Quantitative Analysis of the Chromatin Proteome in Disease Reveals Remodeling Principles and Identifies High Mobility Group Protein B2 as a Regulator of Hypertrophic Growth

Thomas M. Vondriska,Scherise Mitchell-Jordan,Haodong Chen,Sarah Franklin,Yibin Wang,Shuxun Ren

doi:10.1074/mcp.m111.014258

Thomas M. Vondriska, Scherise Mitchell-Jordan + Show 4 more

Open Access

https://doi.org/10.1074/mcp.m111.014258

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Abstract

A fundamental question in biology is how genome-wide changes in gene expression are enacted in response to a finite stimulus. Recent studies have mapped changes in nucleosome localization, determined the binding preferences for individual transcription factors, and shown that the genome adopts a nonrandom structure in vivo. What remains unclear is how global changes in the proteins bound to DNA alter chromatin structure and gene expression. We have addressed this question in the mouse heart, a system in which global gene expression and massive phenotypic changes occur without cardiac cell division, making the mechanisms of chromatin remodeling centrally important. To determine factors controlling genomic plasticity, we used mass spectrometry to measure chromatin-associated proteins. We have characterized the abundance of 305 chromatin-associated proteins in normal cells and measured changes in 108 proteins that accompany the progression of heart disease. These studies were conducted on a high mass accuracy instrument and confirmed in multiple biological replicates, facilitating statistical analysis and allowing us to interrogate the data bioinformatically for modules of proteins involved in similar processes. Our studies reveal general principles for global shifts in chromatin accessibility: altered linker to core histone ratio; differing abundance of chromatin structural proteins; and reprogrammed histone post-translational modifications. Using small interfering RNA-mediated loss-of-function in isolated cells, we demonstrate that the non-histone chromatin structural protein HMGB2 (but not HMGB1) suppresses pathologic cell growth in vivo and controls a gene expression program responsible for hypertrophic cell growth. Our findings reveal the basis for alterations in chromatin structure necessary for genome-wide changes in gene expression. These studies have fundamental implications for understanding how global chromatin remodeling occurs with specificity and accuracy, demonstrating that isoform-specific alterations in chromatin structural proteins can impart these features.

Highlights

From the Departments of ‡Anesthesiology, ¶Medicine/Cardiology, and ࿣Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095
Mass Spectrometric Measurements of the Chromatin Proteome—To investigate changes in chromatin-bound proteins commensurate with global changes in gene expression, adult mice were subjected to cardiac pressure overload by transverse aortic constriction [19], a model that recapitulates the human disease of heart failure, which affects millions of people worldwide [28]
Proteins were separated by SDS-PAGE, in-gel trypsin-digested, and analyzed by quantitative mass spectrometry on an Orbi-trap instrument, and peptide spectra were examined by a combination of traditional database searching (SEQUEST), label-free quantitative analysis using the Elucidator software package [26, 27], and manual inspection

Summary

Introduction

From the Departments of ‡Anesthesiology, ¶Medicine/Cardiology, and ࿣Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095. Mass Spectrometric Measurements of the Chromatin Proteome—To investigate changes in chromatin-bound proteins commensurate with global changes in gene expression, adult mice were subjected to cardiac pressure overload by transverse aortic constriction [19], a model that recapitulates the human disease of heart failure (supplemental Fig. 1), which affects millions of people worldwide [28].

Results

Conclusion