Enhancers Drive Heterogeneity in Embryonic Stem Cells

Abstract

SummaryIn embryonic stem cells (ESCs), heterogeneous gene expression impacts cell-fate decision making and pluripotency. Cell-to-cell variation in gene expression is a key feature of stem cell systems, yet its origins remain unknown. Here we identify a coherent regulatory program of enhancers that are dynamically transcribed across ESCs. Variable enhancers drive heterogeneous expression of developmental genes and transcription factors (TFs). Systematic analysis of enhancer transcription, accessibility, and function demonstrates that variable enhancers regulate cell state-specific gene expression programs. Further, we identify key TFs, Klf4 and Zfp281, that act antagonistically at shared enhancer sites, exerting opposing transcriptional and epigenetic effects and leading to enhancer variation. These results suggest gene expression heterogeneity is established and maintained by enhancers, providing insight into how cellular diversity may be generated during mammalian development.