Digital Reprogramming Decodes Epigenetic Barriers of Cell Fate Changes

The fates of differentiated cells in our body can be induced to change by nuclear reprogramming. In this way, cells valuable for therapeutic purposes and disease modeling can be produced. However, the efficiency of this process is low, partly due to properties of somatic donor nuclei which stabilize their differentiated fate but also act as barriers reprogramming-associated cell fate changes. The identity of these reprogramming barriers is not fully understood. Here, we developed an artificial intelligence-based approach to model nuclear reprogramming and used it to identify the chromatin modification H3K27ac as an epigenetic barrier to reprogramming-induced cell fate changes. Using reprogramming by nuclear transfer (NT) to eggs of Xenopus laevis as a model system, we profiled chromatin modifications in differentiated cell types alongside gene expression patterns before and after reprogramming. Our model integrated the data and by leveraging model predictions, we find that genes resisting inactivation during reprogramming display chromatin modification barcodes. This revealed H3K27ac as a novel candidate barrier to NT reprogramming. Reducing H3K27ac levels using p300/CBP inhibitors before reprogramming led to an improved downregulation of genes linked to H3K27ac-modified enhancers after reprogramming. Importantly, these effects were accompanied by improved embryonic development of the resulting nuclear transfer embryos. In summary, our study identified H3K27ac as a safeguarding mechanism of cellular identities and as a reprogramming barrier during NT. Hence, the here-developed Digital Reprogramming" approach is capable of modelling and improving current cell-fate reprogramming strategies.