Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer
Malou van den Boogaard, L.Y. Elaine Wong, Federico Tessadori, Martijn L. Bakker, Lisa K. Dreizehnter, Vincent Wakker, Connie R. Bezzina, Peter A.C. ‘t Hoen, Jeroen Bakkers, Phil Barnett, Vincent M. Christoffels
Malou van den Boogaard, L.Y. Elaine Wong, Federico Tessadori, Martijn L. Bakker, Lisa K. Dreizehnter, Vincent Wakker, Connie R. Bezzina, Peter A.C. ‘t Hoen, Jeroen Bakkers, Phil Barnett, Vincent M. Christoffels
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Research Article

Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer

Abstract

The contraction pattern of the heart relies on the activation and conduction of the electrical impulse. Perturbations of cardiac conduction have been associated with congenital and acquired arrhythmias as well as cardiac arrest. The pattern of conduction depends on the regulation of heterogeneous gene expression by key transcription factors and transcriptional enhancers. Here, we assessed the genome-wide occupation of conduction system–regulating transcription factors TBX3, NKX2-5, and GATA4 and of enhancer-associated coactivator p300 in the mouse heart, uncovering cardiac enhancers throughout the genome. Many of the enhancers colocalized with ion channel genes repressed by TBX3, including the clustered sodium channel genes Scn5a, essential for cardiac function, and Scn10a. We identified 2 enhancers in the Scn5a/Scn10a locus, which were regulated by TBX3 and its family member and activator, TBX5, and are functionally conserved in humans. We also provided evidence that a SNP in the SCN10A enhancer associated with alterations in cardiac conduction patterns in humans disrupts TBX3/TBX5 binding and reduces the cardiac activity of the enhancer in vivo. Thus, the identification of key regulatory elements for cardiac conduction helps to explain how genetic variants in noncoding regulatory DNA sequences influence the regulation of cardiac conduction and the predisposition for cardiac arrhythmias.

Authors

Malou van den Boogaard, L.Y. Elaine Wong, Federico Tessadori, Martijn L. Bakker, Lisa K. Dreizehnter, Vincent Wakker, Connie R. Bezzina, Peter A.C. ‘t Hoen, Jeroen Bakkers, Phil Barnett, Vincent M. Christoffels

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Figure 3

Scn5a and Scn10a are regulated by TBX3.

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Scn5a and Scn10a are regulated by TBX3. (A) Overview of the ChIP-seq ...
(A) Overview of the ChIP-seq datasets within the Scn5a/Scn10a locus including flanking genes Scn11a and Exog. Top: TBX3, GATA4, NKX2-5, and p300 datasets (present study). Bottom: published ChIP-seq datasets showing tracks for biotinylated TBX5, GATA4, and NKX2-5 expressed in HL-1 cells (35); P300 in ED11.5 embryonic mouse heart (34); and P300 and POL2 in adult mouse heart (37). (B) In situ hybridization of Scn5a and Scn10a in E14.5 WT hearts showing expression pattern overlap, and the resemblance of the Scn5a downstream enhancer fragment F9 (F9 LacZ) with these expression patterns. Arrows denote areas of highest activity, in the atrial body and future ventricular conduction system components. san, sinoatrial node; ra, right atrium; la, left atrium; rv, right ventricle; lv, left ventricle; ivs, interventricular septum; drg, dorsal root ganglion. (C) In situ hybridization of Scn5a and Scn10a in the E17.5 sinoatrial node region showing complementary patterns to Tbx3 and partial overlap with Tbx5. Dotted outlines denote the sinus node region. Original magnification, ×5 (B); ×10 (B, insets, and C).