Cross-lineage Potential of Ascl1 Uncovered by Comparing Diverse Reprogramming Regulatomes [ChIP-seq II]

Direct reprogramming has revolutionized the fields of stem cell biology and regenerative medicine. Direct reprogramming makes it possible to interconvert somatic cell fates without intermediary pluripotency. Although studies have identified different transcription factor (TF) cocktails that can reprogram fibroblasts into different cell types, the common mechanisms governing how reprogramming cells undergo transcriptome and epigenome remodeling (i.e. regulatome remodeling) have not been investigated. Here, by characterizing early changes in the regulatome of three different types of direct reprogramming – induced neurons, induced hepatocytes, and induce cardiomyocytes – we identified two non-cocktail TFs, Tead4 and Atf7, that co-operate with reprogramming TFs to regulate target cell-type specific gene expression. Additionally, by identifying shared pro-cardiac features of iN and iCM reprogramming, we demonstrate Ascl1's cross-lineage potential to induce highly efficient iCM reprogramming in a two-factor cocktail with Mef2c (A+M). Single-cell multi-omics showed that A+M reprogramming terminates in a more mature iCM phenotype than MGT. Finally, through ChIP-seq and RNA-seq, we find that Mef2c drives the shift in Ascl1 binding away from neuronal genes towards cardiac gene, guiding their co-operative epigenetic and transcription activities. These findings demonstrate the existence of common regulators of different direct reprogramming process and argue against the premise that TFs are lineage specific – the basic premise used to develop direct reprogramming approaches. Overall design: H3K27ac, Ascl1, and Mef2c ChIP-seq libraries of Mef2c infected, Ascl1 infected, A+M infected, and MGT infected fibroblast were generated at day 3 post infection using published ChIP-seq protocol