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Mass Spectrometry to Study Chromatin Compaction

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Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Department of System & Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
*
Author to whom correspondence should be addressed.
Biology 2020, 9(6), 140; https://doi.org/10.3390/biology9060140
Received: 1 June 2020 / Revised: 19 June 2020 / Accepted: 23 June 2020 / Published: 26 June 2020
(This article belongs to the Special Issue Chromatin Dynamics)
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease. View Full-Text
Keywords: chromatin; DNA methylation; histone; mass spectrometry; post-translational modification; proteome chromatin; DNA methylation; histone; mass spectrometry; post-translational modification; proteome
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MDPI and ACS Style

Stransky, S.; Aguilan, J.; Lachowicz, J.; Madrid-Aliste, C.; Nieves, E.; Sidoli, S. Mass Spectrometry to Study Chromatin Compaction. Biology 2020, 9, 140.

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