Single-Base RNA Modification Sequencing
– Mapping and Quantification of RNA Modifications at Single-Nucleotide Resolution
RNA modifications are dynamic regulators of RNA structure, stability, processing, translation, and cellular function. Identifying modification sites at single-nucleotide resolution can reveal modification landscapes that are not accessible through conventional region-level enrichment approaches.
Arraystar Single-Nucleotide RNA Modification Sequencing provides modification-specific sequencing solutions for precise mapping and, where applicable, quantitative analysis of diverse RNA modifications, including m6A, pseudouridine (Ψ), m5C, m1A, ac4C, 2′-O-methylation (Nm), dihydrouridine (D), m3C, m7G, and O8G.
Why Choose Single-Nucleotide RNA Modification Sequencing?
Single-Nucleotide Resolution
Precisely localize RNA modification sites at individual nucleotide positions rather than reporting only modification-enriched regions.
Quantitative Modification Analysis
Where supported by the method, modification stoichiometry can be determined at individual sites, enabling quantitative comparisons between biological conditions.
Modification-Specific Strategies
Different RNA modifications have distinct chemical and structural properties. Arraystar applies modification-specific chemical conversion, enzymatic, or enrichment strategies to match the detection principle with the modification of interest.
Transcriptome-Wide Profiling
Depending on the selected method and RNA class, single-nucleotide sequencing can be used to investigate RNA modifications across transcriptomes and specific RNA populations.
Integrated Sample-to-Data Workflow
Arraystar provides an end-to-end workflow covering sample QC, modification-specific treatment or enrichment, library construction, sequencing, and bioinformatics analysis.
Featured Single-Nucleotide RNA Modification Sequencing Services
- m6A Modification
CAM-seq uses cooperative chemical catalysis to selectively deaminate unmodified adenosine while m6A remains resistant, generating an A-to-G sequencing signature for single-base m6A detection and quantitative analysis.
GLORI2-seq uses antibody-free chemical conversion to distinguish m6A from unmodified adenosine, enabling single-base m6A mapping and quantitative profiling.
- Pseudouridine & Inosine
BID-seq exploits the resistance of pseudouridine to bisulfite treatment to generate a characteristic deletion signature for single-base Ψ mapping.
BACS-seq uses controlled bisulfite chemistry to generate a detectable signature for pseudouridine and enables base-resolution Ψ analysis.
Ψ & Inosine BACS-seq combined BACS-seq workflow enables simultaneous profiling of pseudouridine and inosine at single-nucleotide resolution.
- m5C Modification
BS-seq: Bisulfite conversion distinguishes unmodified cytidine from m5C, enabling single-nucleotide mapping of m5C sites.
- m1A Modification
m1A-Quant-seq enables single-nucleotide detection and quantitative profiling of m1A modification sites.
- ac4C Modification
RedaC:T-seq is an antibody-free, base-resolution method for mapping and quantifying N4-acetylcytidine (ac4C), providing site-specific information across protein-coding transcripts.
- 2′-O-Methylation
NM-seq uses periodate-based oxidation-elimination-dephosphorylation chemistry to selectively enrich 2′-O-methylated RNA fragments and map Nm sites at single-nucleotide resolution. The service supports profiling of Nm across mRNA and lncRNA, with additional RNA classes detectable within the same workflow.
- Dihydrouridine
CRACI-seq enables single-nucleotide mapping and quantitative analysis of dihydrouridine (D) using a modification-specific chemical conversion strategy.
- m3C Modification
HAC-seq uses hydrazine-aniline-mediated cleavage to generate a characteristic signal for single-base m3C detection and quantitative profiling.
m3C-IP-seq uses antibody-based enrichment to profile m3C-modified RNA at single-nucleotide resolution and provides an alternative strategy for m3C analysis.
- m7G Modification
m7G-Quant-seq is designed to distinguish internal m7G from the 5′ cap and provides single-base mapping and quantitative analysis of internal m7G.
- O8G Modification
O8G-miSeq combines O8G-specific immunoprecipitation with high-depth sequencing and G-to-T mutation analysis to localize O8G sites at single-nucleotide resolution, with a focus on miRNA and pri-miRNA.
How to Choose the Right RNA Modification Sequencing Method?
The appropriate method depends on four key factors:
- 1. Which RNA modification are you studying?
Select a method specifically designed for the modification of interest. - 2. Which RNA class is your target?
mRNA, lncRNA, miRNA, pri-miRNA, tRNA, and rRNA may require different workflows and sample preparation strategies. - 3. What is your available sample input?
Input requirements vary substantially among modification-specific workflows. Review the individual service requirements before sample preparation.
From Modification Mapping to Biological Insight
Single-nucleotide RNA modification profiles can be integrated with RNA expression, transcript structure, translation, and functional assays to investigate how site-specific RNA modifications contribute to gene regulation and disease biology.
Explore Arraystar’s RNA modification sequencing services to identify, quantify, and interpret RNA modifications at single-nucleotide resolution. Discuss Your Project →