Assembly of multiprotein complexes that control genome function

Journal of Cell Biology

Volumn 185, Issue 1, 2009, Pages 21-26

  Dinant, Christoffel ^a,b,e   Luijsterburg, Martijn S ^c,f   Höfer, Thomas ^d   Von Bornstaedt, Gesa ^d   Vermeulen, Wim ^b   Houtsmuller, Adriaan B ^a   Van Driel, Roel ^c  

^a JOSEPHINE NEFKENS INSTITUTE   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^e DANISH CANCER SOCIETY RESEARCH CENTER   (Denmark)

^f KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

DNA DAMAGE; DNA REPAIR; DNA SEQUENCE; DNA STRUCTURE; DNA TRANSCRIPTION; EXCISION REPAIR; GENE FUNCTION; KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN DNA INTERACTION; SHORT SURVEY; TRANSCRIPTION INITIATION;

CHROMATIN; DNA REPAIR; DNA-BINDING PROTEINS; GENOME; KINETICS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; NUCLEAR PROTEINS; TRANSCRIPTION, GENETIC;

EID: 65249161170     PISSN: 00219525     EISSN: 00219525     Source Type: Journal    
DOI: 10.1083/jcb.200811080     Document Type: Short Survey

References (44)

1. Berg, O.G., R.B. Winter, and P.H. von Hippel. 1981. Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry. 20:6929-6948.
2. Chen, D., C.S. Hinkley, R.W. Henry, and S. Huang. 2002. TBP dynamics in living human cells: constitutive association of TBP with mitotic chromosomes. Mol. Biol. Cell. 13:276-284.
3. Darzacq, X., Y. Shav-Tal, V. de Turris, Y. Brody, S.M. Shenoy, R.D. Phair, and R.H. Singer. 2007. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14:796-806.
4. Dundr, M., U. Hoffmann-Rohrer, Q. Hu, I. Grummt, L.I. Rothblum, R.D. Phair, and T. Misteli. 2002. A kinetic framework for a mammalian RNA poly-merase in vivo. Science. 298:1623-1626.
5. Elf, J., G.W. Li, and X.S. Xie. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science. 316:1191-1194.
6. Erie, D.A., G. Yang, H.C. Schultz, and C. Bustamante. 1994. DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science. 266:1562-1566.
7. Essers, J., A.B. Houtsmuller, L. van Veelen, C. Paulusma, A.L. Nigg, A. Pastink, W. Vermeulen, J.H. Hoeijmakers, and R. Kanaar. 2002. Nuclear dynamics of RAD52 group homologous recombination proteins in response to DNA damage. EMBO J. 21:2030-2037.
8. Essers, J., W. Vermeulen, and A.B. Houtsmuller. 2006. DNA damage repair: anytime, anywhere? Curr. Opin. Cell Biol. 18:240-246.
9. Farla, P., R. Hersmus, B. Geverts, P.O. Mari, A.L. Nigg, H.J. Dubbink, J. Trapman, and A.B. Houtsmuller. 2004. The androgen receptor ligand-binding domain stabilizes DNA binding in living cells. J. Struct. Biol. 147:50-61.
10. Gabdoulline, R.R., and R.C. Wade. 2002. Biomolecular diffusional association. Curr. Opin. Struct. Biol. 12:204-213.
11. Giglia-Mari, G., C. Miquel, A.F. Theil, P.O. Mari, D. Hoogstraten, J.M. Ng, C. Dinant, J.H. Hoeijmakers, and W. Vermeulen. 2006. Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells. PLoS Biol. 4:e156.
12. Gorman, J., and E.C. Greene. 2008. Visualizing one-dimensional diffusion of proteins along DNA. Nat. Struct. Mol. Biol. 15:768-774.
13. Gorski, S.A., M. Dundr, and T. Misteli. 2006. The road much traveled: trafficking in the cell nucleus. Curr. Opin. Cell Biol. 18:284-290.
14. Gorski, S.A., S.K. Snyder, S. John, I. Grummt, and T. Misteli. 2008. Modulation of RNA polymerase assembly dynamics in transcriptional regulation. Mol. Cell. 30:486-497.
15. Gowers, D.M., G.G. Wilson, and S.E. Halford. 2005. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. USA. 102:15883-15888.
16. Hager, G.L., C. Elbi, T.A. Johnson, T. Voss, A.K. Nagaich, R.L. Schiltz, Y. Qiu, and S. John. 2006. Chromatin dynamics and the evolution of alternate promoter states. Chromosome Res. 14:107-116.
17. Halford, S.E., and J.F. Marko. 2004. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32:3040-3052.
18. Hoeijmakers, J.H. 2001. Genome maintenance mechanisms for preventing cancer. Nature. 411:366-374.
19. Hoogstraten, D., A.L. Nigg, H. Heath, L.H. Mullenders, R. van Driel, J.H. Hoeijmakers, W. Vermeulen, and A.B. Houtsmuller. 2002. Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol. Cell. 10:1163-1174.
20. Hoogstraten, D., S. Bergink, V.H. Verbiest, M.S. Luijsterburg, B. Geverts, A. Raams, C. Dinant, J.H. Hoeijmakers, W. Vermeulen, andA.B. Houtsmuller. 2008. Versatile DNA damage detection by the global genome nucleotide excision repair protein XPC. J. Cell Sci. 121:2850-2859.
21. Hopfield, J.J. 1974. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA. 71:4135-4139.
22. Houtsmuller, A.B., and W. Vermeulen. 2001. Macromolecular dynamics in living cell nuclei revealed by fluorescence redistribution after photobleaching. Histochem. Cell Biol. 115:13-21.
23. Houtsmuller, A.B., S. Rademakers, A.L. Nigg, D. Hoogstraten, J.H. Hoeijmakers, and W. Vermeulen. 1999. Action of DNA repair endonuclease ERCC1/ XPF in living cells. Science. 284:958-961.
24. Kalodimos, C.G., N. Biris, A.M. Bonvin, M.M. Levandoski, M. Guennuegues, R. Boelens, and R. Kaptein. 2004. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science. 305:386-389.
25. Kampmann, M. 2004. Obstacle bypass in protein motion along DNA by two-dimensional rather than one-dimensional sliding. J. Biol. Chem. 279:38715-38720.
26. Luijsterburg, M.S., J. Goedhart, J. Moser, H. Kool, B. Geverts, A.B. Houtsmuller, L.H. Mullenders, W. Vermeulen, and R. van Driel. 2007. Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC. J. Cell Sci. 120:2706-2716.
27. Mari, P.O., B.I. Florea, S.P. Persengiev, N.S. Verkaik, H.T. Bruggenwirth, M. Modesti, G. Giglia-Mari, K. Bezstarosti, J.A. Demmers, T.M. Luider, et al. 2006. Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4. Proc. Natl. Acad. Sci. USA. 103:18597-18602.
28. McKinney, K., M. Mattia, V. Gottifredi, and C. Prives. 2004. p53 linear diffusion along DNA requires its C terminus. Mol. Cell. 16:413-424.
29. Misteli, T. 2008. Physiological importance of RNA and protein mobility in the cell nucleus. Histochem. Cell Biol. 129:5-11.
30. Nalley, K., S.A. Johnston, and T. Kodadek. 2006. Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo. Nature. 442:1054-1057.
31. Phair, R.D., and T. Misteli. 2000. High mobility of proteins in the mammalian cell nucleus. Nature. 404:604-609.
32. Phair, R.D., and T. Misteli. 2001. Kinetic modelling approaches to in vivo imaging. Nat. Rev. Mol. Cell Biol. 2:898-907.
33. Politi, A., M.J. Moné, A.B. Houtsmuller, D. Hoogstraten, W. Vermeulen, R. Heinrich, and R. van Driel. 2005. Mathematical modeling of nucleotide excision repair reveals efficiency of sequential assembly strategies. Mol. Cell. 19:679-690.
34. Qian, H. 2008. Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective. Biophys. J. 95:10-17.
35. San Filippo, J., P. Sung, and H. Klein. 2008. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 77:229-257.
36. Seither, P., S. Iben, and I. Grummt. 1998. Mammalian RNA polymerase I exists as a holoenzyme with associated basal transcription factors. J. Mol. Biol. 275:43-53.
37. Soutoglou, E., and T. Misteli. 2008. Activation of the cellular DNA damage response in the absence of DNA lesions. Science. 320:1507-1510.
38. Uematsu, N., E. Weterings, K. Yano, K. Morotomi-Yano, B. Jakob, G. Taucher-Scholz, P.O. Mari, D.C. van Gent, B.P. Chen, and D.J. Chen. 2007. Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks. J. Cell Biol. 177:219-229.
39. van Royen, M.E., P. Farla, K.A. Mattern, B. Geverts, J. Trapman, and A.B. Houtsmuller. 2009. Fluorescence recovery after photobleaching (FRAP) to study nuclear protein dynamics in living cells. Methods Mol. Biol. 464:363-385.
40. Volker, M., M.J. Moné, P. Karmakar, A. van Hoffen, W. Schul, W. Vermeulen, J.H. Hoeijmakers, R. van Driel, A.A. van Zeeland, and L.H. Mullenders. 2001. Sequential assembly of the nucleotide excision repair factors in
41. vivo. Mol. Cell. 8:213-224.
42. Wachsmuth, M., M. Caudron-Herger, and K. Rippe. 2008. Genome organization: balancing stability and plasticity. Biochim. Biophys. Acta. 1783:2061-2079.
43. Yao, J., K.M. Munson, W.W. Webb, and J.T. Lis. 2006. Dynamics of heat shock factor association with native gene loci in living cells. Nature. 442:1050-1053.
44. Zotter, A., M.S. Luijsterburg, D.O. Warmerdam, S. Ibrahim, A. Nigg, W.A. van Cappellen, J.H. Hoeijmakers, R. van Driel, W. Vermeulen, and A.B. Houtsmuller. 2006. Recruitment of the nucleotide excision repair endo-nuclease XPG to sites of UV-induced DNA damage depends on functional TFIIH. Mol. Cell. Biol. 26:8868-8879.