TET1 facilitates specification of early human lineages including germ cells

Fei-Man Hsu; Qiu Ya Wu; Emily B Fabyanic; Alex Wei; Hao Wu; Amander T Clark

doi:10.1016/j.isci.2023.107191

TET1 facilitates specification of early human lineages including germ cells

iScience. 2023 Jun 21;26(7):107191. doi: 10.1016/j.isci.2023.107191. eCollection 2023 Jul 21.

Authors

Fei-Man Hsu^{1

2

3}, Qiu Ya Wu¹, Emily B Fabyanic^{4

5}, Alex Wei^{4

5}, Hao Wu^{4

5}, Amander T Clark^{1

2

3}

Affiliations

¹ Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁴ Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁵ Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.

Abstract

Ten Eleven Translocation 1 (TET1) is a regulator of localized DNA demethylation through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). To examine DNA demethylation in human primordial germ cell-like cells (hPGCLCs) induced from human embryonic stem cells (hESCs), we performed bisulfite-assisted APOBEC coupled epigenetic sequencing (bACEseq) followed by integrated genomics analysis. Our data indicates that 5hmC enriches at hPGCLC-specific NANOG, SOX17 or TFAP2C binding sites on hPGCLC induction, and this is accompanied by localized DNA demethylation. Using CRISPR-Cas9, we show that deleting the catalytic domain of TET1 reduces hPGCLC competency when starting with hESC cultured on mouse embryonic fibroblasts, and this phenotype can be rescued after transitioning hESCs to defined media and a recombinant substrate. Taken together, our study demonstrates the importance of 5hmC in facilitating hPGCLC competency, and the role of hESC culture conditions in modulating this effect.

Keywords: Developmental biology; Embryology; Epigenetics.

Grants and funding

R01 HD079546/HD/NICHD NIH HHS/United States