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Proteomics of a fuzzy organelle: interphase chromatin
Author(s) -
Kustatscher Georg,
Hégarat Nadia,
Wills Karen L H,
Furlan Cristina,
BukowskiWills JimiCarlo,
Hochegger Helfrid,
Rappsilber Juri
Publication year - 2014
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1002/embj.201387614
Subject(s) - library science , sociology , history , biology , art history , classics , computer science
Chromatin proteins mediate replication, regulate expression, and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle, it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead, we propose a new approach that provides a quantitative assessment of a protein's probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. We demonstrate the power of our large‐scale data‐driven annotation during the analysis of cyclin‐dependent kinase ( CDK ) regulation in chromatin. Quantitative protein ontologies may provide a general alternative to list‐based investigations of organelles and complement Gene Ontology.