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Updated: Jun 1, 2026
Rapid and Efficient Spatiotemporal Monitoring of Normal and Aberrant Cytosine Methylation within Intact Zebrafish Embryos
Published on: August 18, 2022
C5-DNA methyltransferase inhibitors: from screening to effects on zebrafish embryo development
Alexandre Ceccaldi1, Arumugam Rajavelu, Christine Champion
1UMR 7196 CNRS, MNHN INSERM U565, Paris, France.
Abstract:
DNA methylation is involved in the regulation of gene expression and plays an important role in normal developmental processes and diseases, such as cancer. DNA methyltransferases are the enzymes responsible for DNA methylation on the position 5 of cytidine in a CpG context. In order to identify and characterize novel inhibitors of these enzymes, we developed a fluorescence-based throughput screening by using a short DNA duplex immobilized on 96-well plates. We have screened 114 flavones and flavanones for the inhibition of the murine catalytic Dnmt3a/3L complex and found 36 hits with IC(50) values in the lower micromolar and high nanomolar ranges. The assay, together with inhibition tests on two other methyltransferases, structure-activity relationships and docking studies, gave insights on the mechanism of inhibition. Finally, two derivatives effected zebrafish embryo development, and induced a global demethylation of the genome, at doses lower than the control drug, 5-azacytidine.
Insights
Researchers screened 114 flavones and flavanones to find inhibitors of DNA methyltransferases (DNMTs). They identified 36 compounds that inhibit DNMTs, with two derivatives impacting zebrafish development and genome demethylation.
Area of Science:
- Biochemistry
- Epigenetics
- Pharmacology
Background:
- DNA methylation regulates gene expression and is crucial in development and diseases like cancer.
- DNA methyltransferases (DNMTs) catalyze DNA methylation at CpG sites.
- Identifying novel DNMT inhibitors is important for therapeutic development.
Purpose of the Study:
- To develop and implement a fluorescence-based high-throughput screening assay.
- To identify and characterize novel inhibitors of the murine catalytic Dnmt3a/3L complex.
- To investigate the mechanism of inhibition and evaluate the in vivo effects of identified compounds.
Main Methods:
- Developed a fluorescence-based throughput screening assay using immobilized DNA duplexes.
- Screened a library of 114 flavones and flavanones against the Dnmt3a/3L complex.
- Conducted inhibition tests on other methyltransferases, structure-activity relationship (SAR) analyses, and molecular docking studies.
- Assessed the effects of two promising derivatives on zebrafish embryo development and global DNA methylation.
Main Results:
- Identified 36 hit compounds inhibiting Dnmt3a/3L with IC(50) values in the low micromolar to high nanomolar range.
- Elucidated structure-activity relationships and potential mechanisms of DNMT inhibition.
- Two flavone derivatives demonstrated efficacy in affecting zebrafish development at lower doses than 5-azacytidine.
- Observed global genome demethylation induced by these derivatives in zebrafish embryos.
Conclusions:
- The developed fluorescence-based assay is effective for screening DNMT inhibitors.
- Flavones and flavanones represent a promising class of compounds for DNMT inhibition.
- The identified derivatives show potential as therapeutic agents due to their efficacy and ability to induce demethylation in vivo.
