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Single-Base RNA Modification Sequencing
Single-Nucleotide RNA m6A Modification Seq(CAM-seq)
Single-Nucleotide RNA m6A Modification Seq(CAM-Seq) is a chemical cooperative catalysis-assisted m6A sequencing method developed by the Chuan He laboratory and published in Nature Chemistry (2025, DOI: 10.1038/s41557-025-01801-3). A carbonyl organocatalyst and a Lewis acid act together to selectively deaminate unmodified adenosine (A) to inosine (I) under mild, near-neutral conditions, while m6A resists deamination and is read as adenine. Because deaminated A is read as guanine during reverse transcription, each m6A site is pinpointed by an A-to-G signature at single-base resolution with quantitative stoichiometry.
Arraystar Single-Nucleotide RNA m6A Modification Seq(CAM-Seq) is provided as an end-to-end sample-to-data service, from RNA sample QC and mild CAM chemical treatment through library construction, sequencing, and bioinformatics analysis. Compared with glyoxal-based deamination methods such as GLORI2-seq, CAM-seq operates under milder near-neutral chemistry with a kethoxal guanine-protecting group, minimizing RNA degradation and reverse-transcription stalling while achieving substantially lower background noise.
Benefits
Unmatched precision: Pinpoints individual m6A modification sites at single-base resolution.
Absolute stoichiometry quantification: Selective A-to-I deamination provides accurate m6A modification ratios.
Gentle near-neutral chemistry: Mild reaction conditions with a reversible kethoxal guanine-protecting group preserve RNA integrity.
Superior specificity and unbiased detection: Antibody-free and motif-unbiased, avoiding cross-reactivity and false negatives.
Low background noise: Optimized reverse transcriptase conditions minimize background for clean, reliable detection.
| Service Name | RNA Class | Price |
|---|---|---|
| Single-Nucleotide RNA m6A Modification Seq(CAM-Seq) | mRNA | |
| Single-Nucleotide RNA m6A Modification Seq(CAM-Seq) | mRNA & lncRNA |
Background
Classic antibody-based m6A profiling (e.g., MeRIP-seq) offers limited resolution and intrinsic motif bias, while earlier chemical deamination methods rely on harsh acidic conditions that degrade RNA and demand high input, putting absolute single-base m6A quantification out of reach. The same workflow extends to long non-coding RNAs (lncRNAs), enabling researchers to profile this modification on lncRNA transcripts in parallel with mRNA in a single assay.
Our Single-Nucleotide RNA m6A Modification Seq(CAM-Seq) overcomes these barriers through cooperative catalysis: a carbonyl organocatalyst and a Lewis acid (boric acid) selectively deaminate unmodified adenosine (A) to inosine (I) under mild, near-neutral conditions, while m6A resists deamination and is read as adenine (Fig. 1). A reversible kethoxal guanine-protecting group preserves RNA integrity, and optimized conditions keep background noise below 0.5%, delivering absolute m6A stoichiometry at true single-base resolution.
Figure 1. CAM-seq m6A detection scheme. Mild near-neutral chemistry (pH ~6) selectively deaminates unmodified adenosine (A) to inosine (I), which is read as G, while m6A resists deamination and is read as A. The A/G ratio at each site yields absolute m6A stoichiometry at single-base resolution.
Key concept: Single-Nucleotide RNA m6A Modification Seq(CAM-seq) is a chemical method in which cooperative catalysis selectively deaminates unmodified adenosine to inosine while m6A resists, enabling absolute single-base m6A quantification.
Workflow
Five steps from RNA sample to single-base m6A data:
Figure 2. Single-Nucleotide RNA m6A Modification Seq workflow.
Bioinformatics
The bioinformatics pipeline maps sequencing reads to the reference genome, detects A-to-G conversion signatures, and quantifies m6A modification stoichiometry at single-nucleotide resolution. Analyses include motif characterization (GAC, AAC, and non-canonical motifs), metagene distribution, differential methylation, functional enrichment, and genome-browser visualization, providing a complete quantitative view of the m6A epitranscriptome.
Deliverables
- Raw m⁶A mRNA sequencing data files (FASTQ format), fully compliant with GEO/SRA submission specifications.
- QC reports plus sorted indexed BAM alignment files with core mapping statistics for m⁶A quantification.
- High-confidence single-base m⁶A site tables (XLSX) with genomic coordinates, host genes, and absolute stoichiometry.
- Single-base m⁶A transcript feature distribution plots and consensus m⁶A motif logos (PDF/PNG format).
- Single-base differential m⁶A methylation tables (XLSX) with quantitative fold change and statistical significance.
- Gene Ontology (GO) enrichment analysis reports for m⁶A-modified genes, available in HTML/PDF/PNG formats.
- Genome browser-compatible m⁶A signal track files (bigWig/bedGraph) and a complete structured project report.
Research Applications
- Plant and crop research: Cross-species single-base m6A maps (111,121 Arabidopsis and 141,990 maize sites) extend epitranscriptomic studies from model plants to crops.
- Neuroscience: Single-base m6A landscapes of brain tissues and neuronal transcripts support studies of m6A in neural function and disease.
- Cancer research: Absolute m6A stoichiometry at individual sites in tumor versus normal samples helps identify dysregulated methylation and candidate biomarkers.
- Stem cell and developmental biology: Resolve m6A dynamics at single sites during cell fate commitment and tissue development.
- Gene regulation and systems biology: Saturated m6A maps with quantified stoichiometry enable unbiased gene-level comparisons across genes, pathways, and conditions.
References
[1] Wang P, Ye C, Zhao M, Jiang B, He C. Small-molecule-catalysed deamination enables transcriptome-wide profiling of N6-methyladenosine in RNA. Nature Chemistry 2025. DOI: 10.1038/s41557-025-01801-3.
[2] Garcia-Campos MA, et al. Deciphering the “m6A code” via antibody-independent quantitative profiling. Cell 2019;178:731-747. DOI: 10.1016/j.cell.2019.06.013.
Sample Requirements
Storage Guidelines
Cells and Tissues: Preserve in TRIzol or an RNA stabilization solution; snap freeze in liquid nitrogen and store at –80 °C.
RNA: Resuspend in ethanol or RNase-free ultrapure water; store at –80 °C and avoid multiple freeze-thaw cycles.
Shipping Instructions
Place the sample in a 1.5 mL RNase-free microcentrifuge tube.
Seal the tube with parafilm or a cap lock to ensure sample integrity.
Ship the package on dry ice with adequate insulation to maintain the required temperature.
| Sample Type | Notes |
|---|---|
| Whole blood | Use EDTA tubes only, as heparin is not compatible with subsequent analytical procedures. |
| Cultured cells | Submission of cell pellets is preferred to ensure high-quality material for processing. |
| Tissue | Provide fresh or frozen specimens, ensuring that necrotic material is strictly avoided. |
| Total RNA | Maintain an OD 260/280 ratio ≥ 1.8 and RIN ≥ 7 with no visible degradation. Submit at least 1 µg total RNA. |
FAQ
What sample types are compatible with Single-Nucleotide RNA m6A Modification Seq(CAM-Seq)?
We accept total RNA extracted from cells, tissues, blood, or other biological sources such as cultured cell pellets and frozen tissue specimens. If you are unsure whether your sample type or preparation is suitable, contact our technical support team for confirmation before submission.
Can CAM-seq identify m6A at single-base resolution?
Yes. Unmodified adenosine is selectively deaminated to inosine and read as guanine during reverse transcription, while m6A resists deamination and is read as adenine. This A-to-G signature pinpoints every m6A site at single-base resolution and simultaneously quantifies its modification stoichiometry with high accuracy.
How does CAM-seq differ from antibody-based or other chemical methods?
Antibody-based methods such as MeRIP-seq offer limited resolution and intrinsic motif bias. CAM-seq is antibody-free and uses mild near-neutral chemistry with a reversible kethoxal guanine-protecting group, avoiding RNA degradation and reverse-transcription stalling, and achieving background noise below 0.5% for unbiased detection.
What advantages does CAM-seq offer over GLORI2-seq?
CAM-seq is built on cooperative catalysis—a carbonyl organocatalyst paired with boric acid as a Lewis acid—that selectively deaminates unmodified adenosines while leaving m6A intact. This antibody-free chemistry delivers robust, single-base m6A quantification with high specificity and consistent performance. Compared with other chemical approaches, CAM-seq offers a clean, efficient conversion and integrates seamlessly into a complete sample-to-data workflow, making it a strong choice for publication-ready, quantitative m6A profiling.
Does this service also profile lncRNA?
Yes. We provide two service options: mRNA modification, and mRNA plus long non-coding RNA (lncRNA) modification. Both transcript types can be analyzed together in a single experiment, so there is no need to split them into two projects, and the scope of your study opens up accordingly.
!This assay is provided for research applications only and is not intended for clinical diagnosis, treatment, or personal health evaluation.