Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression

Biology Biology
Genomics Genomics
Alex K. Shalek Alex K. Shalek
Ben Mead Ben Mead
Marc Wadsworth II Marc Wadsworth II
Riley Drake Riley Drake
Sam Allon Sam Allon

Tsankov et al.▾ Tsankov, A.M., Wadsworth II, M.H., Akopian, V., Charlton, J., Allon, S.J., Arczewska, A., Mead, B.E., Drake, R.S., Smith, Z.D., Mikkelsen, T.S., Shalek, A.K., Meissner, A.

Development , Volume 146

September, 2019


Maintenance of pluripotency and specification towards a new cell fate are both dependent on precise interactions between extrinsic signals and transcriptional and epigenetic regulators. Directed methylation of cytosines by the de novo methyltransferases DNMT3A and DNMT3B plays an important role in facilitating proper differentiation, whereas DNMT1 is essential for maintaining global methylation levels in all cell types. Here, we generated single-cell mRNA expression data from wild-type, DNMT3A, DNMT3A/3B and DNMT1 knockout human embryonic stem cells and observed a widespread increase in cellular and transcriptional variability, even with limited changes in global methylation levels in the de novo knockouts. Furthermore, we found unexpected transcriptional repression upon either loss of the de novo methyltransferase DNMT3A or the double knockout of DNMT3A/3B that is further propagated upon differentiation to mesoderm and ectoderm. Taken together, our single-cell RNA-sequencing data provide a high-resolution view into the consequences of depleting the three catalytically active DNMTs in human pluripotent stem cells.