Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming

Ectopic expression of combinations of transcription factors (TFs) can drive direct lineage conversion, thereby reprogramming a somatic cell’s identity. To determine the molecular mechanisms by which Gata4, Mef2c, and Tbx5 (GMT) induce conversion from a cardiac fibroblast toward an induced cardiomyocyte, we performed comprehensive transcriptomic, DNA-occupancy, and epigenomic interrogation throughout the reprogramming process. Integration of these datasets identified new TFs involved in cardiac reprogramming and revealed context-specific roles for GMT, including the ability of Mef2c and Tbx5 to independently promote chromatin remodeling at previously inaccessible sites. We also find evidence for cooperative facilitation and refinement of each TF’s binding profile in a combinatorial setting. A reporter assay employing newly defined regulatory elements confirmed that binding of a single TF can be sufficient for gene activation, suggesting that co-binding events do not necessarily reflect synergy. These results shed light on fundamental mechanisms by which combinations of TFs direct lineage conversion. [Display omitted] •Integrated scRNA-, ATAC-, and ChIP-seq analyses to interrogate cardiac reprogramming•Gata4, Mef2c, and Tbx5 both facilitate and limit one another's ability to bind to DNA•Mef2c and Tbx5 bind to inaccessible chromatin and promote its remodeling•Context-specific cooperative mechanisms guide cardiac reprogramming Srivastava and colleagues integrate multiple (epi)genomic assays to dissect the mechanisms by which transcription factors function independently and combinatorially to initiate cell fate transitions. Heterogeneous binding relationships between Gata4, Mef2c, and Tbx5 highlight the context-specific mechanisms that dictate cardiac reprogramming.