TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.

TitleTET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells.
Publication TypeJournal Article
Year of Publication2018
AuthorsVerma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang C-J, Papapetrou EP, He C, Elemento O, Huangfu D
JournalNat Genet
Volume50
Issue1
Pagination83-95
Date Published2018 01
ISSN1546-1718
KeywordsAnimals, Cell Differentiation, Cells, Cultured, Dioxygenases, DNA Methylation, DNA-Binding Proteins, Embryonic Stem Cells, Humans, Mice, Mixed Function Oxygenases, Mutation, Neural Plate, PAX6 Transcription Factor, Promoter Regions, Genetic, Proto-Oncogene Proteins
Abstract

TET enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish owing to challenges in distinguishing global versus locus-specific effects. Here we show that TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit prominent bivalent promoter hypermethylation without an overall corresponding decrease in gene expression in the undifferentiated state. Focusing on the bivalent PAX6 locus, we find that increased DNMT3B binding is associated with promoter hypermethylation, which precipitates a neural differentiation defect and failure of PAX6 induction during differentiation. dCas9-mediated locus-specific demethylation and global inactivation of DNMT3B in TKO hESCs partially reverses the hypermethylation at the PAX6 promoter and improves differentiation to neuroectoderm. Taking these findings together with further genome-wide methylation and TET1 and DNMT3B ChIP-seq analyses, we conclude that TET proteins safeguard bivalent promoters from de novo methylation to ensure robust lineage-specific transcription upon differentiation.

DOI10.1038/s41588-017-0002-y
Alternate JournalNat. Genet.
PubMed ID29203910
PubMed Central IDPMC5742051
Grant ListP30 CA008748 / CA / NCI NIH HHS / United States
R01 CA194547 / CA / NCI NIH HHS / United States
R01 DK096239 / DK / NIDDK NIH HHS / United States
T32 CA078207 / CA / NCI NIH HHS / United States