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Assessing Energy Substrate Oxidation In Vitro with 14CO2 Trapping

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Published on: March 23, 2022

Structural insight into substrate preference for TET-mediated oxidation.

Lulu Hu^1,2,3, Junyan Lu⁴, Jingdong Cheng^1,2

¹Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.

|November 3, 2015

Summary

Ten-eleven translocation (TET) proteins oxidize DNA methylation. TET1 and TET2 show higher activity on 5-methylcytosine (5mC) than 5-hydroxymethylcytosine (5hmC) or 5-formylcytosine (5fC) due to substrate conformation and oxidation efficiency. This suggests 5hmC is a stable epigenetic mark.

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Last Updated: Mar 30, 2026

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Area of Science:

Epigenetics
Molecular Biology
Biochemistry

Background:

DNA methylation is a key epigenetic regulator.
Ten-eleven translocation (TET) proteins mediate DNA demethylation by oxidizing 5-methylcytosine (5mC).
TET proteins iteratively convert 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC).

Purpose of the Study:

To investigate the substrate preference of human TET1 and TET2 proteins.
To elucidate the structural basis for TET protein activity on different DNA methylation derivatives.
To understand the implications of TET protein activity for the stability of 5hmC as an epigenetic mark.

Main Methods:

Determination of crystal structures of TET2-5hmC-DNA and TET2-5fC-DNA complexes.
Biochemical analyses of TET protein activity and substrate oxidation efficiency.
Comparative structural analysis of TET2-DNA complexes with 5mC, 5hmC, and 5fC substrates.

Main Results:

Human TET1 and TET2 exhibit higher enzymatic activity on 5mC-DNA compared to 5hmC-DNA and 5fC-DNA.
Crystal structures reveal similar binding of 5mC, 5hmC, and 5fC within the TET2 catalytic cavity, but with distinct orientations of the modified bases.
Biochemical data indicate that restrained conformations of 5hmC and 5fC hinder efficient hydrogen abstraction, leading to lower catalytic efficiency for these substrates.

Conclusions:

TET protein substrate preference is determined by the intrinsic properties of 5mC derivatives, specifically the conformation and hydrogen-bonding potential of the modified cytosine base.
The reduced reactivity of TET proteins towards 5hmC suggests it is a relatively stable epigenetic mark.
TET proteins are evolutionarily optimized to generate and maintain 5hmC, potentially for diverse regulatory functions.