UCSF

Despite numerous advances, direct reprogramming of fibroblasts to induced cardiomyocytes remains an inefficient process with largely unknown underlying mechanisms. To understand the molecular events associated with direct cardiac reprogramming, we characterized genome-wide transcriptional changes in individual and bulk reprogramming cell populations, examined genomic changes in chromatin accessibility and DNA methylation levels during reprogramming, and mapped DNA binding by Gata4, Mef2c, and Tbx5 (GMT) that initiates the transition from fibroblast to induced cardiomyocyte. We discovered that the transition to cardiac-like gene expression occurs within 48 hours of initiating transdifferentiation. This change is accompanied by rapid epigenomic remodeling and includes dynamic chromatin regions enriched for transcription factor motifs in addition to GMT, with different motif families associated with specific patterns of chromatin and DNA methylation changes. We found evidence for binding of the reprogramming factors to dynamically-opening distal regulatory regions linked to cardiac function. In addition, we document the mechanism through which TGFβ and Wnt signaling pathway inhibition improves reprogramming efficiency by limiting aberrant reprogramming outcomes. These results provide insight into the mechanisms that drive direct cardiac reprogramming and provide a hypothesis-building framework for improving this process.