Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development

Abstract

SUMMARY Ten-Eleven Translocation (Tet) family of dioxygenases offers a new mechanism for dynamic regulation of DNA methylation and has been implicated in cell lineage differentiation and oncogenesis. Yet their functional roles and mechanisms of action in gene regulation and embryonic development are largely unknown. Here, we report that Xenopus Tet3 plays an essential role in early eye and neural development by directly regulating a set of key developmental genes. Tet3 is an active 5mC hydroxylase regulating the 5mC/5hmC status at target gene promoters. Biochemical and structural studies further reveal a novel DNA binding mode of the Tet3 CXXC domain that is critical for specific Tet3 targeting. Finally, we show that the enzymatic activity and CXXC domain are crucial for Tet3’s biological function. Together, these findings define Tet3 as a novel transcription factor and reveal a molecular mechanism by which the 5mC hydroxylase and DNA binding activities of Tet3 cooperate to control target gene expression and embryonic development.

Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

“…DNA motif analysis identified a CpG-rich sequence as the highest-ranked motif among Tet3-binding sites (Fig. 2E), also consistent with the previous report (21).…”

“…Tet3-binding sites clustered close to transcription start sites (TSSs), with a low frequency of binding at distal regions relative to the TSSs (Fig. 2D), consistent with a previous report in which Tet3 binding regions were defined by pulldown with a GST fusion of the Tet3 CXXC domain (21). DNA motif analysis identified a CpG-rich sequence as the highest-ranked motif among Tet3-binding sites (Fig.…”

“…The 5hmC generated by Tet family dioxygenases is abundant in neurons (19) and may be critical for neural development (20). In Xenopus, Tet3 plays a vital function in early eye and neural development by directly targeting several key developmental genes (21). All of these studies indicate that TET-family proteins are involved in neural development, which prompted us to further study-through triple deletion of all three TET proteins-the in vivo functions and redundancy of TET proteins during neural development.…”

Methylcytosine dioxygenase TET3 interacts with thyroid hormone nuclear receptors and stabilizes their association to chromatin

“…3D), although it remains to be determined whether TET3 enhances TRα1-specific enrichment at TRE and/or other genomic sites. In an effort to decipher the underlying mechanism, we demonstrated that the CXXC domain, which mediates TET3 direct binding of genomic DNA (14), is dispensable for stabilization of TRα1 recruitment in chromatin (Fig. S7A).…”

The CXXC-TET bridge — mind the methylation gap!

“…Conversion of 5hmC into 5fC and/or 5caC, may result in their replacement by cytosine (C) via a base excision repair (BER) demethylation pathway [5]. Work in the frog suggests that the TET3 CXXC domain is critical for its targeting to the promoters of genes that are essential for eye and neural development [7]. Deletion of the CXXC domain from Xenopus laevis Tet3 (xlTET3) abolishes its ability to occupy target gene promoters, thereby preventing the TET3-driven developmental demethylation event that is normally associated with the activation of these genes.…”