The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

Shinya Ohta, Jimi-Carlo Bukowski-Wills, Luis Sanchez-Pulido, Flavia de Lima Alves, Laura Wood, Zhuo A. Chen, Melpi Platani, Lutz Fischer, Damien F. Hudson, Chris Ponting, Tatsuo Fukagawa, William C. Earnshaw, Juri Rappsilber

Research output: Contribution to journalArticlepeer-review

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 similar to 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 similar to 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.

Original languageEnglish
Pages (from-to)810-821
Number of pages12
JournalCell
Volume142
Issue number5
DOIs
Publication statusPublished - 3 Sep 2010

Keywords

  • HUMAN METAPHASE CHROMOSOMES
  • OUTER KINETOCHORE
  • QUANTITATIVE PROTEOMICS
  • CELL-DIVISION
  • IN-VIVO
  • CENP-A
  • COMPLEX
  • REVEALS
  • IDENTIFICATION
  • QUANTIFICATION

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