Fish-Ing for Enhancers in the Heart

Abstract

Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.

Keywords: enhancers; heart development; heart regeneration; model organism; transcription factors; zebrafish.

Figure 1

Enhancer trapping method. The synthetic transposase mRNA, the transposon donor plasmid containing transposable elements with a minimal promoter, and the gene encoding green fluorescent protein (GFP) are co-injected into fertilized zebrafish eggs. The construct is excised from the donor plasmid and integrated into the endogenous genome. The activity of the “trapped” enhancer can be visualized in the injected embryo when the inserted transgene is expressed under control of nearby enhancers.

Figure 2

Zebrafish gene regulatory programs of heart regeneration. (A,B) Zebrafish mature heart: uninjured, injured heart after ablation, and regenerative heart by cardiomyocyte proliferation. (C) Enhancers that have no detectable activity in uninjured heart direct gene expression during heart regeneration.

Figure 3

Model of enhancer RNA mechanism. (A) Enhancer and gene sequences in chromatin prior to gene activity. (B) Partially or fully assembled sets of TFs can associate with the enhancer and the gene promoter. In the active state, the enhancer and its transcript may physically associate with the gene, triggering formation of a mediator complex [20,21,22,23,24].