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Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics
Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, Milan 20139, Italy
* Author to whom correspondence should be addressed.
Received: 7 November 2012; in revised form: 24 January 2013 / Accepted: 20 February 2013 / Published: 6 March 2013
Abstract: Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs) and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS) has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.
Keywords: chromatin; histone post-translational modifications (hPTMs); combinatorial modifications; epigenetics; mass spectrometry; proteomics; SILAC; histone code readers; histone variants
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Soldi, M.; Cuomo, A.; Bremang, M.; Bonaldi, T. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics. Int. J. Mol. Sci. 2013, 14, 5402-5431.
Soldi M, Cuomo A, Bremang M, Bonaldi T. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics. International Journal of Molecular Sciences. 2013; 14(3):5402-5431.
Soldi, Monica; Cuomo, Alessandro; Bremang, Michael; Bonaldi, Tiziana. 2013. "Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics." Int. J. Mol. Sci. 14, no. 3: 5402-5431.