Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development

Transcriptional enhancers direct precise gene expression patterns during development and harbor the ma-jority of variants associated with phenotypic diversity, evolutionary adaptations, and disease. Pinpointing which enhancer variants contribute to changes in gene expression and phenotypes is a major challenge. Here, we find that suboptimal or low-affinity binding sites are necessary for precise gene expression during heart development. Single-nucleotide variants (SNVs) can optimize the affinity of ETS binding sites, causing gain-of-function (GOF) gene expression, cell migration defects, and phenotypes as severe as extra beating hearts in the marine chordate Ciona robusta. In human induced pluripotent stem cell (iPSC)-derived cardio-myocytes, a SNV within a human GATA4 enhancer increases ETS binding affinity and causes GOF enhancer activity. The prevalence of suboptimal-affinity sites within enhancers creates a vulnerability whereby affinity -optimizing SNVs can lead to GOF gene expression, changes in cellular identity, and organismal-level pheno-types that could contribute to the evolution of novel traits or diseases.

Automated summary

Transcriptional enhancers play a crucial role in directing precise gene expression patterns during development. Suboptimal or low-affinity binding sites are necessary for precise gene expression during heart development. Single-nucleotide variants (SNVs) can optimize the affinity of ETS binding sites and lead to gain-of-function (GOF) gene expression and phenotypic changes.