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The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

2010; Cell Press; Volume: 142; Issue: 5 Linguagem: Inglês

10.1016/j.cell.2010.07.047

1097-4172

Shinya Ohta, Jimi Wills, Luis Sánchez‐Pulido, Flávia de Lima Alves, Laura Wood, Zhuo A. Chen, Melpomeni Platani, Lutz Fischer, Damien F. Hudson, Chris P. Ponting, Tatsuo Fukagawa, William C. Earnshaw, Juri Rappsilber,

Ubiquitin and proteasome pathways

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.