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

TL;DR

This study identifies a 32-base-pair element in a quail gene that evolved from a viral infection and controls atrial-specific protein expression in the heart.

Contribution

The study reveals the evolutionary origin of a cis-regulatory module from a viral element that drives chamber-specific gene expression in the heart.

Findings

The cNRE element controls preferential atrial expression of the SMyHC III gene.

The cNRE evolved from an endogenous viral element in an ancestral host germline.

Atrial activation and ventricular repression motifs work together to achieve chamber-specific expression.

Abstract

Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, 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 show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.

A complex Nuclear Receptor Element (cNRE) of 32 base pairs that emerged from a viral infection drives the quail Slow Myosin Heavy Chain III (SMyHC III) promoter preferential expression to the atria.

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