RNA Cap-Adjacent Methylation Analysis

RNA cap-adjacent modifications are critical epitranscriptomic regulators, exerting precise control over mRNA stability, translation initiation efficiency, and cellular innate immune responses. CD BioSciences offers a comprehensive suite of integrated analytical services designed to precisely map, accurately quantify, and functionally characterize these dynamic modifications.

Overview of RNA Cap-Adjacent Methylation

RNA cap-adjacent methylation refers to specific chemical modifications on the first few nucleotides of eukaryotic mRNA, immediately following the 5' cap structure. The predominant types include 2'-O-methylation (cOMe) of the first transcribed nucleotide (cap1) and often the second (cap2), as well as N6,2'-O-dimethyladenosine (m6Am) when the first nucleotide is an adenosine. These modifications play vital biological roles: they protect mRNA from degradation by exonucleases, enhance translation efficiency by facilitating ribosome binding, and critically, serve as "self" markers to distinguish cellular mRNA from viral RNA, thereby modulating innate immune responses. Studying these marks is essential for understanding post-transcriptional regulation, viral pathogenesis, and developing novel therapeutic strategies.

Fig.1 Cap-adjacent modification by CMTR1, CMTR2, and PCIF1, the latter of which can be reversed by FTO. (Bellows E, et al., 2024)

Our Services

CD BioSciences delivers expert, end-to-end RNA cap-adjacent methylation analysis services. Leveraging state-of-the-art technology and deep expertise in epitranscriptomics, we provide precise, reliable data to accelerate your projects. Our services are designed to help you uncover the roles of cOMe and m6Am in your biological system of interest, from basic mechanism discovery to biomarker identification.

RNA Cap-Adjacent Methylation Analysis Solution

Achieving precise and reliable analysis of cap-adjacent methylations requires a sophisticated, multi-faceted technological approach. Our platform integrates next-generation sequencing (NGS) with advanced biochemical and analytical techniques, allowing for the specific capture, accurate identification, and quantitative profiling of both 2'-O-methylation (cOMe) and N6,2'-O-dimethyladenosine (m6Am). This ensures comprehensive data, from transcriptome-wide mapping to stoichiometric validation.

2'-O-methylation (cOMe) Analysis Service

This service offers comprehensive cOMe analysis, including key cap1 and cap2 modifications as well as internal sites. We provide precise localization and quantification analysis to reveal the dynamic role of cOMe in your biological systems.

1. LC-MS/MS: Quantify global 2'-O-methylation levels with high sensitivity and precision.
2. RiboMeth-seq: Map transcriptome-wide 2'-O-methylation sites at nucleotide resolution.
3. NJU-seq: Precisely identify 2'-O-methylation positions via selective chemical cleavage.
4. Nanopore Sequencing: Directly detect 2'-O-methylation on native RNA in real time.

N6,2'-O-dimethyladenosine (m6Am) Analysis Service

We specialize in the precise detection and quantification of the dual m6Am modification at mRNA caps, revealing its unique role in fine-tuning translation efficiency, transcript stability, and immune signaling.

1. LC-MS/MS: Quantify m6Am abundance and distinguish it from m6A with precision.
2. m6Am-Exo-seq: Profile m6Am sites by sequencing exonuclease-resistant capped RNA.
3. ReCappable-seq: Identify m6Am by selectively sequencing recapped, genuine 5' capped RNAs.
4. CROWN-seq: Map m6Am at nucleotide resolution by direct sequencing of RNA 5' ends.

Workflow of RNA Cap-Adjacent Methylation Analysis Service

Our Advantages

1. Broad Sample Compatibility: Handle a comprehensive range of sample types, including cultured cell lines, primary cells, tissue samples (fresh-frozen and FFPE), blood-derived specimens, and low-input clinical materials.
2. Expertise in Cap Biology & Epitranscriptomics: Apply deep, specialized knowledge of RNA cap structures, modification dynamics, and immune-related pathways to ensure rigorous experimental design and accurate data interpretation.
3. Integrated Multi-Technology Validation: Deliver higher-confidence results through cross-validation with complementary techniques such as sequencing and mass spectrometry.
4. Customized & Flexible Service Packages: Design tailored solutions that align precisely with project goals, sample characteristics, and budget constraints, supporting projects from targeted validation to transcriptome-wide discovery.

At CD BioSciences, we provide comprehensive services not only for RNA cap-adjacent methylation analysis but also for a broad spectrum of RNA modifications, including m6A, m5C, Ψ, ac4C, m7G, m1A, and adenosine-to-inosine (A-to-I) editing. With expertise across multiple platforms, we can customize workflows to meet the unique needs of your research program. Contact us today to discuss how to customize our services to help your projects succeed.

Reference

1. Bellows E, Fray R G, Knight H M, et al. The expanding role of cap-adjacent modifications in animals[J]. Frontiers in RNA Research, 2024, 2: 1485307.