Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer
Malou van den Boogaard, … , Phil Barnett, Vincent M. Christoffels
Malou van den Boogaard, … , Phil Barnett, Vincent M. Christoffels
Published June 18, 2012
Citation Information: J Clin Invest. 2012;122(7):2519-2530. https://doi.org/10.1172/JCI62613.
View: Text | PDF
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

×

Figure 1

In vitro validation of ChIP-seq datasets.

Options: View larger image (or click on image) Download as PowerPoint
In vitro validation of ChIP-seq datasets. (A) Overlap of all ChIP-seq bi...
(A) Overlap of all ChIP-seq binding regions with genes in refGene plus their promoters, defined here as the 1-kb upstream region of those genes. Values are percentage of all peaks. See Methods for a detailed description of peak definition. (B) Results obtained from the MEME motif discovery analysis. Binding motifs were in good agreement with those recently published for the HL-1 based ChIP-seq (35) and JASPAR motifs. (C) Number of overlapping binding regions between heart-derived ChIP-seq datasets. (D) ChIP-qPCR assay validating ChIP-seq peaks. Regions were randomly chosen from the group of ChIP-seq peaks that showed overlap between ChIP sequencing datasets for TBX3, GATA4 and NKX2-5. Shown is enrichment relative to Hprt for NKX2-5, GATA4, and TBX5 in WT adult mouse hearts and for TBX3 in TBX3-induced adult hearts. Ratios below represent the proportion of peaks that showed relative enrichment of more than 10. (E) Of the regions tested with ChIP-qPCR, 11 were tested for their response to NKX2-5, GATA4, and TBX5 or TBX3 in Cos7 cells. All enhancers responded to stimulation with GATA4 and NKX2-5. *P < 0.05.