Signatures of digital 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, hindering their translational application. To explore the causes of this variability, we analysed a panel of ten human iPSC lines, evaluating their differentiation efficiency for two different fates, profiling their transcriptome and chromatin state. Using a machine learning approach, we related chromatin state variability with transcriptional differences. 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 ON/OFF pattern, consistent with a mathematical model based on Polycomb read-write feedback. Notably, altered gene expression patterns of Polycomb-regulated genes were largely propagated into an intermediate state in the differentiation trajectory. Finally, we uncovered a subset of Polycomb-regulated genes with heterogeneous expression and chromatin signatures that were highly predictive of iPSC differentiation efficiencies for two cell types.