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PMID: 20139982 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX.

Nature structural & molecular biology ·Vol. 17 ·No. 3 ·2010-03-00 ·Pages 299-305

Szilard RK, Jacques PE, Laramée L, Cheng B, Galicia S, Bataille AR, Yeung M, Mendez M, Bergeron M, Robert F, Durocher D

Abstract

Phosphorylation of histone H2AX is an early response to DNA damage in eukaryotes. In Saccharomyces cerevisiae, DNA damage or replication-fork stalling results in phosphorylation of histone H2A yielding gamma-H2A (yeast gamma-H2AX) in a Mec1 (ATR)- and Tel1 (ATM)-dependent manner. Here, we describe the genome-wide location analysis of gamma-H2A as a strategy to identify loci prone to engaging the Mec1 and Tel1 pathways. Notably, gamma-H2A enrichment overlaps with loci prone to replication-fork stalling and is caused by the action of Mec1 and Tel1, indicating that these loci are prone to breakage. Moreover, about half the sites enriched for gamma-H2A map to repressed protein-coding genes, and histone deacetylases are necessary for formation of gamma-H2A at these loci. Finally, our work indicates that high-resolution mapping of gamma-H2AX is a fruitful route to map fragile sites in eukaryotic genomes.

MeSH Terms
Cell Cycle Cell Cycle Proteins/genetics,physiology Chromatin Immunoprecipitation Genome, Fungal/genetics Histones/genetics Intracellular Signaling Peptides and Proteins/genetics,metabolism Phosphorylation Polymerase Chain Reaction Protein Serine-Threonine Kinases/genetics,metabolism Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism
Chemicals
Cell Cycle Proteins Histones Intracellular Signaling Peptides and Proteins Saccharomyces cerevisiae Proteins MEC1 protein, S cerevisiae Protein Serine-Threonine Kinases TEL1 protein, S cerevisiae
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Szilard Rachel K
[1] Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. [2] These authors contributed equally to this work.
Jacques Pierre-Etienne
Laramée Louise
Cheng Benjamin
Galicia Sarah
Bataille Alain R
Yeung ManTek
Mendez Megan
Bergeron Maxime
Robert François
Durocher Daniel
References (60)
60 references, click to expand
  1. Two checkpoint complexes are independently recruited to sites of DNA damage in vivo.
    Genes Dev. 2001 Nov 1;15(21):2809-21 PMID: 11691833
  2. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters.
    Cell. 1997 May 2;89(3):365-71 PMID: 9150136
  3. Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway.
    Genes Dev. 1998 Sep 15;12(18):2956-70 PMID: 9744871
  4. DNA rearrangements associated with a transposable element in yeast.
    Cell. 1980 Aug;21(1):239-49 PMID: 6250713
  5. Histone acetylation regulates the time of replication origin firing.
    Mol Cell. 2002 Nov;10(5):1223-33 PMID: 12453428
  6. A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage.
    Cell. 1995 Sep 8;82(5):841-7 PMID: 7671311
  7. Concerted deletions and inversions are caused by mitotic recombination between delta sequences in Saccharomyces cerevisiae.
    Mol Cell Biol. 1987 Mar;7(3):1198-207 PMID: 3550432
  8. The DNA replication checkpoint response stabilizes stalled replication forks.
    Nature. 2001 Aug 2;412(6846):557-61 PMID: 11484058
  9. A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions.
    PLoS Genet. 2007 Aug;3(8):e134 PMID: 17696614
  10. The S. cerevisiae Rrm3p DNA helicase moves with the replication fork and affects replication of all yeast chromosomes.
    Genes Dev. 2006 Nov 15;20(22):3104-16 PMID: 17114583
  11. A role for Saccharomyces cerevisiae histone H2A in DNA repair.
    Nature. 2000 Dec 21-28;408(6815):1001-4 PMID: 11140636
  12. A central role for DNA replication forks in checkpoint activation and response.
    Mol Cell. 2003 May;11(5):1323-36 PMID: 12769855
  13. Yeast histone 2A serine 129 is essential for the efficient repair of checkpoint-blind DNA damage.
    EMBO Rep. 2003 Jul;4(7):678-84 PMID: 12792653
  14. An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
    BMC Bioinformatics. 2006 Mar 07;7:113 PMID: 16522208
  15. Interplay between chromatin and trans-acting factors on the IME2 promoter upon induction of the gene at the onset of meiosis.
    Mol Cell Biol. 2007 Feb;27(4):1254-63 PMID: 17158929
  16. Rad52 forms DNA repair and recombination centers during S phase.
    Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8276-82 PMID: 11459964
  17. ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones.
    Science. 2002 Jul 26;297(5581):602-6 PMID: 12142538
  18. OriDB: a DNA replication origin database.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D40-6 PMID: 17065467
  19. The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes.
    Mol Cell. 2003 Dec;12(6):1525-36 PMID: 14690605
  20. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae.
    EMBO J. 1999 Nov 15;18(22):6448-54 PMID: 10562556
  21. Galactose regulation in Saccharomyces cerevisiae. The enzymes encoded by the GAL7, 10, 1 cluster are co-ordinately controlled and separately translated.
    J Mol Biol. 1979 Jun 15;131(1):41-53 PMID: 385888
  22. The Saccharomyces cerevisiae Esc2 and Smc5-6 proteins promote sister chromatid junction-mediated intra-S repair.
    Mol Biol Cell. 2009 Mar;20(6):1671-82 PMID: 19158389
  23. ATR disruption leads to chromosomal fragmentation and early embryonic lethality.
    Genes Dev. 2000 Feb 15;14(4):397-402 PMID: 10691732
  24. DNA replication forks pause at silent origins near the HML locus in budding yeast.
    Mol Cell Biol. 2001 Aug;21(15):4938-48 PMID: 11438651
  25. Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1.
    Mol Cell. 2007 Aug 3;27(3):393-405 PMID: 17679090
  26. Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals.
    J Cell Biol. 2007 Jul 16;178(2):209-18 PMID: 17635934
  27. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  28. Induction of genome instability by DNA damage in Saccharomyces cerevisiae.
    DNA Repair (Amst). 2003 Mar 1;2(3):243-58 PMID: 12547388
  29. DNA replication fork pause sites dependent on transcription.
    Science. 1996 May 17;272(5264):1030-3 PMID: 8638128
  30. Replication forks pause at yeast centromeres.
    Mol Cell Biol. 1992 Sep;12(9):4056-66 PMID: 1508202
  31. Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair.
    Genes Dev. 1994 Mar 15;8(6):652-65 PMID: 7926756
  32. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break.
    Curr Biol. 2004 Oct 5;14(19):1703-11 PMID: 15458641
  33. Histone H2AX is phosphorylated in an ATR-dependent manner in response to replicational stress.
    J Biol Chem. 2001 Dec 21;276(51):47759-62 PMID: 11673449
  34. Genome-wide location and function of DNA binding proteins.
    Science. 2000 Dec 22;290(5500):2306-9 PMID: 11125145
  35. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae.
    Mol Cell. 2009 Jun 26;34(6):722-34 PMID: 19560424
  36. Break-induced replication: a review and an example in budding yeast.
    Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8255-62 PMID: 11459961
  37. Global position and recruitment of HATs and HDACs in the yeast genome.
    Mol Cell. 2004 Oct 22;16(2):199-209 PMID: 15494307
  38. Replisome instability, fork collapse, and gross chromosomal rearrangements arise synergistically from Mec1 kinase and RecQ helicase mutations.
    Genes Dev. 2005 Dec 15;19(24):3055-69 PMID: 16357221
  39. Chromosome fragile sites.
    Annu Rev Genet. 2007;41:169-92 PMID: 17608616
  40. Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae.
    Mol Biol Cell. 2009 Mar;20(6):1683-94 PMID: 19158388
  41. Overexpression of a kinase-inactive ATR protein causes sensitivity to DNA-damaging agents and defects in cell cycle checkpoints.
    EMBO J. 1998 Jan 2;17(1):159-69 PMID: 9427750
  42. Activation of the G2/M-specific gene CLB2 requires multiple cell cycle signals.
    Mol Cell Biol. 2007 Dec;27(23):8364-73 PMID: 17908798
  43. A new mathematical model for relative quantification in real-time RT-PCR.
    Nucleic Acids Res. 2001 May 1;29(9):e45 PMID: 11328886
  44. Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites.
    Cell. 2005 Mar 11;120(5):587-98 PMID: 15766523
  45. Deletions of a tyrosine tRNA gene in S. cerevisiae.
    Cell. 1979 May;17(1):185-90 PMID: 378404
  46. Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways.
    Genes Dev. 1996 Feb 15;10(4):395-406 PMID: 8600024
  47. H2AX: the histone guardian of the genome.
    DNA Repair (Amst). 2004 Aug-Sep;3(8-9):959-67 PMID: 15279782
  48. Histone H2A phosphorylation in DNA double-strand break repair.
    FEBS J. 2005 Jul;272(13):3231-40 PMID: 15978030
  49. Genome-wide replication profiles of S-phase checkpoint mutants reveal fragile sites in yeast.
    EMBO J. 2006 Aug 9;25(15):3627-39 PMID: 16888628
  50. Saccharomyces cerevisiae chromatin-assembly factors that act during DNA replication function in the maintenance of genome stability.
    Proc Natl Acad Sci U S A. 2003 May 27;100(11):6640-5 PMID: 12750463
  51. Saccharomyces Rrm3p, a 5' to 3' DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA.
    Genes Dev. 2002 Jun 1;16(11):1383-96 PMID: 12050116
  52. Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast.
    Genes Dev. 2006 Jan 15;20(2):159-73 PMID: 16384935
  53. Saccharomyces cerevisiae ATM orthologue suppresses break-induced chromosome translocations.
    Nature. 2008 Jul 24;454(7203):543-6 PMID: 18650924
  54. Replication fork barriers: pausing for a break or stalling for time?
    EMBO Rep. 2007 Apr;8(4):346-53 PMID: 17401409
  55. Telomere dysfunction increases mutation rate and genomic instability.
    Cell. 2001 Aug 10;106(3):275-86 PMID: 11509177
  56. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.
    PLoS Biol. 2005 Dec;3(12):e384 PMID: 16248679
  57. Genome-wide map of nucleosome acetylation and methylation in yeast.
    Cell. 2005 Aug 26;122(4):517-27 PMID: 16122420
  58. Saccharomyces cerevisiae Rrm3p DNA helicase promotes genome integrity by preventing replication fork stalling: viability of rrm3 cells requires the intra-S-phase checkpoint and fork restart activities.
    Mol Cell Biol. 2004 Apr;24(8):3198-212 PMID: 15060144
  59. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139.
    J Biol Chem. 1998 Mar 6;273(10):5858-68 PMID: 9488723
  60. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae.
    Mol Cell Biol. 2004 Jun;24(11):4769-80 PMID: 15143171
Article Info
Journal
Nature structural & molecular biology
Abbr.
Nat Struct Mol Biol
ISSN
1545-9985
DOI
10.1038/nsmb.1754
Published
2010-03-00
Epub
2010-00-07
Pages
299-305
Language
English
Region
United States
NLM ID
101186374
PMCID
PMC3081315
Subset
IM
Grants
CIHR · 82891 · Canada
PHS HHS · MOP82891 · United States
Databases
GEO
GSE18191
External Links
PubMed source DOI: 10.1038/nsmb.1754 PMC Full Text View journal details
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