Signatures of digital epigenetic Polycomb regulation in functional iPSC heterogeneity between individuals

Induced pluripotent stem cells (iPSCs) show substantial heterogeneity between individuals in their capacity to differentiate into various cell types, which is a major hurdle for regenerative cell therapies and disease modelling. To explore the causes of this variability, we assembled a panel of ten human iPSC lines, for which we evaluated the differentiation potential for two different fates, and profiled the transcriptome and epigenome (chromatin accessibility and three post-translational histone modifications). Using a custom-made computational method involving a Support Vector Machine, we dissected the different regulatory modes through which chromatin states affect transcription. We found that regulation of the Polycomb-mediated histone modification H3K27me3 at specific gene loci exhibited the most consistent differences among iPSC lines, frequently displaying a digital pattern (i.e., binary ON/OFF). We developed a mathematical model based on the read-write feedback of the Polycomb complex, which explained this widespread behaviour and showed that even a small change in Polycomb feedback could lead to pronounced changes in histone modification levels. Overall, our findings demonstrate that the heterogeneity in digital Polycomb regulation mirrors the transcriptomic variability across the iPSC lines studied here, and is one of the major sources of iPSC chromatin heterogeneity. Notably, Polycomb heterogeneity was also correlated with the differentiation potentials of the iPSC lines, suggesting that chromatin variability could be one important factor influencing iPSC differentiation potential.