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Single-Base tRNA Modification Sequencing
Single-Nucleotide tRNA m1A Modification Seq(m1A-Quant-seq)
tRNA m1A is a base modification that organises the folded tRNA architecture and stabilises codon–anticodon pairing. m1A-quant-seq passes an engineered reverse transcriptase across N1-methyladenosine in tRNA, so each m1A-bearing position emits a discrete mutation signature that pinpoints and quantifies the site at single-base resolution without disturbing the surrounding tRNA sequence.
Arraystar delivers this as a complete tRNA workflow, from sample QC and tRNA enrichment through reverse transcription, library prep, sequencing and tRNA-aware bioinformatics, returning per-site m1A values and absolute stoichiometry so that laboratories can interpret the biology rather than assemble the assay.
Benefits
Single-base resolution in tRNA: locates m1A across the tRNA transcriptome by reading through every base.
Absolute stoichiometry: derives the m1A fraction at a site from the ratio of reverse-transcription signatures.
Read-through in structured tRNA: the engineered enzyme progresses through modified, tightly folded tRNA regions.
Low sample input: nanogram quantities of tRNA are sufficient, suiting precious or restricted materials.
Antibody-free: bypasses enrichment, removing pull-down bias and cross-reactivity inside compact tRNAs.
Functional annotation: sites are mapped within mature tRNA with anticodon, isotype and isodecoder assignment.
| Service Name | RNA Class | Price |
|---|---|---|
| Single-Nucleotide tRNA m1A Modification Seq(m1A-Quant-seq) | tRNA |
Background
The N1-methyladenosine mark at conserved tRNA positions (for example nucleotide 9, 14 or 58) stabilises the L-shaped fold and tunes aminoacylation and decoding fidelity. Loss or gain of these sites disturbs translation and has been linked to developmental defects and cancer phenotypes.
Antibody-capture strategies provide only coarse resolution and contend with the dense structure of tRNA. m1A-quant-seq instead relies on an engineered reverse transcriptase whose processivity survives m1A; as it crosses the modified base it leaves a reproducible mismatch, and the mutation proportion at that position reflects the m1A level.
Figure 1. m1A-quant-seq scheme for tRNA. The engineered reverse transcriptase reads through the N1-methyladenosine base and produces a characteristic mutation signature; the mutation rate at that base equals m1A%.
Key concept: Single-Nucleotide RNA m1A Modification Seq(m1A-Quant-seq) is an antibody-free method in which an engineered reverse transcriptase reads through m1A and records a reproducible mutation signature, enabling base-resolution mapping and absolute stoichiometry of m1A.
Workflow
Figure 2. m1A-quant-seq workflow for tRNA. Total RNA is depleted of ribosomal and messenger transcripts, fragmented, and divided into a background-control arm and an untreated arm; both arms are copied by the engineered reverse transcriptase, converted into libraries, sequenced and mapped so that m1A is scored and quantified.
tRNA enrichment: total RNA is cleared of ribosomal and messenger RNA by established tRNA isolation.
Fragment sizing: tRNA is broken into uniform pieces to allow efficient reverse transcription.
Background control: one aliquot is demethylated with AlkB as a baseline; the partner aliquot is left native.
Reverse transcription: both aliquots are transcribed by the engineered enzyme into sequencing libraries.
Sequencing and analysis: reads are aligned to a reference tRNA set and m1A is reported as a mutation signature with background correction.
Bioinformatics
The tRNA-aware analysis maps m1A at base resolution, quantifies per-site stoichiometry and flags differential modification. Every site is assigned to the reference tRNA library with anticodon, isodecoder, isotype and structural-domain context, and results are provided as tables, distribution and motif figures, and browser-ready tracks.
Deliverables
- Raw tRNA m1A sequencing reads (FASTQ) for repository deposition.
- Sample and sequencing QC reports with sorted BAM alignment files and mapping statistics.
- High-confidence single-base m1A site tables (XLSX) listing coordinates, tRNA identity and m1A stoichiometry.
- tRNA feature distribution figures and m1A consensus motif logos (PDF/PNG).
- Differential m1A analysis tables (XLSX) with fold-change and significance values.
- Gene Ontology enrichment for the host genes of m1A-modified tRNAs (HTML/PDF/PNG).
- Genome-browser tracks (bigWig/bedGraph) and a structured project report.
Research Applications
- m1A is an adjustable tRNA decoration that influences translational output and tRNA turnover. Since m1A-quant-seq delivers absolute modification levels, it is suited to tying shifts at specific tRNA positions to codon usage, protein synthesis and stress or disease states.
- Translation control: profiling m1A occupancy on particular tRNAs and comparing it with codon-biased translation.
- tRNA structure and stability: linking m1A levels at conserved positions to folding and turnover.
- Cancer and development: mapping m1A changes on tRNA isotypes that participate in tumour or developmental programmes.
References
[1] Li, X., Xiong, X., Zhang, M., Wang, C., Qian, S. B., & Yi, C. (2017). Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts. Molecular Cell, 68(5), 993-1005. DOI: 10.1016/j.molcel.2017.10.019.
[2] Wang, Y., & Zhang, J. (2024). Methyladenosine m1A RNA modification and cancer: Methodologies and clinical perspectives. MDPI Life, 14(10), 1230. DOI: 10.3390/life14101230.
[3] Zhao, Y., et al. (2024). Chemical manipulation of m1A mediates its high-sensitivity detection in human small RNA sequencing. RNA Journal, 30(5), 580-592.
Sample Requirements
Purified total RNA is preferred; the service also offers RNA extraction from cells, tissues, blood or other sources. If the material amount is below the recommended level, contact support@arraystar.com for guidance.
Storage Guidelines
Cells and Tissues: preserve in TRIzol (cells or tissues) or RNAlater (tissues); store at -80 C.
RNA: resuspend in ethanol or RNase-free water; store at -80 C and avoid repeated freeze-thaw.
Shipping Instructions
Place sample in a 1.5 mL RNase-free tube.
Seal with parafilm or a cap lock to protect integrity.
Ship on dry ice with adequate insulation.
| 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 10 µg total RNA. |
FAQ
Can m1A-quant-seq identify m1A in tRNA at single-base resolution?
Yes. During reverse transcription the engineered enzyme records a mutation at the m1A position, so every site is located and quantified to a single nucleotide.
What data will I receive?
You receive raw reads, QC and mapping reports, single-base m1A tables with tRNA annotation and stoichiometry, distribution and motif plots, and a project report.
How does this differ from antibody-based tRNA m1A profiling?
No enrichment is used, so the assay avoids pull-down bias and can interrogate compact, structured tRNA; it delivers quantitative site-level m1A rather than broad regional signal.
What sample type is suitable?
Purified total RNA is preferred, and RNA extraction is available. Nanogram-to-microgram inputs are typical, with options on request.
Why is high-resolution tRNA m1A detection valuable?
Precise positions reveal which isotypes and anticodons carry the mark, giving a clearer link between m1A and translation or disease.
How long does the service take?
Turnaround depends on sample type and scope; contact info@arraystar.com for an estimate.
!This assay is provided for research applications only and is not intended for clinical diagnosis, treatment, or personal health evaluation.