ABSTRACT
E protein transcription factors are crucial for many cell fate decisions. However, the roles of E proteins in the germ-layer specification of human embryonic stem cells (hESCs) are poorly understood. We disrupted the TCF3 gene locus to delete the E protein E2A in hESCs. E2A knockout (KO) hESCs retained key features of pluripotency, but displayed decreased neural ectoderm coupled with enhanced mesoendoderm outcomes. Genome-wide analyses showed that E2A directly regulates neural ectoderm and Nodal pathway genes. Accordingly, inhibition of Nodal or E2A overexpression partially rescued the neural ectoderm defect in E2A KO hESCs. Loss of E2A had little impact on the epigenetic landscape of hESCs, whereas E2A KO neural precursors displayed increased accessibility of the gene locus encoding the Nodal agonist CRIPTO. Double-deletion of both E2A and HEB (TCF12) resulted in a more severe neural ectoderm defect. Therefore, this study reveals critical context-dependent functions for E2A in human neural ectoderm fate specification.
Footnotes
Author contributions
Conceptualization: Y.L., S.Y.; Methodology: S.Y., X.H., Y.Z., S.Z.; Software: Y.Z., S.Z.; Validation: S.Y., X.H.; Formal analysis: Y.Z.; Data curation: S.Y., X.H.; Writing - original draft: S.Y.; Writing - review & editing: Y.L., S.Y., M.K.A., J.C.Z.-P., Q.L.; Supervision: Y.L.; Project administration: Y.L.; Funding acquisition: Y.L.
Funding
This work was funded by the National Key Research and Development Program of China (2018YFE0205300 and 2017YFA0104003 to Y.L.), the National Natural Science Foundation of China (31571517 to Y.L., 81870774 and 81800987 to Q.L.), the Beijing Municipal Natural Science Foundation (7192091 to Y.L.), the Canadian Institutes of Health Research (MOP82861 and PJT153058 to M.K.A.; FND-154332 to J.C.Z.-P.), the National Institutes of Health (1P01AI102853-01 to J.C.Z.P.), the Natural Sciences and Engineering Research Council of Canada (RGPIN-2014-05333 to M.K.A.) and the Krembil Foundation (J.C.Z.-P.). J.C.Z.-P. was supported by a Canada Research Chair in Developmental Immunology. Deposited in PMC for release after 12 months.
Data availability
RNA-seq data and ChIP-seq data have been deposited in GEO under accession number GSE154625.
