title: The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics.
abstract: Despite many decades of study, mitotic chromosome structure and composition remain poorly characterized. Here, we have integrated quantitative proteomics with bioinformatic analysis to generate a series of independent classifiers that describe the approximately 4,000 proteins identified in isolated mitotic chromosomes. Integrating these classifiers by machine learning uncovers functional relationships between protein complexes in the context of intact chromosomes and reveals which of the approximately 560 uncharacterized proteins identified here merits further study. Indeed, of 34 GFP-tagged predicted chromosomal proteins, 30 were chromosomal, including 13 with centromere-association. Of 16 GFP-tagged predicted nonchromosomal proteins, 14 were confirmed to be nonchromosomal. An unbiased analysis of the whole chromosome proteome from genetic knockouts of kinetochore protein Ska3/Rama1 revealed that the APC/C and RanBP2/RanGAP1 complexes depend on the Ska complex for stable association with chromosomes. Our integrated analysis predicts that up to 97 new centromere-associated proteins remain to be discovered in our data set.
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.
authors.forename: Shinya
authors.initials: S
authors.lastname: Ohta
authors.forename: Jimi-Carlo
authors.initials: JC
authors.lastname: Bukowski-Wills
authors.forename: Luis
authors.initials: L
authors.lastname: Sanchez-Pulido
authors.forename: Flavia de Lima
authors.initials: Fde L
authors.lastname: Alves
authors.forename: Laura
authors.initials: L
authors.lastname: Wood
authors.forename: Zhuo A
authors.initials: ZA
authors.lastname: Chen
authors.forename: Melpi
authors.initials: M
authors.lastname: Platani
authors.forename: Lutz
authors.initials: L
authors.lastname: Fischer
authors.forename: Damien F
authors.initials: DF
authors.lastname: Hudson
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Fukagawa
authors.forename: William C
authors.initials: WC
authors.lastname: Earnshaw
authors.forename: Juri
authors.initials: J
authors.lastname: Rappsilber
mesh_terms: D000818:Animals; D002460:Cell Line; D002868:Chromosomal Proteins, Non-Histone / Q000032:analysis* / Q000378:metabolism; D002875:Chromosomes / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D018386:Kinetochores / Q000378:metabolism; D008938:Mitosis; D040901:Proteomics / Q000379:methods*; D008941:Spindle Apparatus / Q000378:metabolism
chemical_list: D002868:Chromosomal Proteins, Non-Histone
references.citation: Genes Cells. 2007 Mar;12(3):269-84
references.pmid: 17352734
references.citation: Chromosoma. 2005 Feb;113(7):385-97
references.pmid: 15609038
references.citation: Nat Rev Mol Cell Biol. 2008 Jan;9(1):33-46
references.pmid: 18097444
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Anal Chem. 2003 Feb 1;75(3):663-70
references.pmid: 12585499
references.citation: EMBO J. 2009 May 20;28(10):1442-52
references.pmid: 19360002
references.citation: J Cell Biol. 2002 May 27;157(5):749-60
references.pmid: 12034769
references.citation: Curr Biol. 2004 Apr 6;14(7):611-7
references.pmid: 15062103
references.citation: BMC Genomics. 2008 Feb 27;9:102
references.pmid: 18304323
references.citation: Chromosoma. 2005 Dec;114(6):377-88
references.pmid: 16136320
references.citation: Cell. 2008 Dec 12;135(6):1039-52
references.pmid: 19070575
references.citation: Mol Cell Biol. 1993 Aug;13(8):4884-93
references.pmid: 8336724
references.citation: Annu Rev Biophys Biomol Struct. 2000;29:291-325
references.pmid: 10940251
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references.pmid: 19920124
references.citation: J Cell Biol. 2009 Jul 27;186(2):173-82
references.pmid: 19620631
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10484-9
references.pmid: 20483991
references.citation: Dev Cell. 2003 Aug;5(2):323-36
references.pmid: 12919682
references.citation: Nature. 2008 Oct 30;455(7217):1251-4
references.pmid: 18820680
references.citation: J Mol Biol. 2000 May 5;298(3):521-37
references.pmid: 10772867
references.citation: Mol Cell. 2009 Oct 23;36(2):290-301
references.pmid: 19854137
references.citation: J Mol Biol. 2000 Sep 8;302(1):205-17
references.pmid: 10964570
references.citation: Cell. 1997 Nov 14;91(4):491-500
references.pmid: 9390558
references.citation: J Biol Chem. 2010 Mar 26;285(13):9322-9326
references.pmid: 20129925
references.citation: Mol Biol Cell. 2008 May;19(5):2300-10
references.pmid: 18305100
references.citation: Mol Cell. 1999 Jul;4(1):21-33
references.pmid: 10445024
references.citation: Nature. 2010 Apr 1;464(7289):721-7
references.pmid: 20360735
references.citation: Cell. 2009 Jan 9;136(1):175-86
references.pmid: 19135898
references.citation: Dev Cell. 2009 Mar;16(3):374-85
references.pmid: 19289083
references.citation: Mol Biol Cell. 2009 May;20(9):2371-80
references.pmid: 19261808
references.citation: Nat Biotechnol. 2008 Dec;26(12):1367-72
references.pmid: 19029910
references.citation: J Biol Chem. 2005 Apr 29;280(17):16994-7004
references.pmid: 15687487
references.citation: BMC Bioinformatics. 2005 Apr 27;6:108
references.pmid: 15857510
references.citation: J Cell Sci. 2010 May 15;123(Pt 10):1623-33
references.pmid: 20392738
references.citation: Dev Cell. 2009 Jan;16(1):105-17
references.pmid: 19154722
references.citation: J Cell Sci. 2009 Jul 15;122(Pt 14):2436-45
references.pmid: 19549680
references.citation: Nat Cell Biol. 2004 Nov;6(11):1135-41
references.pmid: 15502821
references.citation: J Mol Evol. 2003 May;56(5):527-39
references.pmid: 12698291
references.citation: Nature. 2003 Dec 4;426(6966):570-4
references.pmid: 14654843
references.citation: J Chromatogr A. 2002 Dec 6;979(1-2):233-9
references.pmid: 12498253
references.citation: Bioinformatics. 2004 Oct 12;20(15):2479-81
references.pmid: 15073010
references.citation: Science. 2010 Apr 30;328(5978):593-9
references.pmid: 20360068
references.citation: BMC Bioinformatics. 2007 Mar 05;8:73
references.pmid: 17338813
references.citation: Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41
references.pmid: 11517324
references.citation: Science. 2003 Sep 5;301(5638):1380-2
references.pmid: 12958361
references.citation: J Cell Biol. 2007 Oct 22;179(2):187-97
references.pmid: 17938248
references.citation: Nat Struct Mol Biol. 2005 Dec;12(12):1064-71
references.pmid: 16299513
references.citation: Nat Cell Biol. 2006 May;8(5):458-69
references.pmid: 16622419
references.citation: Proc Natl Acad Sci U S A. 2003 May 13;100(10):5813-8
references.pmid: 12724530
references.citation: Mol Cell Proteomics. 2002 May;1(5):376-86
references.pmid: 12118079
references.citation: Nature. 2006 Sep 7;443(7107):101-5
references.pmid: 16943775
references.citation: Nucleic Acids Res. 2002 Dec 1;30(23):5318-27
references.pmid: 12466558
references.citation: Nat Protoc. 2006;1(6):2856-60
references.pmid: 17406544
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D142-4
references.pmid: 14681379
references.citation: Proteins. 2003 Feb 1;50(2):177-83
references.pmid: 12486711
references.citation: Proteomics. 2007 Dec;7(24):4511-27
references.pmid: 18022940
references.citation: EMBO J. 2009 May 20;28(10):1453-65
references.pmid: 19387489
references.citation: Cell. 1982 May;29(1):171-81
references.pmid: 7105181
references.citation: Mol Cell Proteomics. 2005 Sep;4(9):1265-72
references.pmid: 15958392
references.citation: J Biol Chem. 2010 May 21;285(21):15966-77
references.pmid: 20332092
references.citation: Curr Biol. 2009 Sep 15;19(17):1467-72
references.pmid: 19646878
references.citation: J Cell Biol. 2010 May 17;189(4):739-54
references.pmid: 20479470
references.citation: Nat Cell Biol. 2006 May;8(5):446-57
references.pmid: 16622420
references.citation: Genome Res. 2002 Aug;12(8):1231-45
references.pmid: 12176931
references.citation: Chromosoma. 1985;91(3-4):313-21
references.pmid: 2579778