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Genes not previously associated with congenital heart disease have been linked to such conditions, according to new findings from a multi-center study. The researchers also shed new light on the role of CHD4 in inborn heart disease.

This work was led by Frank Conlon, PhD, professor of biology and genetics at the University of North Carolina at Chapel Hill. The study was published this month in Genes & Development.

The team’s results, they write, “Delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.”

Scientists have long known that mutations to three cardiac transcription factors—GATA4, NKX2-5 and TBX5—lead to a range of congenital heart disease states, including atrial and septal defects.

But besides transcription factors, the protein complex subunit CHD4 seems to play a major role in causing such conditions. Chromodomain helicase DNA-binding protein 4 (CHD4) is the catalytic component of NuRD, the nucleosome remodeling and deacetylase (NuRD) complex, which is one of the central chromatin remodeling complexes mediating gene repression. NuRD is essential for numerous developmental events, including heart development.

CHD4 also plays a key role in numerous developmental events, such as ensuring proper timing of the switch from stem cell lineages to differentiated cell types, e.g. heart cells or leg muscle cells. In particular CHD4 is essential for mammalian cardiomyocyte formation and function. Deleting CHD4 causes embryonic death in animal models. Mutations to it cause major problems with proteins involved in skeletal and muscle development.

A long unresolved scientific question has been how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. CDH4 needs to be brought to a specific genetic loci of a cardiac gene to have its effects.

Conlon’s lab, in collaboration with colleagues at UNC-Chapel Hill, Princeton, and Boston Children’s Hospital, used bioinformatics and mass spectrometry to show that GATA4, NKX2-5 and TBX5 interact with and recruit the subunit for action CHD4 inside the embryonic heart.

Using transcriptomics and genome-wide occupancy data, the team characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4–CHD4, NKX2-5–CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes.

Their findings imply congenital heart disease is not only due to loss of cardiac gene expression, but that these genes’ recruitment of CHD4 can lead to a misexpression of non-cardiac genes, leading to faulty heart development.

To test this hypothesis, Conlon and his collaborators removed the binding site for Nkx2-5 in the skeletal muscle gene Acta1 in mice and, independently, the GATA4 binding site in the smooth muscle gene Myh11.

“In both instances, the mutation led to the inappropriate expression of the non-cardiac genes in the heart in a dominant manner,” said Conlon, a member of the UNC McAllister Heart Institute. “This provides a mechanism for the prevalence of congenital heart disease in humans with just one mutated copy of Nkx2-5, Gata4 or Tbx5.”

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