Deciphering the human nucleolar proteome

Mass Spectrometry Reviews

Volumn 25, Issue 2, 2006, Pages 215-234

  Couté, Yohann ^a   Burgess, Jennifer A ^a,f   Diaz, Jean Jacques ^b,g   Chichester, Christine ^c,h   Lisacek, Frédérique ^c,d,e,i   Greco, Anna ^b   Sanchez, Jean Charles ^a,e,j,k,l,m  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b CENTRE DE GÉNÉTIQUE MOLÉCULAIRE ET CELLULAIRE   (France)

^c Geneva Bioinformatics GeneBio SA   (Switzerland)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e Génome and Informatique ^*  (Switzerland)

^f UK for Waters Ltd   (United Kingdom)

^g Centre de Génétique et de Physiologie Moléculaires et Cellulaires   (France)

^h STANFORD UNIVERSITY   (United States)

ⁱ Genome and Informatics Laboratory   (France)

^j GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^k Faculty of Medicine

^l Swiss Proteomics Society   (Switzerland)

^m Phenomics Sciences Consulting

more..

Author keywords

Gene expression regulation; Mass spectrometry; Nucleolus; Ribosome biogenesis; Sub cellular proteomics

Indexed keywords

CELL CYCLE; GENE EXPRESSION REGULATION; NUCLEOLUS; PLURIFUNCTIONAL NUCLEAR; RIBOSOME BIOGENESIS; SUB-CELLULAR PROTEOMICS;

CELLS; DATA MINING; MASS SPECTROMETRY; PATHOLOGY; PHYSIOLOGY; RNA;

PROTEINS;

NUCLEAR PROTEIN; PROTEOME;

ARTICLE; HUMAN; METABOLISM; METHODOLOGY; NUCLEOLUS; PROTEOMICS;

CELL NUCLEOLUS; HUMANS; NUCLEAR PROTEINS; PROTEOME; PROTEOMICS;

EID: 33644917973     PISSN: 02777037     EISSN: None     Source Type: Journal    
DOI: 10.1002/mas.20067     Document Type: Article

References (171)

1. Aebersold R, Mann M. 2003. Mass spectrometry-based proteomics. Nature 422:198-207.
2. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI. 2002. Directed proteomic analysis of the human nucleolus. Curr Biol 12:1-11.
3. Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M. 2005. Nucleolar proteome dynamics. Nature 433:77-83.
4. Bachant JB, Elledge SJ. 1999. Mitotic treasures in the nucleolus. Nature 398:757-758.
5. Bassler J, Grandi P, Gadal O, Lessmann T, Petfalski E, Tollervey D, Lechner J, Hurt E. 2001. Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol Cell 8:517-529.
6. Basu U, Si K, Warner JR, Maitra U. 2001. The Saccharomyces cerevisiae TIF6 gene encoding translation initiation factor 6 is required for 60S ribosomal subunit biogenesis. Mol Cell Biol 21:1453-1462.
7. Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ. 2004. The small-subunit processome is a ribosome assembly intermediate. Eukaryot Cell 3:1619-1626.
8. Blagoev B, Ong SE, Kratchmarova I, Mann M. 2004. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22:1139-1145.
9. Blaschke C, Oliveros JC, Valencia A. 2001. Mining functional information associated with expression arrays. Funct Integr Genomics 1:256-268.
10. Bodnar WM, Blackburn RK, Krise JM, Moseley MA. 2003. Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage. J Am Soc Mass Spectrom 14:971-979.
11. Bond AT, Mangus DA, He F, Jacobson A. 2001. Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing. Mol Cell Biol 21:7366-7379.
12. Brogna S, Sato TA, Rosbash M. 2002. Ribosome components are associated with sites of transcription. Mol Cell 10:93-104.
13. Busch H, Smetana K. 1970. Nucleoli of tumor cells. In: Busch H, Smetana K, editor. The nucleolus. New York: Academic Press, pp 448-471.
14. Busch H, Muramatsu M, Adams H, Steele WJ, Liau MC, Smetana K. 1963. Isolation of nucleoli. Exp Cell Res 24(Suppl 9): 150-163.
15. Cantin GT, Yates JR III. 2004. Strategies for shotgun identification of post-translational modifications by mass spectrometry. J Chromatogr A 1053:7-14.
16. Cargile BJ, Bundy JL, Stephenson JL, Jr. 2004. Potential for false positive identifications from large databases through tandem mass spectrometry. J Proteome Res 3:1082-1085.
17. Cargile BJ, Talley DL, Stephenson JL, Jr. 2004. Immobilized pH gradients as a first dimension in shotgun proteomics and analysis of the accuracy of pi predictability of peptides. Electrophoresis 25:936-945.
18. Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. 2004. The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. Mol Cell Proteomics 3:531-533.
19. Carter KC, Bowman D, Carrington W, Fogarty K, McNeil JA, Fay FS, Lawrence JB. 1993. A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus. Science 259:1330-1335.
20. Chaussabel D, Sher A. 2002. Mining microarray expression data by literature profiling. Genome Biol 3:RESEARCH0055.
21. Chen D, Huang S. 2001. Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells. J Cell Biol 153:169-176.
22. Cooper HJ, Hakansson K, Marshall AG. 2005. The role of electron capture dissociation in biomolecular analysis. Mass Spectrom Rev 24:201-222.
23. Couté Y, Scherl A, Dieckmann R, Callé A, Hoogland C, Kindbeiter K, Déon C, Greco A, Sanchez J-C, Diaz J-J, Hochstrasser DH. 2003. Nucleolar proteomics. In: Cooper DN, editor. Nature encyclopedia of the human genome. London: Macmillan Publishers Ltd., Nature Publishing Group, pp 403-408.
24. Dahlberg JE, Lund E, Goodwin EB. 2003. Nuclear translation: What is the evidence? RNA 9:1-8.
25. Decatur WA, Fournier MJ. 2003. RNA-guided nucleotide modification of ribosomal and other RNAs. J Biol Chem 278:695-698.
26. Dragon F, Gallagher JE, Compagnone-Post PA, Mitchell BM, Porwancher KA, Wehner KA, Wormsley S, Settlage RE, Shabanowitz J, Osheim Y, Beyer AL, Hunt DF, Baserga SJ. 2002. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417:967-970.
27. Dundr M, Misteli T. 2001. Functional architecture in the cell nucleus. Biochem J 356:297-310.
28. El Hage A, Sbai M, Alix JH. 2001. The chaperonin GroEL and other heat-shock proteins, besides DnaK, participate in ribosome biogenesis in Escherichia coli. Mol Gen Genet 264:796-808.
29. Fatica A, Tollervey D. 2002. Making ribosomes. Curr Opin Cell Biol 14:313-318.
30. Fatica A, Cronshaw AD, Dlakic M, Tollervey D. 2002. Ssf1p prevents premature processing of an early pre-60S ribosomal particle. Mol Cell 9:341-351.
31. Finley D. Bartel B, Varshavsky A. 1989. The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis. Nature 338:394-401.
32. Fromont-Racine M. Senger B, Saveanu C. Fasiolo F. 2003. Ribosome assembly in eukaryotes. Gene 313:17-42.
33. Fujiyama S. Yanagida M, Hayano T, Miura Y. Isobe T. Fujimori F, Uchida T. Takahashi N. 2002. Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes. J Biol Chem 277:23773-23780.
34. Gadal O, Strauss D. Braspenning J, Hoepfner D, Petfalski E, Philippsen P. Tollervey D, Hurt E. 2001 a. A nuclear AAA-type ATPase (Rix7p) is required for biogenesis and nuclear export of 60S ribosomal subunits. EMBOJ 20:3695-3704.
35. Gadal O. Strauss D. Kessl J, Trumpower B. Tollervey D, Hurt E. 2001b Nuclear export of 60s ribosomal subunits depends on Xpolp and requires a nuclear export sequence-containing factor, Nmd3p. that associates with the large subunit protein Rpl10p. Mol Cell Biol 21:3405-3415.
36. Gerbi SA. Borovjagin AV. Lange TS. 2003. The nucleolus: A site of ribonucleoprotein maturation. Curr Opin Cell Biol 15:318-325.
37. Geymonat M. Jensen S, Johnston LH. 2002. Mitotic exit: The Cdc14 double cross. Curr Biol 12:R482-R484.
38. Gorlich D. Mattaj IW. 1996. Nucleocytoplasmic transport. Science 271: 1513-1518.
39. Granboulan N. Granboulan P. 1965. Ultrastructure cytochemistry of the nucleolus II. Study of the sites of RNA synthesis in the nucleolus and the nucleus. Exp Cell Res 38:604-619.
40. Grandi P. Rybin V, Bassler J, Petfalski E, Strauss D, Marzioch M, Schafer T, Kuster B, Tschochner H, Tollervey D, Gavin AC, Hurt E. 2002.90S preribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors. Mol Cell 10:105-115.
41. Gruhler A. Olsen JV, Mohammed S, Mortensen P, Faergeman NF, Mann M. Jensen ON. 2005. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 4:310-327.
42. Guilhaus M, Selby D. Mlynski V. 2000. Orthogonal acceleration time-of-flight mass spectrometry. Mass Spectrom Rev 19:65-107.
43. Hadjiolov AA. 1985. The nucleolus and ribosome biogenesis. In: Beermann AM. Goldstein L, Porter KR, Sitte P, editors. Cell biology monographs. Wien/New York: Springer Verlag, pp 1-263.
44. Hager JW. 2002. A new linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 16:512-526.
45. Harnpicharnchai P, Jakovljevic J. Horsey E. Miles T, Roman J. Rout M, Meagher D. Imai B, Guo Y, Brame CJ, Shabanowitz J. Hunt DF, Woolford JL, Jr. 2001. Composition and functional characterization of yeast 66S ribosome assembly intermediates. Mol Cell 8:505-515.
46. Hayano T. Yanagida M, Yamauchi Y, Shinkawa T, Isobe T, Takahashi N. 2003. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes: Possible link between Nop56p and the nucleolar protein treacle responsible for treacher Collins syndrome. J Biol Chem 278:34309-34319.
47. Henderson AS, Warburton D, Atwood KC. 1972. Location of ribosomal DNA in the human chromosome complement. Proc Natl Acad Sci USA 69:3394-3398.
48. Hiscox JA. 2002. The nucleolus - A gateway to viral infection? Arch Virol 147:1077-1089.
49. Ho JH, Kallstrom G, Johnson AW. 2000. Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit. J Cell Biol 151:1057-1066.
50. Horky M, Kotala V. Anton M, Wesierska-Gadek J. 2002. Nucleolus and apoptosis. Ann NY Acad Sci 973:258-264.
51. Horn HF. Vousden KH. 2004. Cancer: Guarding the guardian? Nature 427:110-111.
52. Horsey EW, Jakovljevic J. Miles TD. Harnpicharnchai P. Woolford JL. Jr. 2004. Role of the yeast Rrp1 protein in the dynamics of pre-ribosome maturation. RNA 10:813-827.
53. Huang S. 2002. Building an efficient factory: Where is pre-rRNA synthesized in the nucleolus? J Cell Biol 157:739-741.
54. Huang L, Baldwin MA, Maltby DA. Medzihradszky KF, Baker PR. Allen N. Rexach M. Edmondson RD. Campbell J, Juhasz P. Martin SA. Vestal ML, Burlingame AL. 2002. The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry. Mol Cell Proteomics 1:434-450.
55. Huber LA, Pfaller K. Vietor I. 2003. Organelle proteomics: Implications for subcellular fractionation in proteomics. Circ Res 92:962-968.
56. Huh WK, Falvo JV, Gerke LC. Carroll AS. Howson RW. Weissman JS. O'Shea EK. 2003. Global analysis of protein localization in budding yeast. Nature 425:686-691.
57. Hurt E. Hannus S, Schmelzl B, Lau D, Tollervey D, Simos G. 1999. A novel in vivo assay reveals inhibition of ribosomal nuclear export in ran-cycle and nucleoporin mutants. J Cell Biol 144:389-401.
58. Ibarrola N, Kalume DE, Gronborg M. Iwahori A. Pandey A. 2003. A proteomic approach for quantitation of phosphorylation using stable isotope labeling in cell culture. Anal Chem 75:6043-6049.
59. Ibarrola N, Molina H. Iwahori A. Pandey A. 2004. A novel proteomic approach for specific identification of tyrosine kinase substrates using [13C]tyrosine. J Biol Chem 279:15805-15813.
60. Iborra FJ, Jackson DA. Cook PR. 2001. Coupled transcription and translation within nuclei of mammalian cells. Science 293:1139-1142.
61. Ideue T, Azad AK. Yoshida J. Matsusaka T, Yanagida M. Ohshima Y. Tani T. 2004. The nucleolus is involved in mRNA export from the nucleus in fission yeast. J Cell Sci 117:2887-2895.
62. Isaac C, Yang Y, Meier UT. 1998. Nopp140 functions as a molecular link between the nucleolus and the coiled bodies. J Cell Biol 142:319-329.
63. Jensen ON. 2004. Modification-specific proteomics: Characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol 8:33-41.
64. Jensen LJ, Gupta R. Staerfeldt HH. Brunak S. 2003. Prediction of human protein function according to Gene Ontology categories. Bioinformatics 19:635-642.
65. Jonscher KR, Yates JR III. 1997. The quadrupole ion trap mass spectrometer - A small solution to a big challenge. Anal Biochem 244:1-15.
66. Kaiser J. 2002. PROTEOMICS: Public-private group maps out initiatives. Science 296:827.
67. Keller A, Nesvizhskii AI. Kolker E, Aebersold R. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74:5383-5392.
68. Krauthammer M, Rzhetsky A, Morozov P, Friedman C. 2000. Using BLAST for identifying gene and protein names in journal articles. Gene 259:245-252.
69. Kressler D. Linder P. de La Cruz J. 1999. Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 19:7897-7912.
70. Krogan NJ, Peng WT, Cagney G, Robinson MD, Haw R, Zhong G, Guo X. Zhang X, Canadien V, Richards DP, Beattie BK. Lalev A. Zhang W. Davierwala AP, Mnaimneh S. Starostine A. Tikuisis AP, Grigull J, Datta N. Bray JE, Hughes TR. Emili A, Greenblatt JF. 2004. High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell 13:225-239.
71. Kuhn A. Gottlieb TM. Jackson SP, Grummt I. 1995. DNA-dependent protein kinase: A potent inhibitor of transcription by RNA polymerase I. Genes Dev 9:193-203.
72. Laiko VV. Baldwin MA. Burlingame AL. 2000. Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 72:652-657.
73. Learned RM, Cordes S, Tjian R. 1985. Purification and characterization of a transcription factor that confers promoter specificity to human RNA polymerase I. Mol Cell Biol 5:1358-1369.
74. Leary DJ, Huang S. 2001. Regulation of ribosome biogenesis within the nucleolus. FEES Lett 509:145-150.
75. Leung AK, Andersen JS, Mann M, Lamond AI. 2003. Bioinformatic analysis of the nucleolus. Biochem J 376:553-569.
76. Lewis JD. Tollervey D. 2000. Like attracts like: Getting RNA processing together in the nucleus. Science 288:1385-1389.
77. Link AJ, Eng J, Schieltz DM, Carmack E. Mize GJ, Morris DR, Garvik BM, Yates JR III. 1999. Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17:676-682.
78. Lisacek F, Chichester C, Gonnet P, Jaillet O, Kappus S, Nikitin F, Roland P, Rossier G, Truong L, Appel RD. 2004. Shaping biological knowledge: Applications in proteomics. Comp Funct Genom 5:190-195.
79. Maden BE. 1990. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol 39:241-303. Write to the Help Desk NCBI/ NLM/NIH Department of Health & Human Services Privacy Statement/Freedom of Information Act/Disclaimer.
80. Maden BE, Hughes JM. 1997. Eukaryotic ribosomal RNA: The recent excitement in the nucleotide modification problem. Chromosoma 105:391 -400. Write to the Help Desk NCBI/NLM/NIH Department of Health & Human Services Privacy Statement/Freedom of Information Act/Disclaimer.
81. Maki JA, Schnobrich DJ, Culver GM. 2002. The DnaK chaperone system facilitates 30S ribosomal subunit assembly. Mol Cell 10:129-138.
82. Mann M. Wilm M. 1994. Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66:4390-4399.
83. McLuckey SA, Vanberkel GJ, Goeringer DE, Glish GL. 1994. Ion trap mass spectrometry of externally generated ions. Anal Chem 66:A689-A696.
84. Medzihradszky KF, Campbell JM, Baldwin MA, Falick AM, Juhasz P, Vestal ML, Burlingame AL. 2000. The characteristics of peptide collisioninduced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer. Anal Chem 72:552-558.
85. Melese T, Xue Z. 1995. The nucleolus: An organelle formed by the act of building a ribosome. Curr Opin Cell Biol 7:319-324.
86. Meng F, Forbes AJ, Miller LM, Kelleher NL. 2005. Detection and localization of protein modifications by high resolution tandem mass spectrometry. Mass Spectrom Rev 24:126-134.
87. Milkereit P, Gadal O, Podtelejnikov A, Trumtel S, Gas N, Petfalski E. Tollervey D, Mann M. Hurt E, Tschochner H. 2001. Maturation and intranuclear transport of pre-ribosomes requires Noc proteins. Cell 105:499-509.
88. Milkereit P, Strauss D, Bassler J, Gadal O, Kuhn H, Schutz S, Gas N, Lechner J. Hurt E, Tschochner H. 2003. A Noc complex specifically involved in the formation and nuclear export of ribosomal 40 S subunits. J Biol Chem 278:4072-4081.
89. Misteli T. 2001. Protein dynamics: Implications for nuclear architecture and gene expression. Science 291:843-847.
90. Moy TI, Silver PA. 1999. Nuclear export of the small ribosomal subunit requires the ran-GTPase cycle and certain nucleoporins. Genes Dev 13:2118-2133.
91. Mulder NJ. Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ. Vaughan R, Zdobnov EM. 2003. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31:315-318.
92. Muramatsu M, Onishi T. 1978. Isolation and purification of nucleoli and nucleolar chromatin from mammalian cells. Methods Cell Biol 17: 141-161.
93. Muratani M, Gerlich D, Janicki SM, Gebhard M, Eils R, Spector DL. 2002. Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nat Cell Biol 4:106-110.
94. Nazar RN. 2004. Ribosomal RNA processing and ribosome biogenesis in eukaryotes. IUBMB Life 56:457-465.
95. Neumann S, Petfalski E, Brugger B, Grosshans H, Wieland F, Tollervey D, Hurt E. 2003. Formation and nuclearexport of tRNA, rRNA, and mRNA is regulated by the ubiquitin ligase Rsp5p. EMBO Rep 4:1156-1162.
96. Nissan TA. Bassler J, Petfalski E. Tollervey D, Hurt E. 2002. 60S preribosome formation viewed from assembly in the nucleolus until export to the cytoplasm. EMBO J 21:5539-5547.
97. Nissan TA, Galani K, Maco B, Tollervey D, Aebi U, Hurt E. 2004. A pre-ribosome with a tadpole-like structure functions in ATP-dependent maturation of 60S subunits. Mol Cell 15:295-301.
98. Oda Y, Nagasu T, Chait BT. 2001. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat Biotechnol 19:379-382.
99. Oeffinger M, Dlakic M, Tollervey D. 2004. A pre-ribosome-associated HEAT-repeat protein is required for export of both ribosomal subunits. Genes Dev 18:196-209.
100. Olson MO. 2004. Sensing cellular stress: Another new function for the nucleolus? Sci STKE 2004:pe10.
101. Olson MO, Dundr M, Szebeni A. 2000. The nucleolus: An old factory with unexpected capabilities. Trends Cell Biol 10:189-196.
102. Olson MO, Prestayko AW. Jones CF, Busch H. 1974. Phosphorylation of proteins of ribosomes and nucleolar preribosomal particles from Novikoff hepatmoa ascites cells. J Mol Biol 90:161-168.
103. Ong S-E, Mittler G, Mann M. 2004. Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat Methods 1:119-126.
104. Ong SE, Blagoev B. Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376-386.
105. Opiteck GJ, Lewis KC, Jorgenson JW, Anderegg RJ. 1997. Comprehensive on-line LC/LC/MS of proteins. Anal Chem 69:1518-1524.
106. Opiteck GJ, Ramirez SM, Jorgenson JW, Moseley MA III. 1998. Comprehensive two-dimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping. Anal Biochem 258:349-361.
107. Orrick LR, Olson MO, Busch H. 1973. Comparison of nucleolar proteins of normal rat liver and Novikoff hepatoma ascites cells by two-dimensional polyacrylamide gel electrophoresis. Proc Natl Acad Sci USA 70:1316-1320.
108. Pandolfi PP. 2004. Aberrant mRNA translation in cancer pathogenesis: An old concept revisited comes finally of age. Oncogene 23:3134-3137.
109. Park PC, De Boni U. 1999. Dynamics of structure-function relationships in interphase nuclei. Life Sci 64:1703-1718.
110. Pederson T. 1998. The plurifunctional nucleolus. Nucleic Acids Res 26: 3871-3876.
111. Pederson T, Politz JC. 2000. The nucleolus and the four ribonucleoproteins of translation. J Cell Biol 148:1091-1095.
112. Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M. Lamond AI, Brown JW, Shaw PJ. 2005. Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell 16:260-269.
113. Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. 2003a. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J Proteome Res 2:43-50.
114. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR. 2003b. A panoramic view of yeast noncoding RNA processing. Cell 113:919-933.
115. Perkins DN. Pappin DJ. Creasy DM, Cottrell JS. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551-3567.
116. Phair RD, Misteli T. 2000. High mobility of proteins in the mammalian cell nucleus. Nature 404:604-609.
117. Platani M, Goldberg I. Lamond AI, Swedlow JR. 2002. Cajal body dynamics and association with chromatin are ATP-dependent. Nat Cell Biol 4:502-508.
118. Politz JC. Browne ES, Wolf DE, Pederson T. 1998. Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc Natl Acad Sci USA 95: 6043-6048.
119. Politz JC. Tuft RA, Pederson T, Singer RH. 1999. Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr Biol 9:285-291.
120. Politz JC, Yarovoi S. Kilroy SM, Gowda K, Zwieb C, Pederson T. 2000. Signal recognition particle components in the nucleolus. Proc Natl Acad Sci USA 97:55-60.
121. Prestayko AW, Klomp GR, Schmoll DJ, Busch H. 1974. Comparison of proteins of ribosomal subunits and nucleolar preribosomal particles from Novikoff hepatoma ascites cells by two-dimensional polyacrylamide gel electrophoresis. Biochemistry 13:1945-1951.
122. Proux D, Rechenmann F, Julliard L, Fillet VV, Jacq B. 1998. Detecting gene symbols and names in biological texts: A first step toward pertinent information extraction. Genome Inform Ser Workshop Genome Inform 9:72-80.
123. Rabilloud T. 2002. Two-dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains. Proteomics 2: 3-10.
124. Rabitsch KP, Petronczki M, Javerzat JP. Genier S, Chwalla B, Schleiffer A, Tanaka TU, Nasmyth K. 2003. Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis I. Dev Cell 4:535-548.
125. Raemaekers T, Ribbeck K, Beaudouin J, Annaert W, Van Camp M, Stockmans I, Smets N, Bouillon R, Ellenberg J, Carmeliet G. 2003. NuSAP, a novel microtubule-associated protein involved in mitotic spindle organization. J Cell Biol 162:1017-1029.
126. Ranish JA, Yi EC, Leslie DM, Purvine SO. Goodlett DR, Eng J, Aebersold R. 2003. The study of macromolecular complexes by quantitative proteomics. Nat Genet 33:349-355.
127. Raychaudhuri S, Altman RB. 2003. A literature-based method for assessing the functional coherence of a gene group. Bioinformatics 19:396-401.
128. Reid GE, McLuckey SA. 2002. 'Top down' protein characterization via tandem mass spectrometry. J Mass Spectrom 37:663-675.
129. Roger B, Moisand A. Amalric F, Bouvet P. 2003. Nucleolin provides a link between RNA polymerase I transcription and pre-ribosome assembly. Chromosoma 111:399-407.
130. Ross PL. Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ. 2004. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154-1169.
131. Ruggero D, Pandolfi PP. 2003. Does the ribosome translate cancer? Nat Rev Cancer 3:179-192.
132. Rusnak F, Zhou J, Hathaway G. 2002. Identification of phosphorylated and glycosylated sites in peptides by chemically targeted proteolysis. J Biomol Tech 13:228-237.
133. Sadygov RG, Cociorva D, Yates JR III. 2004. Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book. Nat Methods 1:195-202.
134. Salwinski L. Eisenberg D. 2003. Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol 13:377-382.
135. San-Segundo PA, Roeder GS. 1999. Pch2 links chromatin silencing to meiotic checkpoint control. Cell 97:313-324.
136. Saveanu C, Namane A. Gleizes PE. Lebreton A, Rousselle JC. Noaillac-Depeyre J, Gas N. Jacquier A, Fromont-Racine M. 2003. Sequential protein association with Nascent 60S ribosomal particles. Mol Cell Biol 23:4449-4460.
137. Schafer T, Strauss D, Petfalski E, Tollervey D, Hurt E. 2003. The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes. EMBO J 22:1370-1380.
138. Scheer U. Hock R. 1999. Structure and function of the nucleolus. Curr Opin Cell Biol 11:385-390.
139. Scherl A, Coute Y, Deon C, Calle A, Kindbeiter K, Sanchez JC. Greco A. Hochstrasser D, Diaz JJ. 2002. Functional proteomic analysis of human nucleolus. Mol Biol Cell 13:4100-4109.
140. Scherrer K, Latham H. Darnell JE. 1963. Demonstration of an unstable RNA and of a precursor to ribosomal RNA in HeLa cells. Proc Natl Acad Sci USA 49:240-248.
141. Schwartz JC, Senko MW, Syka JE. 2002. A two-dimensional quadrupole ion trap mass spectrometer. J Am Soc Mass Spectrom 13:659-669.
142. Schweppe RE, Haydon CE, Lewis TS. Resing KA. Ahn NG. 2003. The characterization of protein post-translational modifications by mass spectrometry. Acc Chem Res 36:453-461.
143. Scott M, Boisvert FM, Vieyra D, Johnston RN, Bazett-Jones DP, Riabowol K. 2001. UV induces nucleolar translocation of ING1 through two distinct nucleolar targeting sequences. Nucleic Acids Res 29:2052-2058.
144. Seo J, Lee KJ. 2004. Post-translational modifications and their biological functions: Proteomic analysis and systematic approaches. J Biochem Mol Biol 37:35-44.
145. Sinclair DA, Mills K, Guarente L. 1998. Molecular mechanisms of yeast aging. Trends Biochem Sci 23:131-134.
146. Sleeman JE, Lamond AI. 1999. Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway. Curr Biol 9:1065-1074.
147. Smith RD, Anderson GA. Lipton MS, Pasa-Tolic L, Shen Y, Conrads TP. Veenstra TD, Udseth HR. 2002. An accurate mass tag strategy for quantitative and high-throughput proteome measurements. Proteomics 2:513-523.
148. Stage-Zimmermann T, Schmidt U. Silver PA. 2000. Factors affecting nuclear export of the 60S ribosomal subunit in vivo. Mol Biol Cell 11:3777-3789.
149. Staub E, Fiziev P, Rosenthal A, Hinzmann B. 2004. Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. Bioessays 26:567-581.
150. Syka JE. Marto JA, Bai DL, Horning S, Senko MW, Schwartz JC. Ueberheide B, Garcia B, Busby S, Muratore T, Shabanowitz J. Hunt DE 2004. Novel linear quadrupole ion trap/FT mass spectrometer: Performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J Proteome Res 3:621-626.
151. Tanabe L, Wilbur WJ. 2002. Tagging gene and protein names in biomedical text. Bioinformatics 18:1124-1132.
152. Trere D. 2000. AgNOR staining and quantification. Micron 31:127-131.
153. Trotta CR, Lund E, Kahan L, Johnson AW, Dahlberg JE. 2003. Coordinated nuclear export of 60S ribosomal subunits and NMD3 in vertebrates. EMBO J 22:2841-2851.
154. Tschochner H, Hurt E. 2003. Pre-ribosomes on the road from the nucleolus to the cytoplasm. Trends Cell Biol 13:255-263.
155. Venema J, Tollervey D. 1999. Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33:261-311.
156. Visintin R, Amon A. 2000. The nucleolus: The magician's hat for cell cycle tricks. Curr Opin Cell Biol 12:372-377.
157. Wall DB, Berger SJ, Finch JW, Cohen SA, Richardson K, Chapman R, Drabble D, Brown J, Gostick D. 2002. Continuous sample deposition from reversed-phase liquid chromatography to tracks on a matrix-assisted laser desorption/ionization precoated target for the analysis of protein digests. Electrophoresis 23:3193-3204.
158. Wang H, Hanash S. 2005. Intact-protein based sample preparation strategies for proteome analysis in combination with mass spectrometry. Mass Spectrom Rev 24:413-426.
159. Wattenberg A, Organ AJ, Schneider K, Tyldesley R, Bordoli R, Bateman RH. 2002. Sequence dependent fragmentation of peptides generated by MALDI quadrupole time-of-flight (MALD1 Q-TOF) mass spectrometry and its implications for protein identification. J Am Soc Mass Spectrom 13:772-783.
160. Wienkoop S, Glinski M, Tanaka N, Tolstikov V, Fiehn O, Weckwerth W. 2004. Linking protein fractionation with multidimensional monolithic reversed-phase peptide chromatography/mass spectrometry enhances protein identification from complex mixtures even in the presence of abundant proteins. Rapid Commun Mass Spectrom 18: 643-650.
161. Wilkinson MF, Shyu AB. 2002. RNA surveillance by nuclear scanning? Nat Cell Biol 4:E144-E147.
162. Wilm MS, Mann M. 1994. Electrospray and Taylor-cone theory, Doles beam of macromolecules at last. Int J Mass Spectrom Ion Process 136:167-180.
163. Wilm M, Mann M. 1996. Analytical properties of the nanoelectrospray ion source. Anal Chem 68:1-8.
164. Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG. 2004. System-based proteomic analysis of the Interferon response in human liver cells. Genome Biol 5:R54.
165. Yanagida M, Shimamoto A, Nishikawa K, Furuichi Y, Isobe T, Takahashi N. 2001. Isolation and proteomic characterization of the major proteins of the nucleolin-binding ribonucleoprotein complexes. Proteomics 1:1390-1404.
166. Yanagida M, Hayano T, Yamauchi Y, Shinkawa T, Natsume T, Isobe T, Takahashi N. 2004. Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes. J Biol Chem 279:1607-1614.
167. Yang Y, Chen Y, Zhang C, Huang H, Weissman SM. 2002. Nucleolar localization of hTERT protein is associated with telomerase function. Exp Cell Res 277:201-209.
168. Yates JR III. 2004. Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 33:297-316.
169. Yu H, Hatzivassiloglou V, Friedman C, Rzhetsky A, Wilbur WJ. 2002. Automatic extraction of gene and protein synonyms from MEDLINE and journal articles. Proc AMIA Symp 919-923.
170. Zhou F, Johnston MV. 2004. Protein characterization by on-line capillary isoelectric focusing, reversed-phase liquid chromatography, and mass spectrometry. Anal Chem 76:2734-2740.
171. Zimber A, Nguyen QD, Gespach C. 2004. Nuclear bodies and compartments: Functional roles and cellular signalling in health and disease. Cell Signal 16:1085-1104.