Introduction
Why tRNA Modifications Matter
Transfer RNAs (tRNAs) undergo extensive post-transcriptional modifications that extend far beyond their canonical role in amino acid delivery. These chemical alterations directly govern:
- Structural stability of tRNA folds, particularly in the anticodon loop,
- Decoding fidelity by modulating codon-anticodon interactions,
- Dynamic responses to metabolic shifts or environmental stressors.
Subtle reprogramming of tRNA modifications occurs during metabolic adaptation, cellular stress, and developmental transitions. For investigators studying translational regulation, RNA-protein interactions, or stress signaling networks, profiling tRNA modifications reveals regulatory dimensions inaccessible through transcriptomics alone.
CD Genomics offers two specialized platforms—each tailored to a different analytical goal—enabling researchers to explore tRNA modifications from distinct but complementary angles:
- LC-MS/MS delivers absolute quantification of 36+ modifications (e.g., m⁷G, Ψ, ac⁴C),
- Antibody-based mapping resolves modification sites nucleotide-by-nucleotide. This synergy provides comprehensive coverage—from global modification stoichiometry to context-specific functions—to advance mechanistic studies in epitranscriptomics.
Platform
A Dual-Pronged Platform: Precision Meets Resolution
To meet the diverse needs of tRNA modification research, CD Genomics offers two powerful and distinct analytical strategies. You may choose either approach based on your scientific objective—or combine them for a more comprehensive view.
Option 1: LC-MS/MS for Global Quantification
LC-MS/MS (liquid chromatography–tandem mass spectrometry) enables absolute quantification of multiple tRNA modifications in parallel. Ideal for:
- Measuring overall modification levels
- Tracking global shifts under experimental conditions
- Detecting chemically diverse modifications, including Ψ, m⁵U, ac⁴C, and others
This approach is highly suitable when the focus is on modification abundance and dynamics, rather than positional mapping.
Option 2: Antibody-Enriched Sequencing for Site-Level Detection
For researchers seeking to identify the location of specific modifications on tRNA molecules, antibody-based sequencing (e.g., MeRIP-seq or RIP-seq) offers high-resolution insights. Features include:
- Use of modification-specific antibodies (m⁶A, m¹A, m⁷G, m⁵C, ac⁴C, 2′-O-methylation, etc.)
- Peak-based localization of enriched tRNA regions
- Motif analysis, differential modification comparison, and functional annotation
This method is ideal when your study centers on functional roles or regulatory hotspots of tRNA modifications.
Whether your research demands a global overview or site-specific precision, our platforms are designed to support your goals with flexibility and scientific rigor.
Workflow
Workflow from Your Perspective
We understand that each research project starts with a different question. Whether you're exploring translational fidelity, stress adaptation, or RNA modification dynamics, our service is designed around how you think—not just how we process samples.
"What samples can I use?"
We accept a broad range of input types to match the complexity of your study:
- Total RNA (including small RNA-enriched fractions)
- Cultured cells (adherent/suspension)
- Tissue biopsies
- Blood, serum, plasma, or extracellular vesicles
- FFPE sections (antibody-based workflow only)
Low-input workflows are available for rare or difficult samples.
"Which method fits my research needs?"
- Looking for absolute quantification of modification abundance?
→ Go with LC-MS/MS—ideal for broad profiling and comparative studies.
- Need to map where modifications occur?
→ Choose antibody-enriched sequencing for site-specific resolution.
- Not sure?
→ We're happy to consult on a combined strategy that reveals both stoichiometry and positional context.
"How does the service actually work?"
Here's how our process unfolds—from first contact to data delivery:
Every project is different. We don't force you into a fixed pipeline—we adapt ours to fit your science.
Bioinformatics
Bioinformatics Analysis: From Raw Reads to Functional Insight
High-quality sequencing and mass spectrometry data are only as valuable as the insights they generate. At CD Genomics, our bioinformatics pipeline is engineered specifically for tRNA modification research—bridging analytical depth with biological relevance.
Whether you're investigating global modification trends or zooming in on regulatory sites, we deliver a complete analysis package tailored to your experimental context.
For Antibody-Based Sequencing:
- Read Mapping & Quality Control
Alignment to tRNA and small RNA reference sets with stringent filtering for modification-associated peaks.
- Peak Calling & Enrichment Analysis
Detection of modification-enriched regions using input-normalized immunoprecipitation data.
- Motif Discovery
Identification of conserved sequence motifs within modification sites to reveal enzyme specificity or recognition elements.
- Differential Modification Analysis
Statistical comparison of peak regions across experimental conditions to uncover context-specific regulation.
- Genomic Distribution & Functional Annotation
Classification of peaks relative to tRNA loci and integration with GO/KEGG pathway enrichment for downstream interpretation.
For LC-MS/MS-Based Quantification:
- Modification Profiling Across Conditions
Absolute quantification of dozens of known tRNA modifications with isotopic standard correction.
- Comparative Heatmaps & Clustering
Visualization of modification dynamics across treatment groups, genotypes, or time points.
- Multivariate Analysis (PCA, Hierarchical Clustering)
Dissection of sample-level variation driven by modification composition.
Sample Requirements: Ensuring Quality & Reproducibility
Accurate tRNA modification analysis begins with high-quality input. Our protocols are compatible with a wide range of biological materials, and we maintain rigorous standards to ensure reproducibility across platforms.
Accepted Sample Types
| Sample Type |
Suitable for |
Notes |
| Total RNA |
LC-MS/MS, Antibody-based |
Preferably enriched for small RNA if targeting tRNA only. |
| Cultured Cells |
Both |
Snap-frozen or in RNA-preserving reagents. |
| Tissues |
Both |
Fresh, frozen, or RNAlater-preserved; low-input workflows supported. |
| Plasma/Serum/EVs |
Antibody-based only |
Ultra-low input compatible (≥500 ng total RNA). |
| FFPE Sections |
Antibody-based only |
Requires specialized deparaffinization; consult prior to submission. |
RNA Quality Guidelines
- Concentration: ≥100 ng/μL preferred
- Purity: OD260/280 between 1.8–2.2
- Integrity: RIN ≥7 recommended for optimal data quality
- Avoid: repeated freeze-thaw cycles, phenol contamination, and EDTA-based buffers
Applications
Applications for Research
tRNA modifications are emerging as active regulators, not static marks. By decoding their distribution and dynamics, researchers can access new layers of regulatory control in diverse biological systems. Our platform empowers exploration across multiple fields:
Translational Control & Ribosome Function
- Investigate how specific modifications (e.g., m¹A, Ψ, ac⁴C) affect decoding accuracy, ribosome pausing, and codon bias recognition
- Correlate modification patterns with translation efficiency across cell states
Cellular Stress & Metabolic Adaptation
- Profile stress-induced tRNA reprogramming under hypoxia, nutrient deprivation, oxidative challenge, or heat shock
- Dissect stress granule dynamics and tRNA fragment biogenesis (tRFs)
Developmental Biology & Differentiation
- Track stage-specific or lineage-specific tRNA modification shifts
- Link epitranscriptomic changes with transcriptional and translational rewiring during early development or stem cell fate decisions
Host-Pathogen Interactions & Virology
- Understand how pathogens exploit or disrupt host tRNA modification machinery
- Map changes in tRNA modification profiles during viral replication or immune activation
Neurobiology & Aging Research
- Explore links between tRNA methylation and neural plasticity, axonal growth, or protein homeostasis
- Investigate age-associated tRNA epimutations and their contribution to translation fidelity decline
Advantages
Why CD Genomics
Built for Research. Powered by Precision.
At CD Genomics, we understand that tRNA modification studies demand more than just sequencing—they require accuracy, customization, and interpretability.
Specialist in RNA Epitranscriptomics
Our team brings deep experience in modification mapping, mass spectrometry, and RNA biology. We don't just run protocols—we help refine hypotheses and guide discovery.
Dual-Modality Expertise
Whether you need modification-level quantification via LC-MS/MS or site-specific resolution through antibody-based sequencing, we provide both in a unified service environment, ensuring consistency and cross-validation.
Bioinformatics That Thinks Like You Do
Our in-house bioinformatics team delivers tailored pipelines, not off-the-shelf scripts. From motif discovery to differential modification clustering, we turn raw data into meaningful biological narratives.
Transparent, Researcher-Centric Workflow
You're always in control. We provide detailed QC checkpoints, open communication, and co-interpretation options—no black box processing.
Sample Flexibility & Global Reach
We support a wide range of input types: total RNA, small RNAs, cells, tissues, and even FFPE. No matter your model or system, our team can help build a compatible workflow.
