Dynamic Proteomics of Human Protein Level and Localization across the Cell Cycle

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Farkash Amar, Shlomit ^a   Eden, Eran ^a,c   Cohen, Ariel ^a   Geva Zatorsky, Naama ^a,d   Cohen, Lydia ^a   Milo, Ron ^a   Sigal, Alex ^a,b   Danon, Tamar ^a   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c MeMed Diagnostics   (Israel)

^d HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL CYCLE; CELL CYCLE REGULATION; CELL DIVISION; CELL LEVEL; CELL SYNCHRONIZATION; CELLULAR DISTRIBUTION; CHEMICAL ANALYSIS; COMPUTER MODEL; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; MOLECULAR CLONING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PROTEIN ANALYSIS; PROTEIN CELL LEVEL; PROTEIN LOCALIZATION; PROTEOMICS; SENSITIVITY ANALYSIS;

CELL CYCLE; CELL LINE; DNA REPLICATION TIMING; GENE EXPRESSION PROFILING; HUMANS; PROTEINS; PROTEOMICS; TIME-LAPSE IMAGING;

EID: 84868688518     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048722     Document Type: Article

References (38)

1. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2: 65-73.
2. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
3. Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, et al. (2004) Periodic gene expression program of the fission yeast cell cycle. Nat Genet 36: 809-817 doi:10.1038/ng1377.
4. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13: 1977-2000 doi:10.1091/mbc.02-02-0030.
5. Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, et al. (2001) Transcriptional regulation and function during the human cell cycle. Nat Genet 27: 48-54 doi:10.1038/83751.
6. Cooper S, Shedden K, (2007) Microarrays and the relationship of mRNA variation to protein variation during the cell cycle. J Theor Biol 249: 574-581 doi:10.1016/j.jtbi.2007.08.019.
7. Bar-Joseph Z, Siegfried Z, Brandeis M, Brors B, Lu Y, et al. (2008) Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci USA 105: 955-960 doi:10.1073/pnas.0704723105.
8. Ball DA, Marchand J, Poulet M, Baumann WT, Chen KC, et al. (2011) Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. PLoS ONE 6: e26272 doi:10.1371/journal.pone.0026272.
9. Tully GH, Nishihama R, Pringle JR, Morgan DO, (2009) The anaphase-promoting complex promotes actomyosin-ring disassembly during cytokinesis in yeast. Mol Biol Cell 20: 1201-1212 doi:10.1091/mbc.E08-08-0822.
10. Drapkin BJ, Lu Y, Procko AL, Timney BL, Cross FR, (2009) Analysis of the mitotic exit control system using locked levels of stable mitotic cyclin. Mol Syst Biol 5: 328 doi:10.1038/msb.2009.78.
11. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, et al. (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science 322: 1511-1516 doi:10.1126/science.1160165.
12. Geva-Zatorsky N, Dekel E, Cohen AA, Danon T, Cohen L, et al. (2010) Protein dynamics in drug combinations: a linear superposition of individual-drug responses. Cell 140: 643-651 doi:10.1016/j.cell.2010.02.011.
13. Cohen AA, Kalisky T, Mayo A, Geva-Zatorsky N, Danon T, et al. (2009) Protein dynamics in individual human cells: experiment and theory. PLoS ONE 4: e4901 doi:10.1371/journal.pone.0004901.
14. Sigal A, Danon T, Cohen A, Milo R, Geva-Zatorsky N, et al. (2007) Generation of a fluorescently labeled endogenous protein library in living human cells. Nat Protoc 2: 1515-1527 doi:10.1038/nprot.2007.197.
15. Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, et al. (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nat Methods 3: 525-531 doi:10.1038/nmeth892.
16. Eden E, Geva-Zatorsky N, Issaeva I, Cohen A, Dekel E, et al. (2011) Proteome half-life dynamics in living human cells. Science 331: 764-768 doi:10.1126/science.1199784.
17. Tzur A, Kafri R, LeBleu VS, Lahav G, Kirschner MW, (2009) Cell growth and size homeostasis in proliferating animal cells. Science 325: 167-171 doi:10.1126/science.1174294.
18. McGarry TJ, Kirschner MW, (1998) Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell 93: 1043-1053.
19. Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, et al. (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462: 358-362 doi:10.1038/nature08575.
20. Peng X, Maiers JL, Choudhury D, Craig SW, DeMali KA, (2012) α-Catenin uses a novel mechanism to activate vinculin. J Biol Chem 287: 7728-7737 doi:10.1074/jbc.M111.297481.
21. Peng X, Nelson ES, Maiers JL, DeMali KA, (2011) New insights into vinculin function and regulation. Int Rev Cell Mol Biol 287: 191-231 doi:10.1016/B978-0-12-386043-9.00005-0.
22. Jiang W, Jimenez G, Wells NJ, Hope TJ, Wahl GM, et al. (1998) PRC1: a human mitotic spindle-associated CDK substrate protein required for cytokinesis. Mol Cell 2: 877-885.
23. Zhu C, Jiang W, (2005) Cell cycle-dependent translocation of PRC1 on the spindle by Kif4 is essential for midzone formation and cytokinesis. Proc Natl Acad Sci USA 102: 343-348 doi:10.1073/pnas.0408438102.
24. Wang M, Zhou X, King RW, Wong STC, (2007) Context based mixture model for cell phase identification in automated fluorescence microscopy. BMC Bioinformatics 8: 32 doi:10.1186/1471-2105-8-32.
25. Chebira A, Barbotin Y, Jackson C, Merryman T, Srinivasa G, et al. (2007) A multiresolution approach to automated classification of protein subcellular location images. BMC Bioinformatics 8: 210 doi:10.1186/1471-2105-8-210.
26. Boland MV, Murphy RF, (2001) A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics 17: 1213-1223.
27. Haralick RM, (1979) Statistical and structural approaches to texture. Proceedings of the IEEE 67: 786-804 doi:10.1109/PROC.1979.11328.
28. Haralick RM, Shanmugan K, Dinstein I, (1973) Textural features for image classification. IEEE Transactions on Systems, Man, and Cybernetics SMC-3: 610-621.
29. Rountree MR, Bachman KE, Baylin SB, (2000) DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet 25: 269-277 doi:10.1038/77023.
30. Sun J-M, Chen HY, Moniwa M, Litchfield DW, Seto E, et al. (2002) The transcriptional repressor Sp3 is associated with CK2-phosphorylated histone deacetylase 2. J Biol Chem 277: 35783-35786 doi:10.1074/jbc.C200378200.
31. Hand R, (1978) Eucaryotic DNA: organization of the genome for replication. Cell 15: 317-325.
32. Goldman MA, Holmquist GP, Gray MC, Caston LA, Nag A, (1984) Replication timing of genes and middle repetitive sequences. Science 224: 686-692 doi:10.1126/science.6719109.
33. Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, et al. (2008) Global organization of replication time zones of the mouse genome. Genome Res 18: 1562-1570 doi:10.1101/gr.079566.108.
34. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, et al. (2008) Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6: e245 doi:10.1371/journal.pbio.0060245.
35. White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, et al. (2004) DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci USA 101: 17771-17776 doi:10.1073/pnas.0408170101.
36. Santos SDM, Wollman R, Meyer T, Ferrell Jr JE, (2012) Spatial Positive Feedback at the Onset of Mitosis. Cell 149: 1500-1513 doi:10.1016/j.cell.2012.05.028.
37. Geva-Zatorsky N, Issaeva I, Mayo A, Cohen A, Dekel E, et al. (2012) Using bleach-chase to measure protein half-lives in living cells. Nat Protoc 7: 801-811 doi:10.1038/nprot.2012.028.
38. Zhang B, Kirov S, Snoddy J, (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 33: W741-748 doi:10.1093/nar/gki475.