DNA N4-Methylcytosine (4mC) Analysis

An essential epigenetic mark in prokaryotes with emerging roles in eukaryotes, DNA N4-methylcytosine (4mC) is involved in restriction-modification systems, gene regulation, and genome defense. CD BioSciences provides accurate detection and mapping services for 4mC, enabling researchers to explore its functions in bacterial physiology, host-pathogen interactions, and novel eukaryotic pathways.

Introduction to N4-Methylcytosine (4mC)

DNA N4-methylcytosine (4mC) is a methylation modification where a methyl group is covalently attached to the fourth nitrogen of the cytosine base. It is a well-established and abundant epigenetic mark in bacteria and archaea, primarily known as a key component of restriction-modification (R-M) systems that protect prokaryotic genomes from foreign DNA invasion. Beyond host defense, 4mC also participates in regulating DNA replication, cell cycle control, and gene expression in various microbial species. While historically considered prokaryote-specific, recent studies using sensitive detection methods have reported the presence of 4mC in select eukaryotic genomes—including C. elegans, Drosophila, and plant species—suggesting potential, yet uncharacterized, regulatory functions in higher organisms. Its study is crucial for understanding bacterial virulence, antibiotic resistance mechanisms, and the evolution of epigenetic systems, positioning 4mC as a valuable target for microbial epigenetics and comparative genomics research.

Fig.1 Illustration of the deamination of cytosine, 4mC and 5mC by A3A protein. (Xiong J, et al., 2022)

Our Services

CD BioSciences delivers specialized solutions for the precise identification and quantification of DNA N4-methylcytosine (4mC). Recognizing its distinct chemical nature and genomic context, we employ technologies specifically suited to distinguish 4mC from the more common 5mC. Our services provide researchers with robust data to investigate 4mC's role in microbial genetics, epigenomics, and potential functions in eukaryotic models.

Customized 4mC Analysis Solutions

We offer a comprehensive and advanced technology platform designed for the precise detection of DNA N4-methylcytosine (4mC), a modification that cannot be analyzed using standard bisulfite methods. Our solution utilizes direct single-molecule detection techniques and absolute quantification methods to provide complete and reliable 4mC profiles across diverse genomic contexts.

1. Global DNA Modification Quantification by LC-MS/MS: Provides absolute, quantitative measurement of global 4mC levels as an orthogonal validation method.
2. Nanopore Sequencing: Allows for direct, long-read sequencing that identifies 4mC based on characteristic changes in ionic current.
3. PacBio SMRT DNA Sequencing: Enables single-molecule, real-time detection and genome-wide mapping of 4mC with high confidence through kinetic analysis.

Workflow of DNA 4mC Analysis Service

Our Advantages

1. Direct Detection Expertise: We specialize in SMRT and Nanopore sequencing, the most reliable methods for native 4mC mapping, avoiding indirect inference.
2. Prokaryotic & Eukaryotic Protocol Optimization: Our workflows are validated for both bacterial genomes and challenging eukaryotic samples where 4mC is rare.
3. Single-Molecule Resolution: We capture modification heterogeneity, providing insights into epigenetic diversity within populations.
4. Integrated Quantitative Analysis: Combining sequencing-based mapping with LC-MS/MS quantification offers a complete view of 4mC abundance and distribution.
5. Dedicated Microbial Epigenetics Support: Our bioinformatics and scientific teams have specific expertise in analyzing and interpreting 4mC data in biological contexts.

At CD BioSciences, we support a complete range of DNA modification analyses. In addition to 4mC, our portfolio includes services for 5mC, 5hmC, 5fC, 5caC, 6mA, and 8-oxoG. Whether you are studying restriction-modification systems, microbial pathogenesis, or exploring novel epigenetic marks in eukaryotes, we provide flexible and customized solutions to meet your specific research objectives. If you are interested in our services, please feel free to contact us for more details and quotation information of related services.

Reference 1. Xiong J, Wang P, Shao W X, et al. Genome-wide mapping of N 4-methylcytosine at single-base resolution by APOBEC3A-mediated deamination sequencing[J]. Chemical Science, 2022, 13(34): 9960-9972.