GSE134483
Loss of DNMT3A/B in human ES cells triggers increased cell-cell variability and transcriptional repression
Maintenance of human pluripotent stem cells is dependent on extrinsic signals and cross talk between transcriptional and epigenetic regulators. Methylation of cytosines through the de novo methyltransferases DNMT3A and 3B plays an important role for exiting pluripotency and facilitating proper differentiation. Here, we generated and analyzed single cell expression data from wild-type and DNMT3A/B knockout human embryonic stem cells to better understand the precise effects on pluripotency and differentiation. Although DNA methylation is generally associated with gene silencing, we find unexpected and widespread transcriptional repression upon loss of DNMT3A or DNMT3A/3B. Furthermore, the transcriptional misregulation in DNMT3A knockout cells is largely propagated during differentiation towards mesoderm. Additionally, we observe increased cellular and transcriptional heterogeneity in undifferentiated cells upon deactivation of DNMTs as well as a notable change in cell cycle gene expression. Taken together, our single-cell RNA sequencing data provides several new insights into the role of DNA methylation in human pluripotent stem cells. Overall design: Single-cell RNA-Sequencing of in vitro embryonic stem cells at different stages of differentiation and conditions