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Updated: Jun 8, 2026
Continuous Fluorescence-Based Endonuclease-Coupled DNA Methylation Assay to Screen for DNA Methyltransferase Inhibitors
Published on: August 5, 2022
Identification of preferential target sites for human DNA methyltransferases
Si Ho Choi1, Kyu Heo, Hyang-Min Byun
1Jane Anne Nohl Division of Hematology, Norris Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
Abstract:
DNA methyltransferases (DNMTs) play an important role in establishing and maintaining DNA methylation. Aberrant expression of DNMTs and their isoforms has been found in many types of cancer, and their contribution to aberrant DNA methylation has been proposed. Here, we generated HEK 293T cells stably transfected with each of 13 different DNMTs (DNMT1, two DNMT3A isoforms, nine DNMT3B isoforms and DNMT3L) and assessed the DNA methylation changes induced by each DNMT. We obtained DNA methylation profiles of DNA repetitive elements and 1505 CpG sites from 808 cancer-related genes. We found that DNMTs have specific and overlapping target sites and their DNA methylation target profiles are a reflection of the DNMT domains. By examining H3K4me3 and H3K27me3 modifications in the 808 gene promoter regions using promoter ChIP-on-chip analysis, we found that specific de novo DNA methylation target sites of DNMT3A1 are associated with H3K4me3 modification that are transcriptionally active, whereas the specific target sites of DNMT3B1 are associated with H3K27me3 modification that are transcriptionally inactive. Our data suggest that different DNMT domains are responsible for targeting DNA methylation to specific regions of the genome, and this targeting might be associated with histone modifications.
Insights
DNA methyltransferases (DNMTs) establish and maintain DNA methylation. Different DNMT domains target specific genomic regions, potentially influencing gene activity through histone modifications.
Area of Science:
- Epigenetics and Molecular Biology
- Cancer Genomics
Background:
- DNA methyltransferases (DNMTs) are crucial for DNA methylation, a process vital for normal cellular function.
- Aberrant DNMT expression and DNA methylation are implicated in various cancers.
Purpose of the Study:
- To investigate the specific DNA methylation targeting profiles of 13 different DNMTs and their isoforms.
- To explore the relationship between DNMT targeting and histone modifications in cancer-related genes.
Main Methods:
- Generated HEK 293T cells stably expressing 13 DNMTs (DNMT1, DNMT3A isoforms, DNMT3B isoforms, DNMT3L).
- Assessed DNA methylation changes at repetitive elements and 1505 CpG sites in 808 cancer-related genes.
- Utilized promoter ChIP-on-chip to analyze H3K4me3 and H3K27me3 modifications in gene promoter regions.
Main Results:
- Identified specific and overlapping DNA methylation target sites for different DNMTs, reflecting DNMT domain functions.
- DNMT3A1 specifically targets H3K4me3-marked, transcriptionally active regions.
- DNMT3B1 specifically targets H3K27me3-marked, transcriptionally inactive regions.
Conclusions:
- DNMT domains dictate specific DNA methylation targeting within the genome.
- DNMT-mediated DNA methylation targeting is associated with distinct histone modification patterns, influencing transcriptional states.
