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PreprintCited by 1,040Epigenetics and DNA MethylationGenomics and Chromatin DynamicsCancer-related gene regulation

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Role of TET enzymes in DNA methylation, development, and cancer

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Rasmussen, Kasper Dindler, Helin, Kristian·2016·Genes & Development
DOI 10.1101/gad.276568.115PMC PMC4826392
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Abstract

The pattern of DNA methylation at cytosine bases in the genome is tightly linked to gene expression, and DNA methylation abnormalities are often observed in diseases. The ten eleven translocation (TET) enzymes oxidize 5-methylcytosines (5mCs) and promote locus-specific reversal of DNA methylation. TET genes, and especially TET2 , are frequently mutated in various cancers, but how the TET proteins contribute to prevent the onset and maintenance of these malignancies is largely unknown. Here, we highlight recent advances in understanding the physiological function of the TET proteins and their role in regulating DNA methylation and transcription. In addition, we discuss some of the key outstanding questions in the field.

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Figure 1. Domain structure of TET proteins. The C-terminal core catalytic domain shared by all TET enzymes consists of the DSBH domain, a cysteine-rich (Cys) domain, and binding sites for the Fe(II) and 2-OG cofactors. The DSBH domain contains a large low-complexity region of unknown function. TET1 and TET3 have an N-terminal CXXC domain that can bind directly to DNA and facilitate recruitment to genomic target sites.
Figure 1. Domain structure of TET proteins. The C-terminal core catalytic domain shared by all TET enzymes consists of the DSBH domain, a cysteine-rich (Cys) domain, and binding sites for the Fe(II) and 2-OG cofactors. The DSBH domain contains a large low-complexity region of unknown function. TET1 and TET3 have an N-terminal CXXC domain that can bind directly to DNA and facilitate recruitment to genomic target sites.CC BY-NC · PubMed Central
Figure 2. Pathways of DNA demethylation mediated by TET enzymes. (A) Model of passive replication-dependent DNA demethylation. The diagrams illustrate the two opposite fates of a hemihydroxymethylated CpG dinucleotide through two rounds of DNA replication. The left panel shows the replication-dependent DNA demethylation, in which DNA methylation is lost on the DNA strand opposite to 5hmC. The right panel shows the reverse outcome, in which maintenance of DNA methylation is achieved by DNMT1 in complex with UHRF1/2 or DNMT3A/B. The relative extent of these two opposing outcomes of 5hmC deposition in vivo remains to be determined and is likely influenced by global as well as locus-specific factors. In both cases, newly replicated DNA dilutes 5hmC during cell division. (B) Model of active DNA demethylation by a TET/TDG (thymine–DNA–glycosylase)/BER (base excision repair)-dependent pathway. A cytosine base can be methylated by the DNA methylation machinery (DNMT1 or DNMT3A/B) to form 5mC, which in turn can be iteratively oxidized by TET enzymes to produce 5hmC, 5fC, and 5caC. TDG then recognizes 5fC and 5caC, and the oxidized cytosine base is excised. This yields an abasic site that is repaired by BER and results in restoration of the unmodified cytosine state. Additional pathways of active DNA demethylation have been suggested (for review, see Wu and Zhang 2014). (SAH) S-adenosyl-homocysteine; (SAM) S-adenosyl-methionine.
Figure 2. Pathways of DNA demethylation mediated by TET enzymes. (A) Model of passive replication-dependent DNA demethylation. The diagrams illustrate the two opposite fates of a hemihydroxymethylated CpG dinucleotide through two rounds of DNA replication. The left panel shows the replication-dependent DNA demethylation, in which DNA methylation is lost on the DNA strand opposite to 5hmC. The right panel shows the reverse outcome, in which maintenance of DNA methylation is achieved by DNMT1 in complex with UHRF1/2 or DNMT3A/B. The relative extent of these two opposing outcomes of 5hmC deposition in vivo remains to be determined and is likely influenced by global as well as locus-specific factors. In both cases, newly replicated DNA dilutes 5hmC during cell division. (B) Model of active DNA demethylation by a TET/TDG (thymine–DNA–glycosylase)/BER (base excision repair)-dependent pathway. A cytosine base can be methylated by the DNA methylation machinery (DNMT1 or DNMT3A/B) to form 5mC, which in turn can be iteratively oxidized by TET enzymes to produce 5hmC, 5fC, and 5caC. TDG then recognizes 5fC and 5caC, and the oxidized cytosine base is excised. This yields an abasic site that is repaired by BER and results in restoration of the unmodified cytosine state. Additional pathways of active DNA demethylation have been suggested (for review, see Wu and Zhang 2014). (SAH) S-adenosyl-homocysteine; (SAM) S-adenosyl-methionine.CC BY-NC · PubMed Central
Figure 3. The dynamics of TET-mediated cytosine oxidation and its impact on DNA methylation patterns on regulatory elements in vivo. (A) Diagram illustrating the relative abundance of cytosines in the genome with “stable” levels of modifications as well as the small “transient” fractions that undergo rapid turnover and removal by active DNA demethylation processes. The stable levels of genomic 5caC have not been experimentally determined, as they are often under the detection limit. (B) Model illustrating the dual role of TET enzymes. The rate constant of TET enzymes to produce 5hmC from 5mC is fast, whereas the rate constants for further oxidation to 5fC and 5caC are considerably slower. On a majority of TET target sites, 5mC is oxidized and persists as “stable” 5hmC, likely due to low TET residence time (“stalling TET modification”). On a minority of sites, preferably located in open chromatin associated with regulatory elements, 5mC is oxidized iteratively to 5fC and 5caC and results in net DNA demethylation by the TET/TDG/BER pathway (“processive TET modification”). (C) Model illustrating the impact of loss of TET protein function on different regulatory elements. The protection of active and inactive CpG island promoters by the TET proteins is only one of several mechanisms by which they are protected against ectopic DNA methylation. In contrast, distal regulatory elements such as active enhancers are vulnerable to aberrant DNMT activity and become DNA hypermethylated upon loss of TET activity. (PcG) Polycomb group.
Figure 3. The dynamics of TET-mediated cytosine oxidation and its impact on DNA methylation patterns on regulatory elements in vivo. (A) Diagram illustrating the relative abundance of cytosines in the genome with “stable” levels of modifications as well as the small “transient” fractions that undergo rapid turnover and removal by active DNA demethylation processes. The stable levels of genomic 5caC have not been experimentally determined, as they are often under the detection limit. (B) Model illustrating the dual role of TET enzymes. The rate constant of TET enzymes to produce 5hmC from 5mC is fast, whereas the rate constants for further oxidation to 5fC and 5caC are considerably slower. On a majority of TET target sites, 5mC is oxidized and persists as “stable” 5hmC, likely due to low TET residence time (“stalling TET modification”). On a minority of sites, preferably located in open chromatin associated with regulatory elements, 5mC is oxidized iteratively to 5fC and 5caC and results in net DNA demethylation by the TET/TDG/BER pathway (“processive TET modification”). (C) Model illustrating the impact of loss of TET protein function on different regulatory elements. The protection of active and inactive CpG island promoters by the TET proteins is only one of several mechanisms by which they are protected against ectopic DNA methylation. In contrast, distal regulatory elements such as active enhancers are vulnerable to aberrant DNMT activity and become DNA hypermethylated upon loss of TET activity. (PcG) Polycomb group.CC BY-NC · PubMed Central
Figure 4. Illustration of the mutational landscape of TET2 in hematological diseases. A somatic mutation in TET2 results in premalignant hematopoiesis and clonal expansion. Additional oncogenic events cooperate with the initial TET2 mutation to drive the onset of a wide variety of hematopoietic malignancies. The frequencies of TET2 mutations in the different patient groups are indicated (for review, see Scourzic et al. 2015).
Figure 4. Illustration of the mutational landscape of TET2 in hematological diseases. A somatic mutation in TET2 results in premalignant hematopoiesis and clonal expansion. Additional oncogenic events cooperate with the initial TET2 mutation to drive the onset of a wide variety of hematopoietic malignancies. The frequencies of TET2 mutations in the different patient groups are indicated (for review, see Scourzic et al. 2015).CC BY-NC · PubMed Central

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Metadata

Authors
Rasmussen, K. D., & Helin, K.
Affiliations
University of Copenhagen (DK)
Corresponding author
Helin, Kristian
ORCID
Venue
Genes & Development
Publisher
Cold Spring Harbor Laboratory
Published
2016-04-01
Volume
30
Issue
7
Pages
733-750
ISSN
  • 0890-9369 (ISSN-L)
  • 1549-5477
DOI
10.1101/gad.276568.115
PMC
PMC4826392
OpenAlex
W2325267338
Cited by
1,040
References
162
Citations by year
2026: 56 · 2025: 87 · 2024: 116 · 2023: 100 · 2022: 135 · 2021: 141 · 2020: 131 · 2019: 97 · 2018: 83 · 2017: 60 · 2016: 30
Type
posted content
Language
en
Open access
Licence
cc-by-nc
Locations
  • Genes & Development (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
  • HighWire Press Open Archive (submittedVersion)
Funders
  • Danish Medical Research Council (1333-00120B)
  • European Research Council (294666_DNAMET)
  • Danish Cancer Society
  • Danish National Research Foundation (DNRF 82)
  • Danish Council for Strategic Research
  • Novo Nordisk Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
Keywords
TET enzymes, DNA methylation, 5-methylcytosine oxidation, TET2, demethylation, cancer, developmental regulation, transcriptional regulation, gene expression
MeSH terms
Animals, Cytosine, DNA-Binding Proteins, Humans, Neoplasms, Oxidation-Reduction, Proto-Oncogene Proteins, Gene Expression Regulation, Neoplastic, DNA Methylation, Epigenesis, Genetic, Dioxygenases

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