Pseudouridine (Ψ) Profiling Service

Traditional methods for pseudouridine detection often suffer from low throughput, limited specificity, or inability to achieve transcriptome-wide coverage, constraining systematic studies of its regulatory functions. Pseudouridine (Ψ) profiling technologies overcome these barriers by utilizing Ψ-specific chemical labeling or enzymatic approaches combined with next-generation sequencing, enabling precise, high-resolution mapping across diverse RNA species. CD BioSciences delivers comprehensive pseudouridine profiling services, empowering researchers to decode the roles of Ψ in RNA stability, translation efficiency, and disease mechanisms.

Introduction to Pseudouridine (Ψ) Profiling

Pseudouridine (Ψ) profiling encompasses a suite of high-throughput sequencing techniques designed for transcriptome-wide identification and localization of pseudouridine, the most abundant post-transcriptional RNA modification. The core methodology relies on the unique chemical property of Ψ, which can be specifically labeled using reagents like CMCT (N-cyclohexyl-N’-(2-morpholinoethyl)-carbodiimide methyl-p-toluenesulfonate) or through enzymatic detection approaches. During reverse transcription, these labeled sites cause characteristic truncations or mutations in cDNA synthesis, which are then captured through sequencing. This allows for precise mapping of Ψ sites at nucleotide resolution across mRNAs, non-coding RNAs, and ribosomal RNAs, providing crucial insights into how Ψ modulates RNA structure, protein-RNA interactions, and cellular processes.

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)

Features of Pseudouridine (Ψ) Profiling

Pseudouridine (Ψ) profiling is designed to address the unique challenges of detecting this structurally subtle yet functionally critical RNA modification. By leveraging highly specific chemical reactions or enzymatic recognition, this approach transforms the biochemical signature of Ψ into a detectable sequencing signal, enabling researchers to move beyond qualitative detection to achieve quantitative, transcriptome-wide mapping with the precision needed for mechanistic studies. The key strengths of this technology include:

Transcriptome-Wide Coverage: Enables systematic identification of Ψ sites across all RNA classes without prior knowledge of target regions.
Single-Nucleotide Resolution: Precisely maps Ψ modifications to specific genomic coordinates, allowing detailed mechanistic studies.
High Specificity & Sensitivity: Chemical/enzymatic approaches minimize false positives while detecting low-abundance Ψ sites.
Dynamic Modification Analysis: Supports comparative profiling to track Ψ changes under different biological conditions or treatments.

Our Services

CD BioSciences offers end-to-end pseudouridine (Ψ) profiling services utilizing optimized chemical labeling and sequencing protocols. We provide robust, reproducible detection of Ψ modifications across your RNA samples, delivering data that reveals how this "fifth nucleotide" influences RNA fate and function in development, stress response, and disease pathology.

One-stop Solution for Pseudouridine (Ψ) Profiling

Service	Technological Advantages	Key Applications
CMC-based Ψ Profiling Service	Relies on well-established CMC chemistry for specific Ψ adduct formation. Cost-effective with robust and reproducible results.	Standard transcriptome-wide Ψ discovery in abundant RNA types (e.g., rRNA, snRNA). Initial screening and validation studies.
Pseudo-seq Service	Incorporates photo-crosslinking to improve specificity and reduce false positives. Enhanced signal-to-noise ratio for more precise site calling.	High-confidence mapping of Ψ sites, especially in complex RNA mixtures. Studies requiring stringent site validation.
PSI-seq Service	Utilizes Ψ-specific antibodies for immunoprecipitation prior to sequencing. Effective enrichment of Ψ-containing RNA fragments.	Focused profiling of Ψ modifications in specific RNA populations (e.g., polyA+ mRNA). Investigation of Ψ dynamics under different cellular conditions.
ICE-seq Service	Employs the naturally occurring Ψ-specific endonuclease, ICE (intron-encoded endonuclease). Enables antibody-free, enzyme-mediated direct detection and cleavage at Ψ sites.	Highly specific, enzymatic detection of Ψ without chemical labeling. Ideal for validating Ψ sites identified by chemical methods or studying Ψ in structured RNA regions.
CeU-Seq Service	Combines chemical labeling with biotin pulldown for high-sensitivity enrichment. Exceptionally high signal-to-noise ratio, suitable for low-abundance RNA.	Discovery of Ψ sites in low-input samples or on low-copy-number transcripts. High-resolution mapping where maximum sensitivity is required.

Workflow of Pseudouridine (Ψ) Profiling

Supported Sample Types

Cultured Cells: Adherent cell lines, suspension cells, primary cells, stem cells, organoids.
Animal & Clinical Tissues: Fresh tissues, snap-frozen tissues, FFPE tissue sections, human biopsies.
Specific RNA Populations: Total RNA, poly(A)+ mRNA, rRNA-depleted RNA, tRNA, snRNA, specific non-coding RNA fractions.
Low-Input & Specialized Samples: Sorted cells (e.g., FACS-sorted), rare cell populations, small tissue biopsies, extracellular vesicles (EVs), limited clinical specimens.
Plant, Yeast & Microbial Samples: Plant leaves/tissues, yeast cultures, bacterial RNA (subject to consultation on RNA isolation protocols).

Our Advantages

Multiple Chemistry Options: Expertise in both CMCT-based and emerging enzymatic detection methods for optimal Ψ profiling.
Reduced False Discovery Rates: Advanced bioinformatics pipelines distinguish true Ψ signatures from background noise and other modifications.
Broad Dynamic Range: Capable of detecting Ψ sites across expression levels, from abundant rRNAs to low-copy regulatory RNAs.
Integrated Functional Analysis: Data interpretation includes structural predictions, conservation analysis, and correlation with RBP binding sites.

Accurate mapping of pseudouridine (Ψ) is essential for understanding its multifaceted roles in RNA biology and disease. For comprehensive modification analysis, CD BioSciences also provides complementary services including LC-MS/MS for absolute Ψ quantification and Ψ-specific RNA immunoprecipitation sequencing (RIP-seq), enabling fully customized research strategies. Contact us to discuss how pseudouridine (Ψ) profiling can advance your epitranscriptomic research.

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.