Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers (ChIP-seq data set)

Fibroblasts can be directly reprogrammed toward a cardiac fate by introducing cardiogenic transcription factors (TFs), although the underlying mechanisms of the cardiac reprogramming process remain unclear. Three cardiac TFs, GATA4, MEF2C, and Tbx5 (referred to as GMT) can activate cardiac genes in fibroblasts and their cardiogenic activity is enhanced by the Hand2 TF and the Akt1 kinase. To understand the mechanistic basis of cardiac reprogramming, we performed a genome-wide analysis of cardiogenic TF binding sites and active enhancers, which were annotated by H3K27ac histone modification, during the reprogramming process. We found that cardiogenic TFs rapidly co-occupy core regulatory elements of cardiac genes and activate myriad cardiac enhancers that are enriched predominantly in Mef2 binding sites. Addition of Hand2 and Akt1 to the GMT reprogramming cocktail expands the spectrum of co-occupied active cardiac enhancers. As reprogramming proceeds over time, reprogramming TFs continue to activate additional cardiac enhancers, which are also enriched for Mef2 motifs, while fibroblast enhancers are silenced. This transition of the enhancer landscape strongly correlated with changes in the fibroblast and cardiac transcriptome. To test the relevance of cardiac reprogramming enhancers to the regulation of cardiogenesis in vivo, we assayed a collection of reprogramming enhancers in transgenic mouse embryos and found that they directed highly specific expression patterns in the developing heart. Our findings demonstrate that Hand2 and Akt1 enhance reprogramming by facilitating cardiac enhancer occupancy and identify Mef2 as a central effector of cardiac reprogramming, which coordinates the actions of accessory factors across a broad landscape of cardiac enhancers. To understand the mechanistic basis of cardiac reprogramming, we profiled cardiogenic TF binding sites and epigeomes (using ChIP-seq) and the transcriptiomes (using RNA-seq), of MEFs treated with reprogramming cocktail compared to embroynic heart tissue.