Recombination-induced tag exchange (RITE) cassette series to monitor protein dynamics in saccharomyces cerevisiae

G3: Genes, Genomes, Genetics

Volumn 3, Issue 8, 2013, Pages 1261-1272

  Terweij, Marit ^a   Welsem, Tibor van ^a   Deventer, Sjoerd Van ^a   Verzijlbergen, Kitty F ^a,c   Menendez Benito, Victoria ^a   Ontoso, David ^b   San Segundo, Pedro ^b   Neefjes, Jacques ^a   Leeuwen, Fred van ^a  

^a NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

^b CSIC   (Spain)

^c UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Epitope tag; Inheritance; Protein; Protein turnover; Pulse chase

Indexed keywords

CRE RECOMBINASE; HISTONE; INTEGRASE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; ASSAY; BIOCHEMICAL COMPOSITION; CELL ORGANELLE; CELL TYPE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EPITOPE TAG; GENE CASSETTE; GENE TARGETING; GENE VECTOR; GENETIC ANALYSIS; GENETIC PARAMETERS; GENETIC RECOMBINATION; GENETICS; GENOMICS; INHERITANCE; METABOLISM; MUTANT; NONHUMAN; PROTEIN INHERITANCE; PROTEIN METABOLISM; PROTEIN PROCESSING; PULSE-CHASE; RECOMBINATION INDUCED TAG EXCHANGE; SACCHAROMYCES CEREVISIAE; SPATIOTEMPORAL ANALYSIS; TURNOVER TIME;

SACCHAROMYCES CEREVISIAE;

EPITOPE TAG; PROTEIN INHERITANCE; PROTEIN TURNOVER; PULSE-CHASE;

CHROMATIN IMMUNOPRECIPITATION; GENE KNOCK-IN TECHNIQUES; GENETIC VECTORS; HISTONES; INTEGRASES; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84883426331     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.006213     Document Type: Article

References (42)

1. Adams, S. R., and R. Y. Tsien, 2008 Preparation of the membrane-permanent biarsenicals FlAsH-EDT2 and ReAsH-EDT2 for fluorescent labeling of tetracysteine-tagged proteins. Nat. Protoc. 3: 1527-1534.
2. Albert, I., T. N. Mavrich, L. P. Tomsho, J. Qi, S. J. Zanton et al., 2007 Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576.
3. Brachmann, C. B., A. Davies, G. J. Cost, E. Caputo, J. Li et al., 1998 Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115-132.
4. Butko, M. T., J. Yang, Y. Geng, H. J. Kim, N. L. Jeon et al., 2012 Fluorescent and photo-oxidizing TimeSTAMP tags track protein fates in light and electron microscopy. Nat. Neurosci. 15: 1742-1751.
5. Deal, R., and S. Henikoff, 2010a Capturing the dynamic epigenome. Genome Biol. 11: 218.
6. Deal, R. B., and S. Henikoff, 2010b Catching a glimpse of nucleosome dynamics. Cell Cycle 9: 3389-3390.
7. Deal, R., J. Henikoff, and S. Henikoff, 2010 Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328: 1161-1164.
8. De Vos, D., F. Frederiks, M. Terweij, T. van Welsem, K. F. Verzijlbergen et al., 2011 Progressive methylation of ageing histones by Dot1 functions as a timer. EMBO Rep. 12: 956-962.
9. Dion, M. F., T. Kaplan, M. Kim, S. Buratowski, N. Friedman et al., 2007 Dynamics of replication-independent histone turnover in budding yeast. Science 315: 1405-1408.
10. Dymond, J. S., S. M. Richardson, C. E. Coombes, T. Babatz, H. Muller et al., 2011 Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477: 471-476.
11. Ejlassi-Lassallette, A., E. Mocquard, M. C. Arnaud, and C. Thiriet, 2011 H4 replication-dependent diacetylation and Hat1 promote S-phase chromatin assembly in vivo. Mol. Biol. Cell 22: 245-255.
12. Ghaemmaghami, S., W. K. Huh, K. Bower, R. W. Howson, A. Belle et al., 2003 Global analysis of protein expression in yeast. Nature 425: 737-741.
13. Gietz, R. D., and R. H. Schiestl, 2007 High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2: 31-34.
14. Hager, G., J. McNally, and T. Misteli, 2009 Transcription dynamics. Mol. Cell 35: 741-753.
15. Hinkson, I., and J. Elias, 2011 The dynamic state of protein turnover: it's about time. Trends Cell Biol. 21: 292-303.
16. Hotz, M., C. Leisner, D. Chen, C. Manatschal, T. Wegleiter et al., 2012 Spindle pole bodies exploit the mitotic exit network in metaphase to drive their age-dependent segregation. Cell 148: 958-972.
17. Huh, W. K., J. V. Falvo, L. C. Gerke, A. S. Carroll, R. W. Howson et al., 2003 Global analysis of protein localization in budding yeast. Nature 425: 686-691.
18. Jamai, A., R. M. Imoberdorf, and M. Strubin, 2007 Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication. Mol. Cell 25: 345-355.
19. Jansen, L. E. T., B. E. Black, D. R. Foltz, and D. W. Cleveland, 2007 Propagation of centromeric chromatin requires exit from mitosis. J. Cell Biol. 176: 795-805.
20. Kim, H. J., J. H. Seol, J. W. Han, H. D. Youn, and E. J. Cho, 2007 Histone chaperones regulate histone exchange during transcription. EMBO J. 26: 4467-4474.
21. Kobor, M. S., S. Venkatasubrahmanyam, M. D. Meneghini, J. W. Gin, J. L. Jennings et al., 2004 A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2: E131.
22. Korber, P., T. Luckenbach, D. Blaschke, and W. Horz, 2004 Evidence for histone eviction in trans upon induction of the yeast PHO5 promoter. Mol. Cell. Biol. 24: 10965-10974.
23. Lin, M. Z., and R. Y. Tsien, 2010 TimeSTAMP tagging of newly synthesized proteins. Curr. Protoc. Protein Sci. 26. Unit 26: 25.
24. Lindstrom, D. L., and D. E. Gottschling, 2009 The mother enrichment program: a genetic system for facile replicative life span analysis in Saccharomyces cerevisiae. Genetics 183: 413-422, 411SI2413SI.
25. Logie, C., and A. F. Stewart, 1995 Ligand-regulated site-specific recombination. Proc. Natl. Acad. Sci. USA 92: 5940-5944.
26. Menendez-Benito, V., S. J. vanDeventer, V. Jimenez-Garcia, M. Roy-Luzarraga, F. van Leeuwen et al., 2013 Spatiotemporal analysis of organelle and macromolecular complex inheritance. Proc. Natl. Acad. Sci. USA 110: 175-180.
27. Nelson, J., O. Denisenko, and K. Bomsztyk, 2009 The fast chromatin immunoprecipitation method. Methods Mol. Biol. 567: 45-57.
28. Ouellet, J., and Y. Barral, 2012 Organelle segregation during mitosis: lessons from asymmetrically dividing cells. J. Cell Biol. 196: 305-313.
29. Radman-Livaja, M., K. F. Verzijlbergen, A. Weiner, T. van Welsem, N. Friedman et al., 2011 Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol. 9: e1001075.
30. Ray-Gallet, D., A. Woolfe, I. Vassias, C. Pellentz, N. Lacoste et al., 2011 Dynamics of histone H3 deposition in vivo reveal a nucleosome gap-filling mechanism for H3.3 to maintain chromatin integrity. Mol. Cell 44: 928-941.
31. Rocha, N., C. Kuijl, R. van der Kant, L. Janssen, D. Houben et al., 2009 Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7-RILP-p150 Glued and late endosome positioning. J. Cell Biol. 185: 1209-1225.
32. Rufiange, A., P. E. Jacques, W. Bhat, F. Robert, and A. Nourani, 2007 Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol. Cell 27: 393-405.
33. Russel, D., K. Lasker, J. Phillips, D. Schneidman-Duhovny, J. A. Velazquez- Muriel et al., 2009 The structural dynamics of macromolecular processes. Curr. Opin. Cell Biol. 21: 97-108.
34. Sweet, S. M., M. Li, P. M. Thomas, K. R. Durbin, and N. L. Kelleher, 2010 Kinetics of re-establishing H3K79 methylation marks in global human chromatin. J. Biol. Chem. 285: 32778-32786.
35. Thiriet, C., and J. J. Hayes, 2005 Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev. 19: 677-682.
36. Tong, A. H., and C. Boone, 2006 Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol. Biol. 313: 171-192.
37. van Leeuwen, F., and D. E. Gottschling, 2002 Assays for gene silencing in yeast. Methods Enzymol. 350: 165-186.
38. van Leeuwen, F., P. R. Gafken, and D. E. Gottschling, 2002 Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109: 745-756.
39. Verzijlbergen, K. F., V. Menendez-Benito, T. van Welsem, S. J. van Deventer, D. L. Lindstrom et al., 2010 Recombination-induced tag exchange to track old and new proteins. Proc. Natl. Acad. Sci. USA 107: 64-68.
40. Verzijlbergen, K. F., T. van Welsem, D. Sie, T. L. Lenstra, D. J. Turner et al., 2011 A barcode screen for epigenetic regulators reveals a role for the NuB4/HAT-B histone acetyltransferase complex in histone turnover. PLoS Genet. 7: e1002284.
41. Walsh, P. S., D. A. Metzger, and R. Higuchi, 1991 Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10: 506-513.
42. Zee, B. M., R. S. Levin, B. Xu, G. LeRoy, N. S. Wingreen et al., 2010 In vivo residue-specific histone methylation dynamics. J. Biol. Chem. 285: 3341-3350.