Mechanisms for controlling gene expression during zebrafish heart regeneration

Cardiovascular disease is the leading cause of death worldwide, due in large part to the inability of human cardiomyocytes (CMs) to proliferate and replace damaged tissue.  Instead, human CMs undergo hypertrophy and become polyploid after injury which actively impedes regeneration.  Unlike humans, zebrafish can completely regenerate cardiac tissues through robust CM proliferation.  Retinoic acid (RA) was recently established as a master regulator of regeneration. RA is robustly induced in zebrafish hearts but barely activated in mammals: a key mechanistic distinction between regenerative and non-regenerative species. 

Thousands of transcriptional enhancers emerge during zebrafish heart regeneration, but their origins and how they coordinate the regenerative gene expression program remain unknown. We identified a cardiac enhancer called REN that regulates runx1, a conserved transcription factor implicated in cardiac biology.  REN is active near cardiac valves and at the injury site during regeneration.  Delta-REN causes excess collagen around valves and decreased adamts1 expression; this phenotype is complemented by delta-runx1, indicating REN and runx1 function in different pathways in uninjured hearts.  During regeneration, delta-REN impairs runx1 expression, and both delta-REN and delta-runx1 mutants exhibit increased CM proliferation, suggesting that the REN-runx1 axis acts as a rheostat of tissue proliferation.  This also demonstrates that REN likely switches to regulate different genes.

RA signaling is required for CM proliferation during heart regeneration, yet how RA creates this permissive state is unknown. In zebrafish embryos, RA rewires interactions between enhancers and genes.  REN activity is also dependent on RA suggesting RA is doing something similar between adamts1 and runx1 during regeneration. We propose that RA drives enhancer rewiring to activate regenerative gene programs in the heart.