Unraveling the evolutionary origin of the complex Nuclear Receptor Element (cNRE), a cis-regulatory module required for preferential expression in the atrial chamber

Abstract

Abstract Optimal cardiac function requires appropriate contractile proteins in each heart chamber. Atria require slow myosins to act as variable reservoirs, while ventricles demand fast myosin for swift pumping functions. To achieve this functional distribution, myosins are thus under chamber-biased cis-regulatory control, with a failure in proper regulation of myosin genes leading to severe congenital heart dysfunction. However, the precise regulatory input leading to cardiac chamber-biased expression remains uncharted. To address this, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential gene expression to the atria to define the regulatory information leading to chamber expression and understand its evolutionary origins. We show that SMyHC III gene states are autonomously orchestrated by a complex Nuclear Receptor Element (cNRE), a 32-bp DNA sequence with hexanucleotide binding repeats. Using in vivo transgenic assays in zebrafish and mouse models, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we provide evidence that the cNRE might have emerged from an endogenous viral element, most likely through infection of an ancestral host germline. Our study hence reveals an evolutionary pathway to cardiac chamber-specific expression.