No products in the cart.
Single-Base RNA Modification Sequencing
Single-Nucleotide RNA 2'-O-Me Modification Seq(NM-seq)
Single-Nucleotide RNA 2'-O-Methylation Modification Seq(NM-Seq) maps 2'-O-methylation (Nm) sites with base precision across mRNA and lncRNA. The method exploits the differential reactivity of periodate toward 2'-hydroxyl versus 2'-O-methylated nucleotides, running repeated oxidation-elimination-dephosphorylation (OED) cycles to enrich Nm-containing fragments before sequencing.
Arraystar provides an end-to-end sample-to-data workflow, from RNA QC and OED enrichment through library construction, sequencing, and bioinformatics, delivering an Nm landscape across the transcriptome.
Benefits
Single-base resolution: chemically resolves each 2'-O-methylation site at nucleotide precision.
High-throughput: profiles Nm genome-wide across mRNA and lncRNA in parallel.
Broad RNA coverage: detects Nm on mRNA, lncRNA, pri-miRNA, tRNA, and rRNA.
Chemical method: antibody-free periodate chemistry avoids enrichment bias.
Robust enrichment: repeated OED cycles concentrate methylated fragments.
One-stop service: RNA extraction, preprocessing, library, sequencing, and analysis.
| Service Name | RNA Class | Price |
|---|---|---|
| Single-Nucleotide RNA 2'-O-Methylation Modification Seq(NM-Seq) | mRNA | |
| Single-Nucleotide RNA 2'-O-Methylation Modification Seq(NM-Seq) | mRNA & lncRNA |
Background
2'-O-methylation (Nm) is an abundant modification at the 2'-hydroxyl of the RNA ribose, deposited by 2'-O-methyltransferases (such as the spoUT family) or C/D-box snoRNPs. It is found in rRNA, snRNA, mRNA, tRNA, snoRNA, and siRNA, and regulates RNA stability, structure, biogenesis, splicing, and translation.
In mammals, 2'-O-methylation also marks self versus non-self mRNA and is important in innate immune sensing.
Key concept: Single-Nucleotide RNA 2'-O-Methylation Modification Seq(NM-Seq) is a chemical sequencing method that uses periodate-based oxidation-elimination-dephosphorylation (OED) cycles to selectively degrade unmodified nucleotides, so 2'-O-methylated sites resist cleavage and are mapped at single-base precision.
Figure 1. Single-Nucleotide RNA 2'-O-Me Modification Seq scheme.
Workflow
Five steps from RNA sample to single-base 2'-O-methylation data:
Sample QC: assess RNA integrity, purity, and input amount.
OED enrichment: run oxidation-elimination-dephosphorylation cycles to remove unmodified nucleotides.
Library construction: ligate adapters at the exposed 3' end of methylated fragments.
Sequencing: sequence on an Illumina platform to a depth sufficient for Nm calling.
Bioinformatics: align and quantify Nm sites at single-base resolution.
Figure 2. Single-Nucleotide RNA 2'-O-Me Modification Seq workflow.
Bioinformatics
The pipeline maps reads to the transcriptome and identifies positions where 2'-O-methylation protects the nucleotide from OED degradation, reporting Nm stoichiometry at base resolution. Analyses include motif characterization, differential modification, and genome-browser visualization.
Deliverables
- Raw FASTQ data files, ready for GEO/SRA public database submission.
- QC report with BAM alignment files and core mapping statistics.
- Single-base 2'-O-methylation site tables (XLSX) with coordinates and stoichiometry.
- Nm distribution and motif figures across mRNA and lncRNA (PDF/PNG).
- Differential Nm modification tables (XLSX) with fold change and significance.
- Functional enrichment reports for Nm-bearing transcripts.
- Genome-browser track files (bigWig/bedGraph) and a structured project report.
Research Applications
- mRNA function: link Nm to transcript stability, splicing, and translation.
- Immune response: study Nm as a self/non-self signal in innate immunity.
- Viral RNA: profile Nm on viral transcripts and host immune evasion.
- Development and differentiation: track Nm dynamics across cell states.
- Disease research: identify differentially methylated Nm sites as biomarkers.
- LncRNA biology: assess Nm on long non-coding RNAs and their regulators.
References
[1] Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. Nature Methods 2019; DOI: 10.1038/nmeth.4294.
[2] FTSJ3 is an RNA 2'-O-methyltransferase recruited by HIV to avoid innate immune sensing. Nature 2019; DOI: 10.1038/s41586-018-0841-4.
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 100–300 µg total RNA. |
FAQ
What is 2'-O-methylation?
2'-O-methylation (Nm) is a modification at the 2'-hydroxyl of the ribose, deposited by methyltransferases or C/D-box snoRNPs, regulating RNA stability, structure, splicing, and translation.
How does NM-Seq achieve single-base resolution?
Periodate differential reactivity degrades unmodified nucleotides through OED cycles while 2'-O-methylated sites resist cleavage, mapping Nm at base precision.
What RNA types are covered?
The service profiles Nm across mRNA and lncRNA primarily, and also detects Nm on pri-miRNA, tRNA, and rRNA within the same assay.
How does this differ from antibody-based methods?
NM-Seq is antibody-free chemical sequencing, avoiding enrichment bias and providing base-resolution Nm calling across the transcriptome.
Does the service provide interpretations?
The pipeline reports Nm site tables, CDS/splice-site distribution, motif analysis, differential modification, and enrichment of Nm-bearing transcripts.
!This assay is provided for research applications only and is not intended for clinical diagnosis, treatment, or personal health evaluation.