Ku Regulates the Non-Homologous End Joining Pathway Choice of DNA Double-Strand Break Repair in Human Somatic Cells
The repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic integrity and viability for all organisms. Mammals have evolved at least two genetically discrete ways to mediate DNA DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). In mammalian cells, most DSBs are preferentially repaired by NHEJ. Recent work has demonstrated that NHEJ consists of at least two sub-pathways—the main Ku heterodimer-dependent or “classic” NHEJ (C-NHEJ) pathway and an “alternative” NHEJ (A-NHEJ) pathway, which usually generates microhomology-mediated signatures at repair junctions. In our study, recombinant adeno-associated virus knockout vectors were utilized to construct a series of isogenic human somatic cell lines deficient in the core C-NHEJ factors (Ku, DNA-PKcs, XLF, and LIGIV), and the resulting cell lines were characterized for their ability to carry out DNA DSB repair. The absence of DNA-PKcs, XLF, or LIGIV resulted in cell lines that were profoundly impaired in DNA DSB repair activity. Unexpectedly, Ku86-null cells showed wild-type levels of DNA DSB repair activity that was dominated by microhomology joining events indicative of A-NHEJ. Importantly, A-NHEJ DNA DSB repair activity could also be efficiently de-repressed in LIGIV-null and DNA-PKcs-null cells by subsequently reducing the level of Ku70. These studies demonstrate that in human cells C-NHEJ is the major DNA DSB repair pathway and they show that Ku is the critical C-NHEJ factor that regulates DNA NHEJ DSB pathway choice.
Vyšlo v časopise:
Ku Regulates the Non-Homologous End Joining Pathway Choice of DNA Double-Strand Break Repair in Human Somatic Cells. PLoS Genet 6(2): e32767. doi:10.1371/journal.pgen.1000855
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1000855
Souhrn
The repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic integrity and viability for all organisms. Mammals have evolved at least two genetically discrete ways to mediate DNA DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). In mammalian cells, most DSBs are preferentially repaired by NHEJ. Recent work has demonstrated that NHEJ consists of at least two sub-pathways—the main Ku heterodimer-dependent or “classic” NHEJ (C-NHEJ) pathway and an “alternative” NHEJ (A-NHEJ) pathway, which usually generates microhomology-mediated signatures at repair junctions. In our study, recombinant adeno-associated virus knockout vectors were utilized to construct a series of isogenic human somatic cell lines deficient in the core C-NHEJ factors (Ku, DNA-PKcs, XLF, and LIGIV), and the resulting cell lines were characterized for their ability to carry out DNA DSB repair. The absence of DNA-PKcs, XLF, or LIGIV resulted in cell lines that were profoundly impaired in DNA DSB repair activity. Unexpectedly, Ku86-null cells showed wild-type levels of DNA DSB repair activity that was dominated by microhomology joining events indicative of A-NHEJ. Importantly, A-NHEJ DNA DSB repair activity could also be efficiently de-repressed in LIGIV-null and DNA-PKcs-null cells by subsequently reducing the level of Ku70. These studies demonstrate that in human cells C-NHEJ is the major DNA DSB repair pathway and they show that Ku is the critical C-NHEJ factor that regulates DNA NHEJ DSB pathway choice.
Zdroje
1. HakemR
2008 DNA-damage repair; the good, the bad, and the ugly. EMBO J 27 589 605
2. CahillD
ConnorB
CarneyJP
2006 Mechanisms of eukaryotic DNA double strand break repair. Front Biosci 11 1958 1976
3. LiX
HeyerWD
2008 Homologous recombination in DNA repair and DNA damage tolerance. Cell Res 18 99 113
4. McVeyM
LeeSE
2008 MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends Genet 24 529 538
5. WangH
PerraultAR
TakedaY
QinW
IliakisG
2003 Biochemical evidence for Ku-independent backup pathways of NHEJ. Nucleic Acids Res 31 5377 5388
6. NussenzweigA
NussenzweigMC
2007 A backup DNA repair pathway moves to the forefront. Cell 131 223 225
7. BoultonSJ
JacksonSP
1996 Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res 24 4639 4648
8. MaJL
KimEM
HaberJE
LeeSE
2003 Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol Cell Biol 23 8820 8828
9. HaberJE
2008 Alternative endings. Proc Natl Acad Sci U S A 105 405 406
10. LieberMR
LuH
GuJ
SchwarzK
2008 Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non-homologous DNA end joining: relevance to cancer, aging, and the immune system. Cell Res 18 125 133
11. HendricksonEA
HuffmanJL
TainerJA
2006 Structural aspects of Ku and the DNA-dependent protein kinase complex.
SeideW
KowYW
DoetschPW
DNA Damage Recognition New York, NY Taylor & Francis Group, LLC 629 684
12. MeekK
DangV
Lees-MillerSP
2008 DNA-PK: the means to justify the ends? Adv Immunol 99 33 58
13. ManolisKG
NimmoER
HartsuikerE
CarrAM
JeggoPA
2001 Novel functional requirements for non-homologous DNA end joining in Schizosaccharomyces pombe. EMBO J 20 210 221
14. GottlichB
ReichenbergerS
FeldmannE
PfeifferP
1998 Rejoining of DNA double-strand breaks in vitro by single-strand annealing. Eur J Biochem 258 387 395
15. KabotyanskiEB
GomelskyL
HanJO
StamatoTD
RothDB
1998 Double-strand break repair in Ku86- and XRCC4-deficient cells. Nucl Acids Res 26 5333 5342
16. FeldmannE
SchmiemannV
GoedeckeW
ReichenbergerS
PfeifferP
2000 DNA double-strand break repair in cell-free extracts from Ku80-deficient cells: implications for Ku serving as an alignment factor in non-homologous DNA end joining. Nucl Acids Res 28 2585 2596
17. Guirouilh-BarbatJ
HuckS
BertrandP
PirzioL
DesmazeC
2004 Impact of the Ku80 pathway on NHEJ-induced genome rearrangements in mammalian cells. Mol Cell 14 611 623
18. Guirouilh-BarbatJ
RassE
PloI
BertrandP
LopezBS
2007 Defects in XRCC4 and Ku80 differentially affect the joining of distal nonhomologous ends. Proc Natl Acad Sci U S A 104 20902 20907
19. BennardoN
ChengA
HuangN
StarkJM
2008 Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair. PLoS Genet 4 e1000110 doi:10.1371/journal.pgen.1000110
20. MansourWY
SchumacherS
RosskopfR
RheinT
Schmidt-PetersenF
2008 Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks. Nucleic Acids Res 36 4088 4098
21. Schulte-UentropL
El-AwadyRA
SchlieckerL
WillersH
Dahm-DaphiJ
2008 Distinct roles of XRCC4 and Ku80 in non-homologous end-joining of endonuclease- and ionizing radiation-induced DNA double-strand breaks. Nucleic Acids Res 36 2561 2569
22. WuW
WangM
WuW
SinghSK
MussfeldtT
2008 Repair of radiation induced DNA double strand breaks by backup NHEJ is enhanced in G2. DNA Repair (Amst) 7 329 338
23. BentleyJ
DiggleCP
HarndenP
KnowlesMA
KiltieAE
2004 DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining. Nucleic Acids Res 32 5249 5259
24. Soulas-SprauelP
Le GuyaderG
Rivera-MunozP
AbramowskiV
Olivier-MartinC
2007 Role for DNA repair factor XRCC4 in immunoglobulin class switch recombination. J Exp Med 204 1717 1727
25. YanCT
BoboilaC
SouzaEK
FrancoS
HickernellTR
2007 IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 449 478 482
26. VerkaikNS
Esveldt-van LangeRE
van HeemstD
BruggenwirthHT
HoeijmakersJH
2002 Different types of V(D)J recombination and end-joining defects in DNA double-strand break repair mutant mammalian cells. Eur J Immunol 32 701 709
27. CorneoB
WendlandRL
DerianoL
CuiX
KleinIA
2007 Rag mutations reveal robust alternative end joining. Nature 449 483 486
28. FergusonDO
SekiguchiJM
ChangS
FrankKM
GaoY
2000 The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. Proc Natl Acad Sci U S A 97 6630 6633
29. DifilippantonioMJ
ZhuJ
ChenHT
MeffreE
NussenzweigMC
2000 DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation. Nature 404 510 514
30. WeinstockDM
BrunetE
JasinM
2007 Formation of NHEJ-derived reciprocal chromosomal translocations does not require Ku70. Nat Cell Biol 9 978 981
31. MorrisT
ThackerJ
1993 Formation of large deletions by illegitimate recombination in the HPRT gene of primary human fibroblasts. Proc Natl Acad Sci U S A 90 1392 1396
32. NohmiT
SuzukiM
MasumuraK
YamadaM
MatsuiK
1999 Spi(−) selection: An efficient method to detect gamma-ray-induced deletions in transgenic mice. Environ Mol Mutagen 34 9 15
33. CanningS
DryjaTP
1989 Short, direct repeats at the breakpoints of deletions of the retinoblastoma gene. Proc Natl Acad Sci U S A 86 5044 5048
34. SmanikPA
FurmingerTL
MazzaferriEL
JhiangSM
1995 Breakpoint characterization of the ret/PTC oncogene in human papillary thyroid carcinoma. Hum Mol Genet 4 2313 2318
35. AudebertM
SallesB
CalsouP
2004 Involvement of poly(ADP-ribose) polymerase-1 and XRCC1/DNA ligase III in an alternative route for DNA double-strand breaks rejoining. J Biol Chem 279 55117 55126
36. LiangL
DengL
ChenY
LiGC
ShaoC
2005 Modulation of DNA end joining by nuclear proteins. J Biol Chem 280 31442 31449
37. WangM
WuW
WuW
RosidiB
ZhangL
2006 PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res 34 6170 6182
38. ZhaS
BoboilaC
AltFW
2009 Mre11: roles in DNA repair beyond homologous recombination. Nat Struct Mol Biol 16 798 800
39. ShrivastavM
De HaroLP
NickoloffJA
2008 Regulation of DNA double-strand break repair pathway choice. Cell Res 18 134 147
40. LiG
NelsenC
HendricksonEA
2002 Ku86 is essential in human somatic cells. Proc Natl Acad Sci U S A 99 832 837
41. MyungK
GhoshG
FattahFJ
LiG
KimH
2004 Regulation of telomere length and suppression of genomic instability in human somatic cells by Ku86. Mol Cell Biol 24 5050 5059
42. FattahFJ
LichterNF
FattahKR
OhS
HendricksonEA
2008 Ku70, an essential gene, modulates the frequency of rAAV-mediated gene targeting in human somatic cells. Proc Natl Acad Sci U S A 105 8703 8708
43. IndiviglioSM
BertuchAA
2009 Ku's essential role in keeping telomeres intact. Proc Natl Acad Sci U S A 106 12217 12218
44. WangY
GhoshG
HendricksonEA
2009 Ku86 represses lethal telomere deletion events in human somatic cells. Proc Natl Acad Sci U S A 106 12430 12435
45. KohliM
RagoC
LengauerC
KinzlerKW
VogelsteinB
2004 Facile methods for generating human somatic cell gene knockouts using recombinant adeno-associated viruses. Nucl Acids Res 32 e3
46. RagoC
VogelsteinB
BunzF
2007 Genetic knockouts and knockins in human somatic cells. Nat Protoc 2 2734 2746
47. HendricksonEA
2008 Gene targeting in human somatic cells.
ConnPM
Source Book of Models for Biomedical Research Totowa, NJ Humana Press, Inc 509 525
48. SeluanovA
MittelmanD
Pereira-SmithOM
WilsonJH
GorbunovaV
2004 DNA end joining becomes less efficient and more error-prone during cellular senescence. Proc Natl Acad Sci U S A 101 7624 7629
49. BerdougoE
TerretME
JallepalliPV
2009 Functional dissection of mitotic regulators through gene targeting in human somatic cells. Methods Mol Biol 545 21 37
50. FattahKR
RuisBL
HendricksonEA
2008 Mutations to Ku reveal differences in human somatic cell lines. DNA Repair (Amst) 7 762 774
51. RuisBL
FattahKR
HendricksonEA
2008 The catalytic subunit of DNA-dependent protein kinase regulates proliferation, telomere length, and genomic stability in human somatic cells. Mol Cell Biol 28 6182 6195
52. BennettSE
UmarA
OshimaJ
MonnatRJJr
KunkelTA
1997 Mismatch repair in extracts of Werner syndrome cell lines. Cancer Res 57 2956 2960
53. LengauerC
KinzlerKW
VogelsteinB
1997 DNA methylation and genetic instability in colorectal cancer cells. Proc Natl Acad Sci U S A 94 2545 2550
54. ElliottB
JasinM
2001 Repair of double-strand breaks by homologous recombination in mismatch repair-defective mammalian cells. Mol Cell Biol 21 2671 2682
55. BannisterLA
WaldmanBC
WaldmanAS
2004 Modulation of error-prone double-strand break repair in mammalian chromosomes by DNA mismatch repair protein Mlh1. DNA Repair (Amst) 3 465 474
56. ZhangY
RohdeLH
WuH
2009 Involvement of nucleotide excision and mismatch repair mechanisms in double strand break repair. Curr Genomics 10 250 258
57. FurutaT
TakemuraH
LiaoZY
AuneGJ
RedonC
2003 Phosphorylation of histone H2AX and activation of Mre11, Rad50, and Nbs1 in response to replication-dependent DNA double-strand breaks induced by mammalian DNA topoisomerase I cleavage complexes. J Biol Chem 278 20303 20312
58. MiquelC
JacobS
GrandjouanS
AimeA
ViguierJ
2007 Frequent alteration of DNA damage signalling and repair pathways in human colorectal cancers with microsatellite instability. Oncogene 26 5919 5926
59. DinkelmannM
SpehalskiE
StonehamT
BuisJ
WuY
2009 Multiple functions of MRN in end-joining pathways during isotype class switching. Nat Struct Mol Biol 16 808 813
60. RassE
GrabarzA
PloI
GautierJ
BertrandP
2009 Role of Mre11 in chromosomal nonhomologous end joining in mammalian cells. Nat Struct Mol Biol 16 819 824
61. XieA
KwokA
ScullyR
2009 Role of mammalian Mre11 in classical and alternative nonhomologous end joining. Nat Struct Mol Biol 16 814 818
62. KohKH
KangHJ
LiLS
KimNG
YouKT
2005 Impaired nonhomologous end-joining in mismatch repair-deficient colon carcinomas. Lab Invest 85 1130 1138
63. ChenX
BallinJD
Della-MariaJ
TsaiMS
WhiteEJ
2009 Distinct kinetics of human DNA ligases I, IIIα, IIIβ, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair. DNA Repair (Amst) 8 961 968
64. StarkJM
PierceAJ
OhJ
PastinkA
JasinM
2004 Genetic steps of mammalian homologous repair with distinct mutagenic consequences. Mol Cell Biol 24 9305 9316
65. AdachiN
IshinoT
IshiiY
TakedaS
KoyamaH
2001 DNA ligase IV-deficient cells are more resistant to ionizing radiation in the absence of Ku70: Implications for DNA double-strand break repair. Proc Natl Acad Sci U S A 98 12109 12113
66. KaranjawalaZE
AdachiN
IrvineRA
OhEK
ShibataD
2002 The embryonic lethality in DNA ligase IV-deficient mice is rescued by deletion of Ku: implications for unifying the heterogeneous phenotypes of NHEJ mutants. DNA Repair (Amst) 1 1017 1026
67. LouZ
ChenBP
AsaithambyA
Minter-DykhouseK
ChenDJ
2004 MDC1 regulates DNA-PK autophosphorylation in response to DNA damage. J Biol Chem 279 46359 46362
68. ErramiA
SmiderV
RathmellWK
HeDM
HendricksonEA
1996 Ku86 defines the genetic defect and restores X-ray resistance and V(D)J recombination to complementation group 5 hamster cell mutants. Mol Cell Biol 16 1519 1526
69. LeeSE
PulaskiCR
HeDM
BenjaminDM
VossM
1995 Isolation of mammalian cell mutants that are X-ray sensitive, impaired in DNA double-strand break repair and defective for V(D)J recombination. Mutat Res 336 279 291
70. HeDM
LeeSE
HendricksonEA
1996 Restoration of X-ray and etoposide resistance, Ku-end binding activity and V(D) J recombination to the Chinese hamster sxi-3 mutant by a hamster Ku86 cDNA. Mutat Res 363 43 56
71. PierceAJ
HuP
HanM
EllisN
JasinM
2001 Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells. Genes Dev 15 3237 3242
72. MarvinME
BeckerMM
NoelP
HardyS
BertuchAA
2009 The association of yKu with subtelomeric core X sequences prevents recombination involving telomeric sequences. Genetics 183 453 467, 451SI–413SI
73. RuscettiT
LehnertBE
HalbrookJ
Le TrongH
HoekstraMF
1998 Stimulation of the DNA-dependent protein kinase by poly(ADP-ribose) polymerase. J Biol Chem 273 14461 14467
74. AriumiY
MasutaniM
CopelandTD
MimoriT
SugimuraT
1999 Suppression of the poly(ADP-ribose) polymerase activity by DNA-dependent protein kinase in vitro. Oncogene 18 4616 4625
75. GalandeS
Kohwi-ShigematsuT
1999 Poly(ADP-ribose) polymerase and Ku autoantigen form a complex and synergistically bind to matrix attachment sequences. J Biol Chem 274 20521 20528
76. PleschkeJM
KleczkowskaHE
StrohmM
AlthausFR
2000 Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins. J Biol Chem 275 40974 40980
77. SartoriusCA
TakimotoGS
RicherJK
TungL
HorwitzKB
2000 Association of the Ku autoantigen/DNA-dependent protein kinase holoenzyme and poly(ADP-ribose) polymerase with the DNA binding domain of progesterone receptors. J Mol Endocrinol 24 165 182
78. Van DyckE
StasiakAZ
StasiakA
WestSC
1999 Binding of double-strand breaks in DNA by human Rad52 protein. Nature 398 728 731
79. FinnieNJ
GottliebTM
BluntT
JeggoPA
JacksonSP
1995 DNA-dependent protein kinase activity is absent in xrs-6 cells: implications for site-specific recombination and DNA double-strand break repair. Proc Natl Acad Sci U S A 92 320 324
80. DeChiaraTM
2001 Gene targeting in ES cells. Methods Mol Biol 158 19 45
81. KonishiH
LauringJ
GarayJP
KarakasB
AbukhdeirAM
2007 A PCR-based high-throughput screen with multiround sample pooling: application to somatic cell gene targeting. Nat Protoc 2 2865 2874
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