Abstract
Cellular localization and activity of most proteins are highly dependent on the formation of complexes with other proteins and/or other biomolecules. Moreover, protein–protein interactions and the nature of the complexes formed are modulated in cell differentiation, de-differentiation, and carcinogenesis. Therefore, identification of protein interactors is essential to the understanding of protein biological activity in given cell states. Formation of DNA-binding complexes implicating proteins such as DNA repair enzymes, DNA- and histone-modifying enzymes, transcription factors, and gene activators, repressors, and silencers greatly affect DNA integrity and gene expression associated with multiple processes including cellular division and cancer development and progression. Protein–protein interaction mapping proved to be particularly difficult for chromatin-bound protein complexes due to the insolubility of these high molecular weight biomolecule assemblies. Recently, DNA-based methods were developed to isolate DNA-bound protein complexes formed at a specific locus. Techniques were also developed to purify the breath of proteins associated with a particular protein target using modified chromatin immunoprecipitation. The isolated proteins are then identified by tandem mass spectrometry and protein complexes are represented using dedicated softwares. In this chapter, we present the recently developed methods allowing for the isolation and identification of chromatin-bound protein complexes and to assign biological functions to these biomolecule. We also discuss the future challenges in the field of chromatin-bound protein interactor isolation and identification.
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Abbreviations
- CENPA:
-
Centromer protein A
- ChAP-MS:
-
Chromatin affinity purification with mass spectrometry
- CTCF:
-
CCCTC-binding factor
- E-MAP:
-
Epistasis mini-array profile
- GENECAPP:
-
Global exonuclease-based enrichment of chromatin-associated proteins for proteomics
- H3K4me3:
-
Histone H3 lysine 4 (K4) tri-methylation (me3)
- HJURP:
-
Holliday junction recognition protein
- HSP90:
-
Heat shock protein 90
- Kog1p:
-
Kontrol of growth protein
- Lge1p:
-
Depletion of large cell 1
- MChIP:
-
Modified chromatin immunoprecipitation
- NPM1:
-
Nnucleophosmin1
- PICh:
-
Proteomics of isolated chromatin segment
- SMYD2:
-
SET and MYND-containing protein 2.
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Acknowledgments
D.F. Acknowledges a Canada Research Chair in Proteomics and Systems Biology.
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Doucet, A., Figeys, D. (2014). Identification of Chromatin-Binding Protein Complexes. In: Emili, A., Greenblatt, J., Wodak, S. (eds) Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7931-4_6
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DOI: https://doi.org/10.1007/978-1-4614-7931-4_6
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