Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass (original) (raw)
Kerscher, O., Felberbaum, R. & Hochstrasser, M. Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol.22, 159–180 (2006). ArticleCASPubMed Google Scholar
Deshaies, R. J. & Joazeiro, C. A. RING domain E3 ubiquitin ligases. Annu. Rev. Biochem.78, 399–434 (2009). CASPubMed Google Scholar
Nijman, S. M. et al. A genomic and functional inventory of deubiquitinating enzymes. Cell123, 773–786 (2005). ArticleCASPubMed Google Scholar
Al-Hakim, A. et al. The ubiquitous role of ubiquitin in the DNA damage response. DNA Repair (Amst)9, 1229–1240 (2010). ArticleCAS Google Scholar
Ulrich, H. D. & Walden, H. Ubiquitin signalling in DNA replication and repair. Nat. Rev. Mol. Cell Biol.11, 479–489 (2010). ArticleCASPubMed Google Scholar
Bekker-Jensen, S. & Mailand, N. Assembly and function of DNA double-strand break repair foci in mammalian cells. DNA Repair (Amst)9, 1219–1228 (2010). ArticleCAS Google Scholar
Bergink, S. & Jentsch, S. Principles of ubiquitin and SUMO modifications in DNA repair. Nature458, 461–467 (2009). ArticleCASPubMed Google Scholar
Lehmann, A. R. et al. Translesion synthesis: Y-family polymerases and the polymerase switch. DNA Repair (Amst)6, 891–899 (2007). ArticleCAS Google Scholar
Moldovan, G. L., Pfander, B. & Jentsch, S. PCNA, the maestro of the replication fork. Cell129, 665–679 (2007). ArticleCASPubMed Google Scholar
Friedberg, E. C. Suffering in silence: the tolerance of DNA damage. Nat. Rev. Mol. Cell Biol.6, 943–953 (2005). ArticleCASPubMed Google Scholar
Bienko, M. et al. Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science310, 1821–1824 (2005). ArticleCASPubMed Google Scholar
Huang, T. T. et al. Regulation of monoubiquitinated PCNA by DUB autocleavage. Nat. Cell Biol.8, 339–347 (2006). CASPubMed Google Scholar
Wagner, S. A. et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol. Cell Proteomics10, M111 013284 (2011). ArticlePubMedPubMed Central Google Scholar
Xu, G., Paige, J. S. & Jaffrey, S. R. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat. Biotechnol.28, 868–873 (2010). ArticleCASPubMedPubMed Central Google Scholar
Gillet, L. C. & Scharer, O. D. Molecular mechanisms of mammalian global genome nucleotide excision repair. Chem. Rev.106, 253–276 (2006). ArticleCASPubMed Google Scholar
Sugasawa, K. et al. UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex. Cell121, 387–400 (2005). ArticleCASPubMed Google Scholar
Xiao, A. et al. WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature457, 57–62 (2009). ArticleCASPubMed Google Scholar
Chen, Z. J. & Sun, L. J. Nonproteolytic functions of ubiquitin in cell signaling. Mol. Cell33, 275–286 (2009). ArticleCASPubMed Google Scholar
Altun, M. et al. Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes. Chem. Biol.18, 1401–1412 (2011). ArticleCASPubMed Google Scholar
Emanuele, M. J., Ciccia, A., Elia, A. E. & Elledge, S. J. Proliferating cell nuclear antigen (PCNA)-associated KIAA0101/PAF15 protein is a cell cycle-regulated anaphase-promoting complex/cyclosome substrate. Proc. Natl Acad. Sci. USA108, 9845–9850 (2011). ArticleCASPubMedPubMed Central Google Scholar
Williamson, A. et al. Regulation of ubiquitin chain initiation to control the timing of substrate degradation. Mol. Cell42, 744–757 (2011). ArticleCASPubMedPubMed Central Google Scholar
Jackson, D. A. & Pombo, A. Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J. Cell Biol.140, 1285–1295 (1998). ArticleCASPubMedPubMed Central Google Scholar
Niimi, A. et al. Regulation of proliferating cell nuclear antigen ubiquitination in mammalian cells. Proc. Natl Acad. Sci. USA105, 16125–16130 (2008). ArticleCASPubMedPubMed Central Google Scholar
Choi, J. H. & Pfeifer, G. P. The role of DNA polymerase eta in UV mutational spectra. DNA Repair (Amst)4, 211–220 (2005). ArticleCAS Google Scholar
Havens, C. G. & Walter, J. C. Mechanism of CRL4(Cdt2), a PCNA-dependent E3 ubiquitin ligase. Gen. Dev.25, 1568–1582 (2011). ArticleCAS Google Scholar
Havens, C. G. & Walter, J. C. Docking of a specialized PIP Box onto chromatin-bound PCNA creates a degron for the ubiquitin ligase CRL4Cdt2. Mol. Cell35, 93–104 (2009). ArticleCASPubMedPubMed Central Google Scholar
Ong, S. E., Foster, L. J. & Mann, M. Mass spectrometric-based approaches in quantitative proteomics. Methods29, 124–130 (2003). ArticleCASPubMed Google Scholar
MacCoss, M. J., Wu, C. C., Matthews, D. E. & Yates, J. R. 3rd. Measurement of the isotope enrichment of stable isotope-labeled proteins using high-resolution mass spectra of peptides. Anal. Chem.77, 7646–7653 (2005). ArticleCASPubMed Google Scholar
Nielsen, M. L. et al. Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nat. Methods5, 459–460 (2008). ArticleCASPubMed Google Scholar
Wagner, S. A. et al. Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues. Mol. Cell Proteomicshttp://dx.doi.org/10.1074/mcp.M112.017905 (2012).
Michalski, A. et al. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell Proteomics10, M111 011015 (2011). ArticlePubMedPubMed Central Google Scholar
Olsen, J. V. et al. A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol. Cell Proteomics8, 2759–2769 (2009). ArticleCASPubMedPubMed Central Google Scholar
Kelstrup, C. D., Young, C., Lavallee, R., Nielsen, M. L. & Olsen, J. V. Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. J. Proteome Res.11, 3487–3497 (2012). ArticleCASPubMed Google Scholar
Olsen, J. V. et al. Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods4, 709–712 (2007). ArticleCASPubMed Google Scholar
Cox, J. et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat. Protoc.4, 698–705 (2009). ArticleCASPubMed Google Scholar
Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res.10, 1794–1805 (2011). ArticleCASPubMed Google Scholar
Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol.26, 1367–1372 (2008). ArticleCASPubMed Google Scholar
Olsen, J. V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell127, 635–648 (2006). ArticleCASPubMed Google Scholar
Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods4, 207–214 (2007). ArticleCASPubMed Google Scholar
Craig, R. & Beavis, R. C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics20, 1466–1467 (2004). ArticleCASPubMed Google Scholar
Szklarczyk, D. et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res.39, D561–D568 (2011). ArticleCASPubMed Google Scholar
Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L. & Ideker, T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics27, 431–432 (2011). ArticleCASPubMed Google Scholar
Danielsen, J. M. et al. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol. Cell Proteomics10, M110 003590 (2011). ArticlePubMed Google Scholar
Mailand, N. et al. RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell131, 887–900 (2007). ArticleCASPubMed Google Scholar
Mailand, N., Bekker-Jensen, S., Bartek, J. & Lukas, J. Destruction of Claspin by SCFbetaTrCP restrains Chk1 activation and facilitates recovery from genotoxic stress. Mol. Cell23, 307–318 (2006). ArticleCASPubMed Google Scholar
Maya-Mendoza, A., Petermann, E., Gillespie, D. A., Caldecott, K. W. & Jackson, D. A. Chk1 regulates the density of active replication origins during the vertebrate S phase. EMBO J.26, 2719–2731 (2007). ArticleCASPubMedPubMed Central Google Scholar
Parris, C. N. & Seidman, M. M. A signature element distinguishessibling and independent mutations in a shuttle vector plasmid. Gene117, 1–5 (1992). ArticleCASPubMed Google Scholar