TET3 controls the expression of the H3K27me3 demethylase Kdm6b during neural commitment

Abstract

The acquisition of cell identity is associated with developmentally regulated changes in the cellular histone methylation signatures. For instance, commitment to neural differentiation relies on the tightly controlled gain or loss of H3K27me3, a hallmark of polycomb-mediated transcriptional gene silencing, at specific gene sets. The KDM6B demethylase, which removes H3K27me3 marks at defined promoters and enhancers, is a key factor in neurogenesis. Therefore, to better understand the epigenetic regulation of neural fate acquisition, it is important to determine how Kdm6b expression is regulated. Here, we investigated the molecular mechanisms involved in the induction of Kdm6b expression upon neural commitment of mouse embryonic stem cells. We found that the increase in Kdm6b expression is linked to a rearrangement between two 3D configurations defined by the promoter contact with two different regions in the Kdm6b locus. This is associated with changes in 5hydroxymethylcytosine (5hmC) levels at these two regions, and requires a functional teneleven-translocation (TET) 3 protein. Altogether, our data support a model whereby Kdm6b induction upon neural commitment relies on an intronic enhancer the activity of which is defined by its TET3-mediated 5-hmC level. This original observation reveals an unexpected interplay between the 5-hmC and H3K27me3 pathways during neural lineage commitment in mammals. It also questions to which extent KDM6B-mediated changes in H3K27me3 level account for the TET-mediated effects on gene expression.

Gene body methylation in cancer: molecular mechanisms and clinical applications

“…In addition, bioinformatic analyses have shown that CGIs themselves exhibit enhancer histone modifications and show greater transcription factor binding [ 75 ]. Such signatures have been identified at a gene body CGI within Kdm6b, which exhibits H3K4me1 and loops to the promoter CGI to enhance Kdm6b expression [ 76 ]. In addition, the distribution of enhancer CGIs plays an important role in enhancer function; enhancers enriched in CGIs (i) are more highly conserved, (ii) are more highly enriched in R loops and 3D genomic contacts, (iii) on average provide stronger signals in functional assays, and (iv) are prone to hypermethylation in cancer [ 77 ].…”

Intragenic CpG Islands and Their Impact on Gene Regulation

“…Bioinformatic analyses show that iCGIs themselves exhibit enhancer histone modifications, are actively transcribed to eRNAs, are conserved across mammalian species (Bell and Vertino, 2017) and show greater transcription factor binding (Steinhaus et al, 2020). Such signatures have been identified at an iCGI within Kdm6b, which exhibits H3K4me1 and loops to the promoter CGI to enhance Kdm6b expression (Montibus et al, 2021). Given that transcription of enhancer regions is required to deposit enhancer histone marks, it is unclear how CGIs are initially defined as enhancer regions (Kaikkonen et al, 2013).…”

TET Enzymes and 5-Hydroxymethylcytosine in Neural Progenitor Cell Biology and Neurodevelopment

“…This is in line with DNA hypermethylation in the embryonic cerebral cortex of Tet2 knockout mice ( Lister et al, 2013 ). TET3 plays a role in the epigenetic regulation of NPC specification and maintenance of cellular identity ( Montibus et al, 2020 ; Santiago et al, 2020 ). During differentiation of mouse ESCs to NPCs, the catalytic activity of TET3 promotes expression of histone demethylase Kdm6b , an epigenetic regulator critical for gene regulation during neurogenesis ( Montibus et al, 2020 ), and loss of TET3 promotes NPC apoptosis ( Li T. et al, 2015 ).…”

“…TET3 plays a role in the epigenetic regulation of NPC specification and maintenance of cellular identity ( Montibus et al, 2020 ; Santiago et al, 2020 ). During differentiation of mouse ESCs to NPCs, the catalytic activity of TET3 promotes expression of histone demethylase Kdm6b , an epigenetic regulator critical for gene regulation during neurogenesis ( Montibus et al, 2020 ), and loss of TET3 promotes NPC apoptosis ( Li T. et al, 2015 ). Knockdown of Tet3 in NPCs promotes de-repression of pluripotency genes Oct4 and Nanog , implicating TET3 in the maintenance of NPC identity ( Santiago et al, 2020 ).…”

“…Tet1 knockout mice have fewer NPCs in the dentate gyrus of the hippocampus and conditional deletion of Tet1 or Tet2 in NPCs compromises hippocampal neurogenesis ( Zhang et al, 2013 ; Gontier et al, 2018 ). While most functions of TETs in NPCs are attributed to their enzymatic activity ( Zhang et al, 2013 ; Li et al, 2017 ; Montibus et al, 2020 ), some functions are independent of enzymatic activity, such as transcriptional repression of the imprinted gene Snrnp by TET3 ( Montalban-Loro et al, 2019 ). Investigating these dual roles of TETs and dissecting their requirements in NPC biology and neurogenesis will be essential.…”