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

ABSTRACT: 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 unclear. 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 differentiation, we show that GATA4 is essential for timely topological activation of key cardiac genes, while partial depletion of CTCF, anticipating physiological downregulation during development, 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 sequencing of chamber-specific cardiac organoids shows that loss of GATA4 delays differentiation and sustains proliferation of early cardiomyocytes, whereas premature CTCF depletion accelerates yet confounds cardiomyocyte maturation. These findings suggest that CTCF and GATA4 have antagonistic roles on chromatin dynamics during cardiomyogenesis, forming a rheostat that maintains accurate developmental tempo. Disruption of this mechanism may contribute to congenital heart defects caused by mutations in these factors. This repository contains the support data files to reproduce the bioinformatic codes deposited in our GitHub. Refer to the README of the GitHub repository for all the details on how to use these supporting data.