Advisor(s)

Jianyi Zhang
Manuel Rosa-Garrido

Committee Member(s)

Isidoro Cobo
Suresh Verma
Thanh Nguyen
Yuji Nakada

Document Type

Dissertation

Date of Award

1-29-2026

Degree Name

Doctor of Philosophy (PhD)

School

Joint Health Sciences (Interdisciplinary)

Department

Biomedical Engineering

Abstract

Chromatin structure is a central regulator of gene expression and cellular identity, yet the chromatin structural factors driving cardiac disease and regeneration remain incompletely defined. This dissertation investigates how modulation of chromatin architecture shapes pathological and regenerative cardiac phenotypes through integrated single-cell transcriptomic, epigenomic, and functional analyses. To determine whether chromatin structural regulators distinguish healthy from diseased cardiac states, we curated a comprehensive list of chromatin structural genes and applied it to single-nuclei RNA sequencing datasets from human hearts with and without dilated cardiomyopathy (DCM). Chromatin structural gene expression effectively stratified cardiomyocyte and fibroblast populations by disease status. Diseased cardiomyocytes exhibited reduced expression of contractile genes and increased cardiomyopathy markers, while fibroblasts displayed activated phenotypes. Among these regulators, HMGN3 was consistently downregulated in DCM patients and in mouse pressure overload and pig myocardial infarction models. Functional studies in AC16 cardiomyocyte-like cells showed that HMGN3 depletion promotes apoptosis, alters transcriptional programs, and reorganizes chromatin accessibility, including redistribution of H3K27ac, identifying HMGN3 as a regulator of chromatin structure in the diseased heart. In parallel, this work examines chromatin architecture during cardiomyocyte proliferation and regeneration. Reanalysis of mouse and pig single-nuclei RNA sequencing datasets using cell cycle– and chromatin structural factor–specific autoencoders identified a conserved proliferative cardiomyocyte population following injury. Gene ontology analyses revealed coordinated activation of cell-cycle and chromatin remodeling pathways. Cross-species comparisons uncovered a conserved chromatin structural signature associated with cardiomyocyte proliferation, among which CTCF emerged as a key regulator. CTCF expression declined after birth but was reactivated after injury, and its overexpression promoted cardiomyocyte-like cell proliferation accompanied by redistribution of CTCF binding at cell-cycle regulatory loci. Together, these findings demonstrate that chromatin structural regulators play critical roles in cardiac disease progression and regenerative competence and identify HMGN3 and CTCF as key modulators of chromatin architecture in pathological remodeling and cardiomyocyte proliferation.

ProQuest Publication Number

32404755

ISBN

9798273398719

Download

Share

COinS