Journal of Molecular Biology
Volume 432, Issue 23, 20 November 2020, Pages 6075-6091
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Research Article
TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues

https://doi.org/10.1016/j.jmb.2020.10.008Get rights and content
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Highlights

  • TET1 and NANOG interact via multiple independent binding regions.

  • TET1 and NANOG interactions are mediated by aromatic and hydrophobic residues.

  • TET1 residues that bind NANOG are highly conserved in mammals.

  • Co-localisation of TET1 and NANOG on chromatin is enriched at NANOG target genes.

  • NANOG and TET1 have regulatory roles in maintaining and reprogramming pluripotency.

Abstract

The DNA demethylase TET1 is highly expressed in embryonic stem cells and is important both for lineage commitment, and reprogramming to naïve pluripotency. TET1 interacts with the pluripotency transcription factor NANOG which may contribute to its biological activity in pluripotent cells. However, how TET1 interacts with other proteins is largely unknown. Here, we characterise the physical interaction between TET1 and NANOG using embryonic stem cells and bacterial expression systems. TET1 and NANOG interact through multiple binding sites that act independently. Critically, mutating conserved hydrophobic and aromatic residues within TET1 and NANOG abolishes the interaction. On chromatin, NANOG is predominantly localised at ESC enhancers. While TET1 binds to CpG dinucleotides in promoters using its CXXC domain, TET1 also binds to enhancers, though the mechanism involved is unknown. Comparative ChIP-seq analysis identifies genomic loci bound by both TET1 and NANOG, that correspond predominantly to pluripotency enhancers. Importantly, around half of NANOG transcriptional target genes are associated with TET1-NANOG co-bound sites. These results indicate a mechanism by which TET1 protein may be targeted to specific sites of action at enhancers by direct interaction with a transcription factor.

Keywords

protein–protein interactions
embryonic stem cells
chromatin
pluripotency
enhancers

Abbreviations

DSBH
double stranded beta helix domain
ESC
embryonic stem cell
NID
NANOG-interacting domain
OGT
O-linked N-acetylglucosamine transferase
TET
ten-eleven-translocation
WR
tryptophan-repeat

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