High G/C content of cohesive overhangs renders DNA end joining Ku-independent

DNA Repair

Volumn 3, Issue 1, 2004, Pages 13-21

  Sandoval, Ana ^a   Labhart, Paul ^a  

^a TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

Author keywords

Cohesive overhangs; DNA ligation; Ku; Non homologous DNA end joining; Protruding single strands; Xenopus egg extract

Indexed keywords

DNA; KU ANTIGEN;

ACCURACY; ARTICLE; BASE PAIRING; BINDING AFFINITY; CROSS LINKING; DNA REPAIR; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; THERMODYNAMICS;

EID: 0346249706     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2003.08.014     Document Type: Article

References (37)

1. Lieber M.R. The biochemistry and biological significance of nonhomologous DNA end joining: an essential repair process in multicellular eukaryotes. Genes Cells. 4:1999;77-85.
2. Grawunder U., Wilm M., Wu X., Kulesza P., Wilson T.E., Mann M., Lieber M.R. Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature. 388:1997;492-495.
3. Leber R., Wise T.W., Mizuta R., Meek K. The XRCC4 gene product is a target for and interacts with the DNA-dependent protein kinase. J. Biol. Chem. 273:1998;1794-1801.
4. Kurimasa A., Kumano S., Boubnov N.V., Story M.D., Tung C.S., Peterson S.R., Chen D.J. Requirement of the kinase activity of human DNA-dependent protein kinase catalytic subunit in DNA strand break rejoining. Mol. Cell. Biol. 19:1999;3877-3884.
5. Göttlich B., Reichenberger S., Feldmann E., Pfeiffer P. Rejoining of DNA double-strand breaks in vitro by single-strand annealing. Eur. J. Biochem. 258:1998;387-395.
6. Huang J., Dynan W.S. Reconstitution of the mammalian DNA double-strand break end-joining reaction reveals a requirement for an Mre11/Rad50/NBS1- containing fraction. Nucleic Acids Res. 30:2002;667-674.
7. Taccioli G.E., Gottlieb T.M., Blunt T., Priestley A., Demengeot J., Mizuta R., Lehmann A.R., Alt F.W., Jackson S.P., Jeggo P.A. Ku80: product of the XRCC5 gene and its role in DNA repair and V(D)J recombination. Science. 265:1994;1442-1445.
8. Smider V., Rathmell W.K., Lieber M.R., Chu G. Restoration of X-ray resistance and V(D)J recombination in mutant cells by Ku cDNA. Science. 266:1994;288-291.
9. Falzon M., Fewell J.W., Kuff E.L. EBP-80, a transcription factor closely resembling the human autoantigen Ku, recognizes single- to double-strand transitions in DNA. J. Biol. Chem. 268:1993;10546-10552.
10. Giffin W., Torrance H., Rodda D.J., Préfontaine G.G., Pope L., Haché R.J.G. Sequence-specific DNA binding by Ku autoantigen and its effects on transcription. Nature. 380:1996;265-268.
11. Mimori T., Hardin J.A. Mechanism of interaction between Ku protein and DNA. J. Biol. Chem. 261:1986;10375-10379.
12. Blier P.R., Griffith A.J., Craft J., Hardin J.A. Binding of Ku protein to DNA. Measurement of affinity for ends and demonstration of binding to nicks. J. Biol. Chem. 268:1993;7594-7601.
13. Pang D., Yoo S., Dynan W.S., Jung M., Dritschilo A. Ku proteins join DNA fragments as shown by atomic force microscopy. Cancer Res. 57:1997;1412-1415.
14. Wang J., Dong X., Reeves W.H. A model for Ku heterodimer assembly and interaction with DNA. J. Biol. Chem. 273:1998;31068-31074.
15. Walker J.R., Corpina R.A., Goldberg J. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature. 412:2001;607-614.
16. Dynan W.S., Yoo S. Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucleic Acids Res. 26:1998;1551-1559.
17. Jones J.M., Gellert M., Yang W. A Ku bridge over broken DNA. Structure (Camb.). 9:2001;881-884.
18. Pfeiffer P., Vielmetter W. Joining of nonhomologous DNA double strand breaks in vitro. Nucleic Acids Res. 16:1988;907-924.
19. Thode S., Schäfer A., Pfeiffer P., Vielmetter W. A novel pathway of DNA end-to-end joining. Cell. 60:1990;921-928.
20. Feldmann E., Schiemann V., Goedecke W., Reichenberger S., Pfeiffer P. 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. Nucleic Acids Res. 28:2000;2585-2596.
21. Chen S., Inamdar K.V., Pfeiffer P., Feldmann E., Hannah M.F., Yu Y., Lee J.-W., Zhou T., Lees-Miller S.P., Povirk L.F. Accurate in vitro end joining of a DNA double strand break with partially cohesive 3′-overhangs and 3′-phosphoglycolate termini. J. Biol. Chem. 276:2001;24323-24330.
22. Boulton S.J., Jackson S.P. Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 24:1996;4639-4648.
23. Baumann P., West S.C. DNA end-joining catalyzed by human cell-free extracts. Proc. Natl. Acad. Sci. U.S.A. 95:1998;14066-14070.
24. Labhart P. Ku-dependent nonhomologous DNA end joining in Xenopus egg extracts. Mol. Cell. Biol. 19:1999;2585-2593.
25. Yoo S., Dynan W.S. Characterization of the RNA binding properties of Ku protein. Biochemistry. 37:1998;1336-1343.
26. Sandoval A., Labhart P. Joining of DNA ends bearing non-matching 3′-overhangs. DNA Repair (Amst.). 1:2002;397-410.
27. Toth J., Biggin M.D. The specificity of protein-DNA crosslinking by formaldehyde: in vitro and in drosophila embryos. Nucleic Acids Res. 28:2000;e4.
28. Kuo M.H., Allis C.D. In vivo cross-linking and immunoprecipitation for studying dynamic protein: DNA associations in a chromatin environment. Methods. 19:1999;425-433.
29. Orlando V. Mapping chromosomal proteins in vivo by formaldehyde- crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 25:2000;99-104.
30. de Vries E., van Driel W., Bergsma W.G., Arnberg A.C., van der Vliet P.C. HeLa nuclear protein recognizing DNA termini and translocating on DNA forming a regular DNA-multimeric protein complex. J. Mol. Biol. 208:1989;65-78.
31. Paillard S., Strauss F. Analysis of the mechanism of interaction of simian Ku protein with DNA. Nucleic Acids Res. 19:1991;5619-5624.
32. Smith J., Riballo E., Kysela B., Baldeyron C., Manolis K., Masson C., Lieber M.R., Papadopoulo D., Jeggo P. Impact of DNA ligase IV on the fidelity of end joining in human cells. Nucleic Acids Res. 31:2003;215-2167.
33. Kysela B., Doherty A.J., Chovanec M., Stiff T., Ameer-Beg S.M., Vojnovic B., Girard P.-M., Jeggo P.A. Ku stimulation of DNA ligase IV-dependent ligation requires inward movement along the DNA molecule. J. Biol. Chem. 278:2003;22466-22474.
34. Boulton S.J., Jackson S.P. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 15:1996;5093-5103.
35. Liang F., Jasin M. Ku80-deficient cells exhibit excess degradation of extrachromosomal DNA. J. Biol. Chem. 271:1996;14405-14411.
36. Kabotyanski E.B., Gomelsky L., Han J.O., Stamato T.D., Roth D.B. Double-strand break repair in Ku86- and XRCC4-deficient cells. Nucleic Acids Res. 26:1998;5333-5342.
37. Nick McElhinny S.A., Snowden C.M., McCarville J., Ramsden D.A. Ku recruits the XRCC4-ligase IV complex to DNA ends. Mol. Cell. Biol. 20:2000;2996-3003.