TET (Ten-eleven translocation) family proteins: structure, biological functions and applications

Abstract

Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.

Fig. 1

Function and structure of TET proteins. a The dynamic cycle of DNA methylation and demethylation. DNA methyltransferases (DNMTs) catalyzed the formation of 5-methylcytosine (5mC), which can be removed by TET-mediated oxidation, coupled with thymine-DNA glycosylase (TDG)-involved excision and base excision repair (BER). b Domain structure of TET proteins. All TET proteins possessed one core catalytic domain in C-terminal. A CXXC domain, located in the N-terminal of TET1 and TET3, but not in TET2, conferred DNA binding ability directly

Fig. 2

Expression levels of TET1(a), TET2(b), and TET3(c) in different tissues. The data were obtained from the proteinatlas. Modified from images available for TET1 (https://www.proteinatlas.org/ENSG00000138336-TET1/tissue), for TET2 (https://www.proteinatlas.org/ENSG00000168769-TET2/tissue), and for TET3(https://www.proteinatlas.org/ENSG00000187605-TET3/tissue). nTPM: consensus normalized expression

Fig. 3

TETs working models. a A particular transcription factor (TF) recruited TETs to specific DNA areas of promoters to increase the downstream gene expression in a dioxygenase activity-dependent manner.^, b TETs binding with other epigenetic regulatory enzymes, such as HDAC, together regulated the particular gene expression independent of TETs enzyme activity.^, c, d TET1/2 oxidated mRNA (c)^, and TET2 oxidated tRNA (d) to exhibit regulatory functions in RNA levels

Fig. 4

The timeline of key discoveries in basic research of TETs

Fig. 5

Primary factors in positive(red) and negative(blue) regulation of TETs activity and the outmost layer described the involved mechanism. FOXA1, Vitamin C, CRL4(VprBP), P300, and AMPK enhanced TETs activity, while Vpr, IDAX, Calpain 1, 2HG and miR-29b decreased TETs activity

Fig. 6

Representative schematic diagrams of 5hmC detection approaches. a Schematic diagrams of hMe-Seal, TAB-seq, oxBS-seq, hmC-CATCH, CAPS, Jump-Seq, ACE-Seq, and CAM-Seq. b Structural formula of representative molecules

Fig. 7

Representative working models of targeted demethylation. a With the gDNA, a DNA modification domain, such as TET1, fused to dCas9, led to the erasure of specific DNA methylation. b GCN4 repeats fused to dCas9, recruited many copies of an anti-GCN4 antibody (scFV)-fused TET1, to amplify demethylation efficiently. c Multiple effectors were used to increase the efficacy of demethylation. The modified gRNA with PUF binding sites, recruited protein fusions of PUF, TET1, and NEIL2 to particular DNA methylation sites. Among these, PUF were used for binding to the modified gRNA, and TET1 oxidated 5mC and NEIL2 worked as a DNA glycosylase to promote DNA demethylation. d Without tethering an effector such as TET1, only gRNA-dCas9 led to specific DNA demethylation, by sterically blocking DNA methyltransferase