RNA Pseudouridine (Ψ) Analysis

Pseudouridine (Ψ), known as the "fifth nucleoside," is a pervasive and functionally critical RNA modification that stabilizes RNA structure and fine-tunes genetic decoding. CD BioSciences provides state-of-the-art, end-to-end pseudouridine analysis services, enabling researchers to precisely locate, quantify, and understand the role of Ψ across diverse RNA species and biological contexts.

Overview of Pseudouridine (Ψ)

Pseudouridine (Ψ) is the most abundant post-transcriptional modification found in RNA. It is formed through an isomerization reaction that rotates the uracil base 180 degrees and creates a carbon-carbon glycosidic bond (instead of the usual carbon-nitrogen bond), linking it to the ribose sugar. This unique "C-glycosidic" bond confers greater structural stability to the RNA molecule. Ψ plays essential and multifaceted biological roles: it acts as a key structural stabilizer for non-coding RNAs (e.g., rRNA, tRNA), ensures translational fidelity by fine-tuning codon-anticodon interactions, and functions as a dynamic cellular regulator in mRNA to influence splicing, translation, and stop codon recognition.

The research significance of Ψ is profound, as its dysregulation is implicated in human diseases such as cancers and mitochondrial disorders, while its unique capacity to evade innate immune detection has made synthetic Ψ a critical component in the development of next-generation mRNA therapeutics and vaccines. Therefore, precise mapping and quantification of Ψ are indispensable for advancing both fundamental molecular biology and applied biomedical innovation.

Pseudouridine (Ψ) modification and techniques that can be used to draw Ψ maps.

Fig.1 Pseudouridine (Ψ) modification and available technologies for mapping Ψs. (Ramakrishnan M, et al., 2022)

Our Services

Leveraging cutting-edge sequencing and mass spectrometry platforms, CD BioSciences empowers your research with a complete suite of pseudouridine (Ψ) analysis solutions. We combine robust experimental biochemistry with deep bioinformatics expertise to transform your RNA samples into reliable, interpretable data. From discovery-phase profiling to targeted validation, our tailored services are designed to help you uncover the functional impact of Ψ modifications in your system of interest.

Comprehensive Pseudouridine (Ψ) Analysis Solution

Our integrated approach combines cutting-edge chemical biology, high-throughput sequencing, and precise mass spectrometry to deliver not just data, but actionable insights into the location, abundance, and biological impact of this pivotal RNA modification across diverse RNA species.

Ψ-Seq Service
CeU-Seq Service
Pseudo-Seq Service
PSI-Seq Service
ICE-Seq Service

RIP-Seq Service
RTL-P Service
Ψ-qPCR Service
LC-MS/MS for Ψ Quantification
CMC-based Ψ Profiling Service

Workflow of RNA Ψ Analysis Service

To ensure consistent, high-quality results across our diverse technology portfolio, CD BioSciences has established a standardized yet flexible project workflow. This end-to-end process is built on rigorous quality control, expert execution at every stage, and transparent communication, guiding your project from initial consultation to the delivery of reliable, publication-ready data.

Core Steps	Description
Project Consultation & Design	We begin with a collaborative consultation where our specialists analyze your research objectives, sample type, and desired outcomes. Based on this, we recommend the optimal profiling strategy and co-design a detailed project plan that outlines experimental steps, controls, deliverables, and timelines.
Sample Preparation & Stringent QC	Upon receiving your RNA samples, we perform a comprehensive quality assessment. This includes evaluating RNA integrity (RIN), purity, and concentration using Bioanalyzer, spectrophotometry, and fluorometric methods. Samples must meet our strict QC benchmarks before proceeding to the core analytical stage.
Core Analysis Execution (Technology-Specific)	This pivotal step is customized to the chosen service. For sequencing-based methods (e.g., Ψ-Seq, Pseudo-Seq), it involves Ψ-specific chemical treatment and high-quality library construction. For quantification services (e.g., LC-MS/MS), it entails sample digestion and instrumental setup. All protocols follow optimized SOPs to ensure specificity and reproducibility.
Data Generation & Primary Processing	Processed samples are run on our dedicated platforms: sequencing libraries on Illumina systems or prepared digests on high-sensitivity mass spectrometers. We perform real-time monitoring of key metrics (e.g., sequencing depth, chromatographic peaks) and conduct primary data processing (e.g., base calling, spectral analysis) to generate raw data files.
Bioinformatics & Advanced Data Analysis	Our bioinformatics team processes the raw data through specialized pipelines. For sequencing data, this includes read alignment, Ψ site calling, differential analysis between sample groups, and motif discovery. For MS data, it involves precise peak integration and stoichiometry calculation. Integration with orthogonal datasets (e.g., RNA-Seq) is available for functional insights.
Comprehensive Reporting & Delivery	You receive a final project report containing all raw and processed data, publication-ready visualizations (e.g., genome browser tracks, scatter plots), and a clear biological interpretation of the results. We highlight significant findings, such as differentially modified sites or quantitative changes, and provide context for their potential functional implications in your research system.

Our Advantages

Broad RNA Type Compatibility: Our optimized protocols are validated for a wide range of RNA types, including mRNA, tRNA, rRNA, snoRNA and more, allowing comprehensive profiling across the transcriptome.
High-Resolution Mapping Expertise: We specialize in chemical-based sequencing methods (Ψ-Seq/CeU-Seq) that achieve single-nucleotide resolution, providing precise localization of Ψ sites without antibody dependency.
Integrated Quantification & Validation: We seamlessly combine discovery-grade sequencing with absolute LC-MS/MS quantification and site-specific validation assays, offering a complete verification loop for your findings.
Dedicated Bioinformatics Support: Our analysis goes beyond basic site calling to include differential analysis, functional enrichment, and correlation with RNA expression data, delivering actionable biological insights.

At CD BioSciences, our expertise in the epitranscriptome extends beyond pseudouridine (Ψ). We provide a comprehensive portfolio of services for the analysis of other critical RNA modifications and editing events, including m6A, m5C, ac4C, m6Am, m7G, m1A and RNA adenosine-to-inosine (A-to-I) editing analysis. Whether your focus is on fundamental mechanism discovery, biomarker identification, or therapeutic RNA optimization, we offer fully customized, end-to-end solutions to meet your specific research objectives and drive your projects to success. To propel your research forward, please feel free to contact us for detailed consultation and a customized project quotation.

Reference

1. Ramakrishnan M, Rajan K S, Mullasseri S, et al. The plant epitranscriptome: revisiting pseudouridine and 2'‐O‐methyl RNA modifications[J]. Plant biotechnology journal, 2022, 20(7): 1241-1256.