Long-range Pitx2c Enhancer-Promoter Interactions Prevent Predisposition to Atrial Fibrillation

Proc Natl Acad Sci U S A. 2019 Nov 5;116(45):22692-22698. doi: 10.1073/pnas.1907418116. Epub 2019 Oct 21.

Abstract

Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia, is associated with noncoding sequence variants located in proximity to PITX2 Cardiomyocyte-specific epigenomic and comparative genomics uncovered 2 AF-associated enhancers neighboring PITX2 with varying conservation in mice. Chromosome conformation capture experiments in mice revealed that the Pitx2c promoter directly contacted the AF-associated enhancer regions. CRISPR/Cas9-mediated deletion of a 20-kb topologically engaged enhancer led to reduced Pitx2c transcription and AF predisposition. Allele-specific chromatin immunoprecipitation sequencing on hybrid heterozygous enhancer knockout mice revealed that long-range interaction of an AF-associated region with the Pitx2c promoter was required for maintenance of the Pitx2c promoter chromatin state. Long-range looping was mediated by CCCTC-binding factor (CTCF), since genetic disruption of the intronic CTCF-binding site caused reduced Pitx2c expression, AF predisposition, and diminished active chromatin marks on Pitx2 AF risk variants located at 4q25 reside in genomic regions possessing long-range transcriptional regulatory functions directed at PITX2.

Keywords: PITX2; atrial fibrillation; epigenetics; genome topology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atrial Fibrillation / genetics*
  • CRISPR-Cas Systems
  • Chromosome Mapping
  • Enhancer Elements, Genetic*
  • Epigenesis, Genetic
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study
  • Homeodomain Proteins / genetics*
  • Mice
  • Mice, Knockout
  • Promoter Regions, Genetic*
  • Transcription Factors / genetics*

Substances

  • Homeodomain Proteins
  • Transcription Factors
  • homeobox protein PITX2