Dissecting gene regulatory networks and regeneration enhancer elements for zebrafish heart regeneration

PROJECT SUMMARY/ABSTRACT Adult mammals poorly regenerate injured hearts. In contrast, adult zebrafish possess a remarkable capacity to regenerate damaged hearts. Combined with available genetic tools, this capacity makes zebrafish a powerful system for deciphering the innate mechanisms underlying heart regeneration. In the previous funding period, our laboratory uncovered that interleukin11a (il11a) signaling plays dual roles as a regenerative and fibrotic factor in adult zebrafish hearts. We demonstrated that these opposite outcomes are caused by cell-type-dependent effects. By integrating epigenome and transcriptome analyses with transgenic assays, we also identified the importance of enhancer and promoter pairing in transcriptional activation and cell types emerging in regenerating hearts and their molecular identity. However, critical gaps remain in our understanding regeneration-associated genetic and epigenetic mechanisms. First, we know little about transcriptional regulators of il11 signaling responsible for regenerative processes. Second, while numerous cardiac regeneration enhancers have been discovered, we still lack a comprehensive understanding of how DNA sequences and their composition encode regeneration-dependent expression. Third, there is a need to delineate the differences between injury- and regeneration-associated gene regulatory networks. The current application aims to address these central questions using cutting-edge genetic and epigenetic analysis tools. We hypothesize that a cardiac mitogen activates dedicated cardiac regeneration enhancers to initiate the repair process. In Aim 1, we will elucidate transcription factors (TFs) mediating il11a-triggered cardiomyocyte (CM) proliferation and related gene regulatory networks (GRNs). Epigenome and biochemical analyses with zebrafish genetic models will identify the foxm1/e2f8/mybl2b/znf367 complex and their related GRNs as key players for CM proliferation. In Aim 2, we will define a cluster of cardiac regeneration enhancers (regeneration-cistrome) that ensures precise transcriptional control of the regeneration response. Our computational analyses with zebrafish transgenic and regeneration assays will identify enhancer logics of cardiac regeneration enhancers and related cistrome in the zebrafish genome. In Aim 3, we will employ zebrafish genetic models and CUT&Tag approaches to identify regeneration-dedicated enhancers to discriminate injury and regeneration processes. Overall, this project will articulate TF networks and epigenetic factors for heart regeneration, illuminating innate mechanisms promoting heart repair and uncovering strategies for mammalian heart repair.