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Genome-Wide Analysis Identifies an Essential Human TBX3 Pacemaker Enhancer.

Vincent W W van Eif1, Stephanie I Protze2, Fernanda M Bosada1

  • 1Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam (V.W.W.v.E., F.M.B., K.v.D., R.A.M., V.W., C.d.G.-d.V., I.B.H., A.O.V., B.J.B., V.M.C.).

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|October 12, 2020
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Summary

Researchers identified regulatory DNA elements controlling heart pacemaker cells. Genetic variants linked to heart rate recovery were found to influence TBX3 expression in these crucial cells.

Keywords:
geneticsheart ratehumanmyocyte, cardiacstem cell

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Area of Science:

  • Cardiovascular Biology
  • Genomics
  • Epigenetics

Background:

  • Sinoatrial node (SAN) pacemaker cell development and function are regulated by transcription factors like TBX3, ISL1, and SHOX2.
  • The specific regulatory DNA elements (REs) governing gene expression in SAN pacemaker cells remain largely undefined.

Purpose of the Study:

  • To identify the regulatory landscape of human SAN-like pacemaker cells.
  • To functionally assess SAN-specific REs involved in pacemaker cell gene regulation.

Main Methods:

  • Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed on human pluripotent stem cell-derived SAN-like and ventricle-like cells.
  • CRISPR-mediated deletion of mouse orthologs of candidate REs in the SHOX2 and TBX3 loci.
  • Functional assessment in transgenic mouse embryos and adult mice.

Main Results:

  • Thousands of putative REs specific to human SAN-like or ventricle-like cells were identified.
  • Deletion of a SHOX2 locus RE caused selective loss of Shox2 expression in the developing SAN, leading to embryonic lethality.
  • Deletion of a TBX3 locus RE, harboring variants associated with heart rate recovery, caused selective loss of Tbx3 expression in the SAN and cardiac ganglia, resulting in neonatal lethality and altered heart rate recovery in adult mice.

Conclusions:

  • A genome-wide collection of candidate human pacemaker-specific REs, including those near SHOX2, TBX3, and ISL1, was established.
  • A functional link between human genetic variants affecting heart rate recovery and a conserved RE driving TBX3 expression in the SAN was identified.