Opposing CTCF and GATA4 activities set the pace of chromatin topology remodeling during cardiomyogenesis

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Abstract
SUMMARY: Reorganization of the three-dimensional chromatin structure is a critical feature of human embryonic development. Yet, the mechanisms regulating integrative remodelling of local structures (e.g., loops) and global architecture (e.g., A/B compartmentalization) remain un-clear. Here, we investigate this aspect in the context of cardiomyogenesis, characterized by pronounced B-to-A remodelling of several cardiac-specific genes such as TTN . We focus on the roles of the pioneer transcription factor GATA4 and the architectural protein CTCF. Using an inducible knockdown system during human induced pluripotent stem cell differ-entiation, we show that GATA4 is essential for timely topological activation of key cardiac genes, while partial depletion of CTCF, anticipating physiological downregulation during de-velopment, enhances this process. Deletion of a single CTCF binding site on TTN leads to modest gene decompaction and transcriptional activation. Bulk and single-cell RNA se-quencing of chamber-specific cardiac organoids reveals that loss of GATA4 delays differ-entiation and sustains proliferation of early cardiomyocytes, whereas premature CTCF de-pletion accelerates yet alters cardiomyocyte maturation. These findings suggest that CTCF and GATA4 have antagonistic roles on chromatin dynamics during cardiomyogenesis, form-ing a rheostat that maintains accurate developmental tempo. Disruption of this mecha-nism may contribute to congenital heart defects caused by mutations in these factors.
Funding Information
  • Federation of European Biochemical Societies (Excellence Award 2022)
  • Additional Ventures (Single Ventricle Research Fund 2022)

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