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Control of Cardiac Gene Expression by Chromatin Architectural Proteins: Mechanisms at the Level of Chromatin Fiber, Transcriptome Remodeling and Cellular Phenotype

  • Author(s): Monte, Emma Marie
  • Advisor(s): Vondriska, Thomas M
  • et al.
Abstract

When faced with chronic stress, the heart enters a compensatory hypertrophic stage; without intervention it eventually succumbs to decompensation marked by a dilated left ventricular chamber and decreased ejection fraction. While the morphological cardiac remodeling that occurs during the progression of heart failure is well characterized, the exact molecular cause for this gradual switch to failure is not known. In addition to the numerous alterations in signaling pathways, a conserved switch in the transcriptome, known as the fetal gene program, occurs during hypertrophy as a protective effort to sustain contractility by reverting to fetal isoforms of metabolic, contractile and calcium handling genes. We hypothesize that the reproducible, coordinated reprogramming of gene expression is orchestrated by a change in chromatin structure that enables pathologic gene expression.

To determine the proteins involved in repackaging chromatin during cardiac pathology, we performed quantitative proteomic analyses of nuclear proteins in a mouse model of pressure overload hypertrophy and failure. Among the hundreds of proteins we measured on chromatin, my subsequent analyses have focused on two candidates that had the potential to alter gene expression by directly affecting chromatin packing. The first was Nucleolin, a major component of the nucleolus where it mediates ribosomal biogenesis. Using isolated myocytes and the developing zebrafish embryo, we uncovered a role for Nucleolin to regulate cardiac looping, with its effect on hypertrophy context dependent, such that in isolated myoctyes knockdown can promote pathologic gene expression, but loss of Nucleolin during development does not alter myocyte size, instead affecting differentiation along the cardiac lineage.

The second protein I functionally validated was High mobility group protein B2 (HMGB2), a non-histone chromatin structural protein that increases 3-fold in our proteomic analyses. We show that HMGB2 is necessary for ribosomal RNA transcription and is enriched in the nucleolus in hypertrophy; however, overexpression of HMGB2 shuts down transcription globally by compacting DNA. Furthermore, we find HMGB2 knockdown alters the chromatin environment of individual gene promoters in the same manner as hypertrophic agonist signaling in isolated myocytes. Finally, we find that the effect of HMGB2 abundance on the expression of individual genes can be partially explained by the chromatin context, and specifically identify a novel relationship between HMGB2 and CTCF. These studies add to the growing body of work characterizing chromatin remodeling in hypertrophy, and demonstrate that this remodeling extends outside of gene bodies and promoters. Finally, this work begins to uncover what features of chromatin are responsible for tailoring the effects of ubiquitous chromatin proteins toward a cell-type specific outcome.

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