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

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 posttranslational modifications. Using small interfering RNAmediated 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 isoformspecific alterations in chromatin structural proteins can impart these features. Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.014258, 1-12, 2012.Transcriptional regulation must be preceded by nonrandom structural reorganization of the genome, such that stimulusspecific transcriptional regulators are recruited to the correct genomic regions and excluded from the wrong ones. During mitosis, eukaryotic chromosomes adapt an ordered and stunningly reproducible three-dimensional structure. During interphase, however, and in cells that do not divide (such as adult cardiomyocytes and neurons), the structure of the genome is much less clear. Chromosome territories have been described (1) that are thought to facilitate co-localization of similarly regulated genes within the nucleus, and recent advances in chromosomal conformation capture techniques have provided exciting new insights into the global structure of the interphase genome suggesting that the structure resembles a fractal globule (2). However, changes in this structu...

High-mobility group box 2 (HMGB2) modulates radioresponse and is downregulated by p53 in colorectal cancer cell

“…They suggest 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. 37 Finally, like HMGB1, HMGB2 might be involved in regulation of telomerase activity and lead to telomere dysfunction. Knockout of the HMGB1 gene in mouse embryonic fibroblasts results in chromosomal abnormalities, enhanced colocalization of γH2AX foci at telomeres and a moderate shortening of telomere lengths.…”

Reciprocal Regulation of the Cardiac Epigenome by Chromatin Structural Proteins Hmgb and Ctcf

“…Different cell types ought to have different chromatin structure underpinning their different transcriptomes, although most of the knowledge on endogenous chromatin structure (4,14,15) and the non-nucleosome proteins that regulate it (16,17) comes from non-cardiac cells, with some exceptions (18). At the level of the whole nucleus, we have reported a decrease in trimethylation of lysine 9 on histone H3 (H3K9me3), 8 a marker of constitutively silenced DNA (19), and an increase in H3K4me3 abundance, a marker of active expression (20), in failing hearts after transverse aortic constriction (21). Similarly, decreased H3K9me2 and increased H3K4me2 in the heart were observed in a mouse model of diabetes with glomerulosclerosis, a condition that can lead to heart disease in humans and induces hypertrophy of the cardiomyocytes in mice (22).…”

“…Gene Expression-We previously found that hmgb2-regulated genes are enriched in pathways important to cardiac hypertrophy (21). We next asked how Hmgb2 and Ctcf regulate mRNA expression to explain why some hmgb2-regulated genes are up-regulated and others are down-regulated in response to hmgb2 knockdown in cardiomyocytes (21).…”

“…We next asked how Hmgb2 and Ctcf regulate mRNA expression to explain why some hmgb2-regulated genes are up-regulated and others are down-regulated in response to hmgb2 knockdown in cardiomyocytes (21). We used ENCODE date from the adult mouse heart and our Hmgb2 ChIP-seq data.…”

“…We previously found that Hmgb2 abundance is altered in heart disease (21), and in this study we sought to test the molecular mechanisms for its actions at the level of both the chromatin fiber and the entire genome. Herein, we uncover a previously unknown relationship between Hmgb2 and Ctcf, and we use this relationship to explore the role of chromatin architectural proteins in regulating cardiac gene expression in disease.…”