9207020
  65. Increased mutagenesis and unique mutation signature associated with mitotic gene conversion.
    Science. 2010 Jul 2;329(5987):82-5 PMID: 20595613
  66. DNA end resection: many nucleases make light work.
    DNA Repair (Amst). 2009 Sep 2;8(9):983-95 PMID: 19473888
  67. Hiding at the ends of yeast chromosomes: telomeres, nucleases and checkpoint pathways.
    J Cell Sci. 2003 Oct 15;116(Pt 20):4057-65 PMID: 12972499
  68. Mutability and importance of a hypermutable cell subpopulation that produces stress-induced mutants in Escherichia coli.
    PLoS Genet. 2008 Oct 03;4(10):e1000208 PMID: 18833303
  69. Hypermutability of damaged single-strand DNA formed at double-strand breaks and uncapped telomeres in yeast Saccharomyces cerevisiae.
    PLoS Genet. 2008 Nov;4(11):e1000264 PMID: 19023402
  70. A time-invariant principle of genome evolution.
    Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13004-9 PMID: 20615949
  71. Perspective: Sign epistasis and genetic constraint on evolutionary trajectories.
    Evolution. 2005 Jun;59(6):1165-74 PMID: 16050094
  72. Recombination in adaptive mutation.
    Science. 1994 Apr 8;264(5156):258-60 PMID: 8146657
  73. The unexpected landscape of in vivo somatic mutation in a human epithelial cell lineage.
    Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1437-42 PMID: 11818556
  74. Sequence space and the ongoing expansion of the protein universe.
    Nature. 2010 Jun 17;465(7300):922-6 PMID: 20485343
  75. Error-prone DNA polymerases: when making a mistake is the only way to get ahead.
    Annu Rev Genet. 2003;37:31-66 PMID: 14616055
  76. Strand-biased spreading of mutations during somatic hypermutation.
    Science. 2007 Aug 31;317(5842):1227-30 PMID: 17761884
  77. Mutation as a stress response and the regulation of evolvability.
    Crit Rev Biochem Mol Biol. 2007 Sep-Oct;42(5):399-435 PMID: 17917874
  78. High mutability of the tumor suppressor genes RASSF1 and RBSP3 (CTDSPL) in cancer.
    PLoS One. 2009 May 29;4(5):e5231 PMID: 19478941
  79. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion.
    Genome Res. 2007 Oct;17(10):1420-30 PMID: 17785536
  80. Human SNP variability and mutation rate are higher in regions of high recombination.
    Trends Genet. 2002 Jul;18(7):337-40 PMID: 12127766
  81. Revealing evolutionary pathways by fitness landscape reconstruction.
    Crit Rev Biochem Mol Biol. 2009 Jul-Aug;44(4):169-74 PMID: 19552615
  82. Pathway correcting DNA replication errors in Saccharomyces cerevisiae.
    EMBO J. 1993 Apr;12(4):1467-73 PMID: 8385605
Article Info
Journal
Cell cycle (Georgetown, Tex.)
Abbr.
Cell Cycle
ISSN
1551-4005
Published
2011-04-01
Epub
2011-00-01
Pages
1073-85
Language
English
Region
United States
NLM ID
101137841
PMCID
PMC3100884
Subset
IM
Grants
NIEHS NIH HHS · P30 ES010126 · United States
NIEHS NIH HHS · RC1 ES018091 · United States
Intramural NIH HHS · Z01 ES065073 · United States
NIEHS NIH HHS · P30ES010126 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com