DNA double strand break repair via non-homologous end-joining.

DNA double-stranded breaks (DSB) are among the most dangerous forms of DNA damage. Unrepaired DSBs results in cells undergoing apoptosis or senescence whereas mis-processing of DSBs can lead to genomic instability and carcinogenesis. One important pathway in eukaryotic cells responsible for the repair of DSBs is non-homologous end-joining (NHEJ). In this review we will discuss the interesting new insights into the mechanism of the NHEJ pathway and the proteins which mediate this repair process. Furthermore, the general role of NHEJ in promoting genomic stability will be discussed.

[1]  Yunmei Ma,et al.  The DNA-dependent Protein Kinase Catalytic Subunit Phosphorylation Sites in Human Artemis* , 2005, Journal of Biological Chemistry.

[2]  David J. Chen,et al.  Solution structure of the C-terminal domain of Ku80 suggests important sites for protein-protein interactions. , 2004, Structure.

[3]  A. Fischer,et al.  Partial T and B lymphocyte immunodeficiency and predisposition to lymphoma in patients with hypomorphic mutations in Artemis. , 2003, The Journal of clinical investigation.

[4]  D. Ramsden,et al.  Ku complex interacts with and stimulates the Werner protein. , 2000, Genes & development.

[5]  D. V. van Gent,et al.  The mechanism of non-homologous end-joining: a synopsis of synapsis. , 2004, DNA repair.

[6]  D. Ramsden,et al.  Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus. , 2002, Nucleic acids research.

[7]  B. Chait,et al.  Ku80 removal from DNA through double strand break–induced ubiquitylation , 2008, The Journal of cell biology.

[8]  J. Tainer,et al.  XLF regulates filament architecture of the XRCC4·ligase IV complex. , 2010, Structure.

[9]  L. Postow,et al.  An SCF complex containing Fbxl12 mediates DNA damage-induced Ku80 ubiquitylation , 2013, Cell cycle.

[10]  J. Wang,et al.  DNA looping by Ku and the DNA-dependent protein kinase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Lees-Miller,et al.  Autophosphorylation of DNA-Dependent Protein Kinase Regulates DNA End Processing and May Also Alter Double-Strand Break Repair Pathway Choice , 2005, Molecular and Cellular Biology.

[12]  David J. Chen,et al.  Persistently bound Ku at DNA ends attenuates DNA end resection and homologous recombination. , 2012, DNA repair.

[13]  R. Guérois,et al.  Delineation of the Xrcc4-interacting Region in the Globular Head Domain of Cernunnos/XLF* , 2010, The Journal of Biological Chemistry.

[14]  J. Walker,et al.  Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair , 2001, Nature.

[15]  David J. Chen,et al.  Defining interactions between DNA-PK and ligase IV/XRCC4. , 2002, DNA repair.

[16]  K. Caldecott,et al.  APLF (C2orf13) Is a Novel Human Protein Involved in the Cellular Response to Chromosomal DNA Strand Breaks , 2007, Molecular and Cellular Biology.

[17]  P. Jeggo,et al.  The C-terminal conserved domain of DNA-PKcs, missing in the SCID mouse, is required for kinase activity. , 2000, Nucleic acids research.

[18]  Burkhard Jakob,et al.  Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks , 2007, The Journal of cell biology.

[19]  Qi Ding,et al.  The DNA-Dependent Protein Kinase Catalytic Subunit Is Phosphorylated In Vivo on Threonine 3950, a Highly Conserved Amino Acid in the Protein Kinase Domain , 2006, Molecular and Cellular Biology.

[20]  P. Jeggo,et al.  Identification of a defect in DNA ligase IV in a radiosensitive leukaemia patient , 1999, Current Biology.

[21]  S. Lees-Miller,et al.  N-terminal constraint activates the catalytic subunit of the DNA-dependent protein kinase in the absence of DNA or Ku , 2011, Nucleic acids research.

[22]  S. West,et al.  The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates , 2006, Nature.

[23]  Jeroen A. A. Demmers,et al.  Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4 , 2006, Proceedings of the National Academy of Sciences.

[24]  K. Meek,et al.  The leucine rich region of DNA-PKcs contributes to its innate DNA affinity , 2005, Nucleic acids research.

[25]  D. Durocher,et al.  The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase. , 2005, Molecular cell.

[26]  Anthony W. Parker,et al.  The dynamics of Ku70/80 and DNA-PKcs at DSBs induced by ionizing radiation is dependent on the complexity of damage , 2012, Nucleic acids research.

[27]  M. Lieber,et al.  XRCC4:DNA ligase IV can ligate incompatible DNA ends and can ligate across gaps , 2007, The EMBO journal.

[28]  L. Povirk,et al.  Processing of 3′-Phosphoglycolate-terminated DNA Double Strand Breaks by Artemis Nuclease* , 2006, Journal of Biological Chemistry.

[29]  F. Alt,et al.  A Critical Role for DNA End-Joining Proteins in Both Lymphogenesis and Neurogenesis , 1998, Cell.

[30]  S. Jackson,et al.  The DNA-dependent protein kinase: Requirement for DNA ends and association with Ku antigen , 1993, Cell.

[31]  P. Wu,et al.  Structural and Functional Interaction between the Human DNA Repair Proteins DNA Ligase IV and XRCC4 , 2009, Molecular and Cellular Biology.

[32]  Gaudenz Danuser,et al.  Positional stability of single double-strand breaks in mammalian cells , 2007, Nature Cell Biology.

[33]  B. Chen,et al.  Role of DNA-dependent protein kinase catalytic subunit in cancer development and treatment. , 2012, Translational cancer research.

[34]  M. Lieber,et al.  The Mechanism of Human Nonhomologous DNA End Joining* , 2008, Journal of Biological Chemistry.

[35]  David J. Chen,et al.  The N-terminal Region of the DNA-dependent Protein Kinase Catalytic Subunit Is Required for Its DNA Double-stranded Break-mediated Activation* , 2013, The Journal of Biological Chemistry.

[36]  E. Makarov,et al.  A novel splice variant of the DNA-PKcs gene is associated with clinical and cellular radiosensitivity in a patient with xeroderma pigmentosum , 2009, Journal of Medical Genetics.

[37]  S. Lees-Miller,et al.  Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining. , 2009, The Biochemical journal.

[38]  David J. Chen,et al.  Functional significance of the interaction with Ku in DNA double‐strand break recognition of XLF , 2011, FEBS letters.

[39]  K. Khanna,et al.  DNA double-strand breaks: signaling, repair and the cancer connection , 2001, Nature Genetics.

[40]  Stephen P. Jackson,et al.  Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage , 2005, Nature.

[41]  S. Nakajima,et al.  A novel human AP endonuclease with conserved zinc‐finger‐like motifs involved in DNA strand break responses , 2007, The EMBO journal.

[42]  F. Alt,et al.  The nonhomologous end-joining pathway of DNA repair is required for genomic stability and the suppression of translocations. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Christopher J Bakkenist,et al.  Initiating Cellular Stress Responses , 2004, Cell.

[44]  Thomas Ried,et al.  DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation , 2000, Nature.

[45]  Yunmei Ma,et al.  Hairpin Opening and Overhang Processing by an Artemis/DNA-Dependent Protein Kinase Complex in Nonhomologous End Joining and V(D)J Recombination , 2002, Cell.

[46]  David J. Chen,et al.  A DNA-PKcs mutation in a radiosensitive T-B- SCID patient inhibits Artemis activation and nonhomologous end-joining. , 2008, The Journal of clinical investigation.

[47]  David J. Chen,et al.  Ataxia Telangiectasia Mutated (ATM) Is Essential for DNA-PKcs Phosphorylations at the Thr-2609 Cluster upon DNA Double Strand Break* , 2007, Journal of Biological Chemistry.

[48]  D. Ramsden,et al.  Ku Recruits the XRCC4-Ligase IV Complex to DNA Ends , 2000, Molecular and Cellular Biology.

[49]  O. Hammarsten,et al.  DNA-dependent protein kinase: DNA binding and activation in the absence of Ku. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Y Taya,et al.  Enhanced phosphorylation of p53 by ATM in response to DNA damage. , 1998, Science.

[51]  F Chen,et al.  The three-dimensional structure of the C-terminal DNA-binding domain of human Ku70. , 2001, The Journal of biological chemistry.

[52]  A. Nussenzweig,et al.  Hypersensitivity of Ku80-deficient cell lines and mice to DNA damage: the effects of ionizing radiation on growth, survival, and development. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[53]  U. Pannicke,et al.  Length-dependent Binding of Human XLF to DNA and Stimulation of XRCC4·DNA Ligase IV Activity* , 2007, Journal of Biological Chemistry.

[54]  H. Akiyama,et al.  Molecular mechanism of protein assembly on DNA double-strand breaks in the non-homologous end-joining pathway. , 2009, Journal of radiation research.

[55]  R. Ghirlando,et al.  Crystal structure of the Xrcc4 DNA repair protein and implications for end joining , 2000, The EMBO journal.

[56]  B. Reina-San-Martin,et al.  PARP-3 and APLF function together to accelerate nonhomologous end-joining. , 2011, Molecular cell.

[57]  David J. Chen,et al.  Cell Cycle Dependence of DNA-dependent Protein Kinase Phosphorylation in Response to DNA Double Strand Breaks* , 2005, Journal of Biological Chemistry.

[58]  D. Durocher,et al.  APLF (C2orf13) facilitates nonhomologous end-joining and undergoes ATM-dependent hyperphosphorylation following ionizing radiation. , 2008, DNA repair.

[59]  B. L. Sibanda,et al.  Crystal Structure of DNA-PKcs Reveals a Large Open-Ring Cradle Comprised of HEAT Repeats , 2009, Nature.

[60]  Robert T Abraham,et al.  PI 3-kinase related kinases: 'big' players in stress-induced signaling pathways. , 2004, DNA repair.

[61]  J. Little,et al.  Some unsolved problems and unresolved issues in radiation cytogenetics: a review and new data on roles of homologous recombination and non-homologous end joining. , 2010, Mutation research.

[62]  Z. Zeng,et al.  APLF promotes the assembly and activity of non‐homologous end joining protein complexes , 2012, The EMBO journal.

[63]  N. Kleckner,et al.  The ATRs, ATMs, and TORs Are Giant HEAT Repeat Proteins , 2003, Cell.

[64]  S. Lees-Miller,et al.  The DNA-dependent protein kinase interacts with DNA to form a protein-DNA complex that is disrupted by phosphorylation. , 2002, Biochemistry.

[65]  Laurence H Pearl,et al.  Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair. , 2006, Molecular cell.

[66]  S. Schreiber,et al.  FKBP12-Rapamycin-associated Protein (FRAP) Autophosphorylates at Serine 2481 under Translationally Repressive Conditions* , 2000, The Journal of Biological Chemistry.

[67]  C. Brenner,et al.  The ataxia-oculomotor apraxia 1 gene product has a role distinct from ATM and interacts with the DNA strand break repair proteins XRCC1 and XRCC4. , 2004, DNA repair.

[68]  David J. Chen,et al.  Live cell imaging of XLF and XRCC4 reveals a novel view of protein assembly in the non-homologous end-joining pathway , 2008, Cell cycle.

[69]  David J. Chen,et al.  The endless tale of non-homologous end-joining , 2008, Cell Research.

[70]  David J. Chen,et al.  Role of non-homologous end joining (NHEJ) in maintaining genomic integrity. , 2006, DNA repair.

[71]  F. Alt,et al.  Leaky Scid phenotype associated with defective V(D)J coding end processing in Artemis-deficient mice. , 2002, Molecular cell.

[72]  E. Koonin,et al.  SAP - a putative DNA-binding motif involved in chromosomal organization. , 2000, Trends in biochemical sciences.

[73]  J. Cerhan,et al.  Mutational analysis of thirty-two double-strand DNA break repair genes in breast and pancreatic cancers. , 2008, Cancer research.

[74]  P. Cortés,et al.  Role of non-homologous end joining in V(D)J recombination , 2012, Immunologic Research.

[75]  K. Mahajan,et al.  Association of terminal deoxynucleotidyl transferase with Ku. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[76]  L. Pearl,et al.  Structural model of full‐length human Ku70–Ku80 heterodimer and its recognition of DNA and DNA‐PKcs , 2007, EMBO reports.

[77]  A. Griffith,et al.  Binding of Ku protein to DNA. Measurement of affinity for ends and demonstration of binding to nicks. , 1993, The Journal of biological chemistry.

[78]  M. Lieber,et al.  The nonhomologous DNA end joining pathway is important for chromosome stability in primary fibroblasts , 1999, Current Biology.

[79]  F. Alt,et al.  Interplay of p53 and DNA-repair protein XRCC4 in tumorigenesis, genomic stability and development , 2000, Nature.

[80]  D. Weinstock,et al.  Formation of NHEJ-derived reciprocal chromosomal translocations does not require Ku70 , 2007, Nature Cell Biology.

[81]  David J. Chen,et al.  Congenital bone marrow failure in DNA-PKcs mutant mice associated with deficiencies in DNA repair , 2011, The Journal of cell biology.

[82]  S. Jackson,et al.  Mapping of protein-protein interactions within the DNA-dependent protein kinase complex. , 1999, Nucleic acids research.

[83]  John A. Tainer,et al.  XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair , 2011, The Journal of Biological Chemistry.

[84]  S. Brunak,et al.  Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis , 2010, Science Signaling.

[85]  D. Ramsden,et al.  Ku is a 5'dRP/AP lyase that excises nucleotide damage near broken ends , 2010, Nature.

[86]  S. Jackson,et al.  XLF Interacts with the XRCC4-DNA Ligase IV Complex to Promote DNA Nonhomologous End-Joining , 2006, Cell.

[87]  P. Jeggo,et al.  Interaction of the Ku heterodimer with the DNA ligase IV/Xrcc4 complex and its regulation by DNA-PK. , 2007, DNA repair.

[88]  B. Chen,et al.  ATR-Dependent Phosphorylation of DNA-Dependent Protein Kinase Catalytic Subunit in Response to UV-Induced Replication Stress , 2006, Molecular and Cellular Biology.

[89]  D. Durocher,et al.  Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV , 2004, The EMBO journal.

[90]  Stephen P. Jackson,et al.  A means to a DNA end: the many roles of Ku , 2004, Nature Reviews Molecular Cell Biology.

[91]  Martin Pelikan,et al.  Ku and DNA-dependent Protein Kinase Dynamic Conformations and Assembly Regulate DNA Binding and the Initial Non-homologous End Joining Complex* , 2009, The Journal of Biological Chemistry.

[92]  Xiaofeng Jiang,et al.  A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[93]  T. Halazonetis,et al.  Emerging common themes in regulation of PIKKs and PI3Ks , 2009, The EMBO journal.

[94]  B. L. Sibanda,et al.  Crystal structure of an Xrcc4–DNA ligase IV complex , 2001, Nature Structural Biology.

[95]  Y. Hosoi,et al.  The association of DNA-dependent protein kinase activity with chromosomal instability and risk of cancer. , 2006, Carcinogenesis.

[96]  Laurence H Pearl,et al.  Three-dimensional structure and regulation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). , 2005, Structure.

[97]  Takashi Kohno,et al.  Polynucleotide Kinase and Aprataxin-like Forkhead-associated Protein (PALF) Acts as Both a Single-stranded DNA Endonuclease and a Single-Stranded DNA 3′ Exonuclease and Can Participate in DNA End Joining in a Biochemical System* , 2011, The Journal of Biological Chemistry.

[98]  Timothy Woods,et al.  Autophosphorylation of the Catalytic Subunit of the DNA-Dependent Protein Kinase Is Required for Efficient End Processing during DNA Double-Strand Break Repair , 2003, Molecular and Cellular Biology.

[99]  T. Kunkel,et al.  A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. , 2005, Molecular cell.

[100]  F. Alt,et al.  Growth retardation and leaky SCID phenotype of Ku70-deficient mice. , 1997, Immunity.

[101]  D. Ramsden,et al.  Dual Modes of Interaction between XRCC4 and Polynucleotide Kinase/Phosphatase , 2010, The Journal of Biological Chemistry.

[102]  P. Jeggo,et al.  The C Terminus of Ku80 Activates the DNA-Dependent Protein Kinase Catalytic Subunit , 1999, Molecular and Cellular Biology.

[103]  Junjie Chen,et al.  The E3 ligase RNF8 regulates KU80 removal and NHEJ repair , 2012, Nature Structural &Molecular Biology.

[104]  C. Wyman,et al.  A human XRCC4–XLF complex bridges DNA , 2012, Nucleic acids research.

[105]  D. Ramsden,et al.  Werner protein cooperates with the XRCC4-DNA ligase IV complex in end-processing. , 2008, Biochemistry.

[106]  G. Chu,et al.  Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends , 2007, Proceedings of the National Academy of Sciences.

[107]  M. Lieber,et al.  Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells , 1997, Nature.

[108]  Shengfang Jin,et al.  Binding of Ku and c-Abl at the Kinase Homology Region of DNA-dependent Protein Kinase Catalytic Subunit* , 1997, The Journal of Biological Chemistry.

[109]  P. Jeggo,et al.  Genetic variants of NHEJ DNA ligase IV can affect the risk of developing multiple myeloma, a tumour characterised by aberrant class switch recombination , 2002, Journal of medical genetics.

[110]  M. Connelly,et al.  DNA-dependent protein kinase catalytic subunit: A relative of phosphatidylinositol 3-kinase and the ataxia telangiectasia gene product , 1995, Cell.

[111]  F. Alt,et al.  DNA ligase IV deficiency in mice leads to defective neurogenesis and embryonic lethality via the p53 pathway. , 2000, Molecular cell.

[112]  David J. Chen,et al.  Requirement for the Kinase Activity of Human DNA-Dependent Protein Kinase Catalytic Subunit in DNA Strand Break Rejoining , 1999, Molecular and Cellular Biology.

[113]  Phoebe L Stewart,et al.  Cryo-EM structure of the DNA-dependent protein kinase catalytic subunit at subnanometer resolution reveals alpha helices and insight into DNA binding. , 2008, Structure.

[114]  W. Dynan,et al.  Geometry of a complex formed by double strand break repair proteins at a single DNA end: recruitment of DNA-PKcs induces inward translocation of Ku protein. , 1999, Nucleic acids research.

[115]  David J. Chen,et al.  WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing , 2006, Nature Structural &Molecular Biology.

[116]  D. Barnes,et al.  Targeted disruption of the gene encoding DNA ligase IV leads to lethality in embryonic mice , 1998, Current Biology.

[117]  David J. Chen,et al.  Ku recruits XLF to DNA double‐strand breaks , 2008, EMBO reports.

[118]  J. Danska,et al.  V(D)J recombination activates a p53-dependent DNA damage checkpoint in scid lymphocyte precursors. , 1996, Genes & development.

[119]  David J. Chen,et al.  Autophosphorylation of the DNA-dependent protein kinase catalytic subunit is required for rejoining of DNA double-strand breaks. , 2002, Genes & development.

[120]  Chen Wang,et al.  Phosphorylation of polynucleotide kinase/ phosphatase by DNA-dependent protein kinase and ataxia-telangiectasia mutated regulates its association with sites of DNA damage , 2011, Nucleic acids research.

[121]  J. Hoeijmakers.  Genome maintenance mechanisms for preventing cancer , 2001, Nature.

[122]  M. Jung,et al.  Ku proteins join DNA fragments as shown by atomic force microscopy. , 1997, Cancer research.

[123]  David J. Chen,et al.  The Ku80 Carboxy Terminus Stimulates Joining and Artemis-Mediated Processing of DNA Ends , 2008, Molecular and Cellular Biology.

[124]  J. Steitz,et al.  Characterization of the DNA-binding protein antigen Ku recognized by autoantibodies from patients with rheumatic disorders. , 1986, The Journal of biological chemistry.

[125]  D. Ramsden,et al.  Association of DNA Polymerase μ (pol μ) with Ku and Ligase IV: Role for pol μ in End-Joining Double-Strand Break Repair , 2002, Molecular and Cellular Biology.

[126]  R. West,et al.  Productive and Nonproductive Complexes of Ku and DNA-Dependent Protein Kinase at DNA Termini , 1998, Molecular and Cellular Biology.

[127]  Samuel H. Wilson,et al.  The X family portrait: structural insights into biological functions of X family polymerases. , 2007, DNA repair.