2024 AIChE Annual Meeting
(132d) Single Base-Pair Changes within Heart Enhancers Increase Transcription Factor Binding Affinity and Disrupt Embryonic Heart Development
Authors
Alexis Bantle, University of California, San Diego
Joe Solvason, University of California, San Diego
Jessica Grudzien, University of California, San Diego
Agnieszka D'Antonio-Chronowska, University of California, San Diego
Fabian Lim, University of California, San Diego
Sophia Le, University of California, San Diego
Benjamin Song, University of California, San Diego
Michelle Ragsac, University of California, San Diego
Adam Klie, University of California, San Diego
Reid Larsen, University of California, San Diego
Kelly Frazer, University of California, San Diego
Emma Farley, University of California, San Diego
Transcriptional enhancers direct precise gene expression patterns during embryonic development, upon binding of transcription factors. Enhancers harbor the majority of variants associated with phenotypic diversity, evolutionary adaptations, and disease, but pinpointing which enhancer variants contribute to changes in gene expression and phenotypes is a major challenge. Here we find that low-affinity transcription factor binding sites are necessary for precise gene expression during heart development. Strikingly, in Ciona robusta embryos, we find that single base-pair changes can optimize the binding affinity of ETS binding sites, causing excess gene expression, cell migration defects, and phenotypes as severe as an extra beating heart. Mouse and human developmental heart enhancers also contain low-affinity transcription factor binding sites that are likely important for encoding precise gene expression patterns. Indeed, in human induced pluripotent stem cell-derived cardiomyocytes, a single base-pair change within a GATA4 enhancer increases ETS transcription factor binding affinity and causes excess enhancer activity. Our work illustrates a potential vulnerability in genomes created by the prevalence of low-affinity transcription factor binding sites, namely that single base-pair affinity-optimizing variants within enhancers can lead to excess gene expression and changes in cellular identity and organismal-level phenotypes. Understanding how tissue-specific enhancers in genomes encode specificity could inform the design of synthetic tissue-specific enhancers.