What is lncRNA translation, and why is it important?

lncRNA translation refers to the process by which long non-coding RNAs (lncRNAs) produce small functional peptides, known as micropeptides. These short peptides can regulate cell signalling, metabolism, and disease progression. Studying lncRNA translation helps researchers uncover previously hidden protein-coding potential within the non-coding genome, providing new insights into gene regulation, cancer biology, and therapeutic target discovery.

How does Ribo-seq differ from RNA-seq in identifying translated regions?

RNA-seq measures overall gene expression by sequencing all RNA molecules, while Ribo-seq captures only RNA fragments protected by ribosomes during translation. This difference allows Ribo-seq to reveal which transcripts are actively translated into proteins or peptides. Combining both technologies provides a dual-omics view of gene regulation, distinguishing between transcriptional activity and translational output.

Can Ribo-seq detect novel peptides encoded by lncRNAs?

Yes. Ribo-seq detects ribosome occupancy at codon-level resolution, enabling the identification of small open reading frames (sORFs) and non-canonical translation events that are often missed by standard RNA-seq. This makes it a powerful tool for discovering new micropeptides encoded by lncRNAs and characterizing their functional roles.

What kind of samples can be used for lncRNA translation analysis?

Most biological materials suitable for RNA extraction can be used, including cell lines, animal tissues, and clinical specimens. The key requirement is maintaining RNA integrity and ribosome-mRNA complexes during sample preparation. CD Genomics provides detailed guidance on sample quality assessment and library construction to ensure accurate detection of translation signals.

How reliable are the results of lncRNA translation profiling?

All experiments undergo rigorous quality control and data validation, including triplet periodicity checks, read alignment accuracy, and functional enrichment verification. Advanced bioinformatics pipelines distinguish genuine translation signals from background noise, ensuring that identified lncRNA-derived peptides are statistically supported and biologically relevant.

What are the applications of micropeptide profiling?

Micropeptide profiling can reveal peptides involved in cancer growth, immune activation, and metabolic regulation. It supports drug target discovery, biomarker identification, and translational research in various disease models. By mapping lncRNA translation, researchers can explore new layers of gene expression regulation and uncover potential therapeutic peptides.

Can lncRNA translation analysis be integrated with other omics studies?

Yes. Data from Ribo-seq and RNA-seq can be combined with proteomics, metabolomics, or epigenomics for a more complete view of cellular regulation. Integration with proteomic validation or third-generation RNA sequencing further enhances accuracy and biological interpretation, allowing comprehensive exploration of functional non-coding elements.

How does CD Genomics ensure data confidentiality and reproducibility?

All client data is handled through secure, access-controlled systems under strict confidentiality agreements. Every project follows standardized, traceable workflows from sequencing to reporting. Reproducibility is ensured through internal controls, consistent QC checkpoints, and transparent reporting formats suitable for peer-reviewed publication or regulatory submission.

How do I start a lncRNA translation or micropeptide profiling project?

Clients can contact CD Genomics through the online inquiry form to discuss study design and sample requirements. Our technical specialists assist in project planning, from experimental setup to data interpretation. After sequencing and analysis, clients receive publication-ready reports, annotated datasets, and expert consultation to support further research or collaboration.

lncRNA Translation & Micropeptide Profiling Service– Ribo-seq & RNA-seq Platform

Unlock the Hidden Coding Potential of lncRNAs

Uncover the translation potential of long non-coding RNAs (lncRNAs) through CD Genomics' integrated Ribo-seq and RNA-seq platform.

Our service enables precise lncRNA translation analysis and micropeptide profiling, helping researchers reveal short, functional peptides that were previously undetectable by conventional transcriptomic methods.

We provide an end-to-end workflow—from sample preparation and sequencing to bioinformatics interpretation—for decoding translation activity, identifying novel micropeptides, and connecting transcriptional and translational regulation across disease models.

What Problems We Solve

Difficulty confirming whether lncRNAs are actively translated
Limited detection of novel short peptides in traditional RNA-seq datasets
Fragmented workflows between transcriptional and translational profiling
Lack of publication-ready, high-resolution datasets

Submit Your Request Now

Infographic of lncRNA translation and micropeptide profiling platform integrating Ribo-seq and RNA-seq workflows for detecting translated ORFs and novel peptides.

Introduction

Unveiling the Hidden Layer of Gene Expression

Although over 80% of the human genome is transcribed into RNA, only a small fraction encodes proteins.

Recent studies have revealed that many long non-coding RNAs (lncRNAs) actually harbor small open reading frames (sORFs) that can produce functional micropeptides—a discovery that is reshaping our understanding of gene regulation.

Traditional RNA-seq identifies which RNAs are expressed but cannot confirm whether they are actively translated.

This creates a critical information gap: researchers can detect transcription but not verify translation.

Our integrated Ribo-seq and RNA-seq platform bridges this gap by providing codon-resolution translation analysis and precise quantification of lncRNA translation events.

Learn how Ribo-seq precisely maps translation events in our Ribosome Footprinting Service.

Research Scope & Scientific Objectives

Study Focus

Our lncRNA Translation & Micropeptide Profiling Service is designed to uncover the hidden protein-coding potential of long noncoding RNAs (lncRNAs) and their functional peptides.

Through integrated Ribo-seq and RNA-seq analysis, we support translational research projects aiming to:

Compare global translation profiles between control and treatment groups
Identify genes with significantly altered translation efficiency
Detect tumor-specific short peptides and novel open reading frames (ORFs)
Map codon usage and translation signatures in cancer cells
Discover tumor-associated neoantigens for immunological research
Validate micropeptide expression and investigate molecular mechanisms

Scientific Innovation

This workflow represents a next-generation approach for studying lncRNA-derived peptide translation.

While most studies focus on lncRNAs as regulatory RNA molecules, our platform integrates ribosome profiling and long RNA sequencing to reveal translation events previously considered noncoding.

The discovery of these micropeptides opens new perspectives on tumor biology, providing a theoretical and technical basis for biomarker development and therapeutic exploration.

Key Scientific Questions Addressed

Are specific lncRNAs abnormally expressed in disease or tumor tissues?
Do these dysregulated lncRNAs contain translatable small ORFs encoding micropeptides?
How do these micropeptides influence cell signalling and disease progression?
Can newly discovered micropeptides serve as diagnostic markers or therapeutic targets?

Our platform answers these questions with high-resolution translational data derived from Ribo-seq and RNA-seq, offering quantitative evidence for functional lncRNA translation.

Our Integrated Solution — lncRNA Translation & Micropeptide Profiling

Technology Overview

CD Genomics provides a unified Ribo-seq and RNA-seq platform designed to characterize lncRNA translation with codon-level precision.

This dual-omics workflow integrates ribosome profiling, which captures active translation, and transcriptome sequencing, which measures RNA expression levels.

By combining both datasets, we identify lncRNAs with active open reading frames (ORFs), predict micropeptide sequences, and assess translation efficiency under different biological conditions.

Our advanced pipeline detects:

Translated ORFs including non-canonical start codons
Novel micropeptides derived from lncRNAs
Upstream ORFs (uORFs) and alternative translation initiation sites
Dynamic changes in translation in response to treatment or stress

Complementary workflows such as RNA Third-Generation Sequencing, Polysome Profiling, and Enhanced Ribosome Profiling are available for researchers requiring deeper translational resolution and quantitative accuracy.

Enhanced vs standard ribosome profiling comparison showing translation accuracy and sensitivity

End-to-end workflow for lncRNA translation and micropeptide profiling

Workflow Summary

Step 1: Sample Preparation

High-quality cells or tissues are lysed to preserve ribosome-mRNA complexes.

Ribosome-protected fragments are isolated using controlled nuclease digestion.

Step 2: Library Construction

Parallel Ribo-seq and RNA-seq libraries are prepared after removing rRNA to ensure high data purity.

Step 3: High-Throughput Sequencing

Libraries are sequenced using Illumina platforms to generate codon-resolution data.

Step 4: Bioinformatics Integration

Sequencing reads are aligned to the reference genome.

Custom algorithms calculate translation efficiency, identify ORFs, and predict peptide sequences.

Step 5: Data Interpretation and Reporting

Functional enrichment analysis (GO and KEGG) links identified peptides to biological pathways.

Final deliverables include annotated ORFs, differential translation reports, and publication-ready visualizations.

Complementary workflows, such as RNA Third-Generation Sequencingand Polysome Profiling, are available for deeper translational analysis.

Integrated Bioinformatics Workflow: Ribo-seq and longRNA-seq Analysis

Ribo-seq Analysis Workflow	longRNA-seq Analysis Workflow
1. Raw data preprocessing	1. Data quality control
2. FastQC quality assessment	2. Gene alignment and read statistics
3. Genome alignment	3. Differential mRNA expression analysis
4. Transcriptome mapping	4. Differential circRNA expression analysis
5. Ribo-seq library QC	5. GO enrichment analysis of differential genes
6. Ribosome-protected fragment (RPF) counting	6. KEGG pathway enrichment analysis
7. FPKM normalization (quantification)	—
8. Genome coverage distribution	—
9. Translation efficiency calculation	—
10. Differential translation efficiency calculation	—
11. GO and KEGG functional analysis	—
12. Open Reading Frame (ORF) identification	—
13. Start-codon analysis	—
14. Codon usage frequency analysis	—
15. Screening RNAs with translational potential	—
16. Identification of tumor-specific short peptides	—
17. Tumor neoantigen identification (for cancer studies)	—

The pipeline ensures comprehensive insight into both transcriptional and translational layers, enabling accurate detection of translated ORFs and potential micropeptides.

Scientific Basis and Data Reliability

Proven Methods and Analytical Precision

CD Genomics applies validated Ribo-seq and RNA-seq protocols derived from leading scientific standards to ensure reliable detection of translation events.

Our platform captures ribosome-protected fragments (RPFs) with single-nucleotide resolution, offering codon-level insight into the translational landscape.

Each dataset undergoes multi-layer quality control, including read distribution analysis, triplet periodicity validation, and mapping accuracy checks.

This rigorous process guarantees that every identified lncRNA translation event is biologically meaningful, not a sequencing artifact.

We follow globally recognized best practices:

Experimental design referencing Nature Methods and Cell Reports workflows
RNA integrity evaluation using Bioanalyzer RIN ≥ 8
Sequencing depth ensuring coverage of >10 million reads per library
Internal spike-in controls for normalization and reproducibility

Bioinformatics Expertise and Interpretation

Our bioinformatics team combines advanced statistical models with biological insight to interpret complex translation data.

Machine-learning-assisted ORF prediction algorithms distinguish true translation signals from background noise.

Comprehensive analysis integrates:

RPF coverage patterns for active translation verification
ORF classification (canonical, non-canonical, upstream, overlapping)
Cross-validation with transcript expression data to confirm functional peptides

Each report is supported by high-resolution plots—metagene profiles, codon occupancy heatmaps, and peptide sequence predictions—delivered in both raw and visual formats for direct publication use.

Data Integrity and Reproducibility

To meet the standards expected by academic and pharmaceutical clients, CD Genomics maintains strict data security and traceability measures.

Results are reproducible across runs and instruments, enabling direct comparison between biological replicates or treatment conditions.

Our expertise in high-fidelity sequencing extends beyond this service.

Explore RNA Sequencing Service for complementary transcriptome profiling solutions.

Applications — Turning Data into Biological Insight

Cancer Biology: Revealing Hidden Oncogenic Peptides

Many lncRNAs encode previously unrecognized peptides that can modulate tumour pathways.

Our integrated Ribo-seq and RNA-seq platform identifies such lncRNA-derived micropeptides, revealing how they influence cell proliferation, apoptosis regulation, and metastasis.

This insight helps oncology researchers pinpoint new biomarkers and develop therapeutic targets that traditional mRNA profiling cannot detect.

Example:

Functional micropeptides like HOXB-AS3 and SPAR, discovered through ribosome profiling, have been linked to cancer metabolism and resistance mechanisms—illustrating how translation-level data can inform drug strategy.

Immunology and Neoantigen Discovery

Ribo-seq analysis can uncover short peptides that elicit immune responses, offering opportunities for neoantigen identification in immunotherapy.

By combining lncRNA translation profiling with peptide prediction, our service helps immunologists explore the repertoire of noncanonical antigens generated from the non-coding genome.

Such discoveries support vaccine design, autoimmune research, and immune-oncology development.

Metabolic and Stress Response Studies

Under conditions such as nutrient deprivation or oxidative stress, lncRNA translation patterns shift significantly.

Our micropeptide profiling service quantifies these dynamic changes, linking translation efficiency with cellular stress adaptation and energy metabolism.

This enables researchers to connect translational control to physiological outcomes and understand disease-specific metabolic signatures.

Drug Discovery and Target Validation

The integration of transcriptomic and translatomic data offers valuable insights for drug mechanism research.

Identifying micropeptides encoded by lncRNAs can highlight new molecular targets and pathways previously overlooked in proteomics.

CD Genomics supports pharmaceutical clients in correlating compound treatment with translation-level alterations, accelerating target validation and preclinical screening.

Beyond Discovery — Translational Systems Biology

By mapping both RNA expression and ribosome occupancy, this platform extends beyond single-gene studies.

It supports systems-level modeling of gene regulation, enabling comprehensive views of how transcription and translation interact across entire networks.

Comprehensive Data Packages

CD Genomics provides complete, high-resolution datasets that integrate both transcriptome and translation-level information.

Each project includes raw data, processed results, and interpretive analytics suitable for publication or downstream validation.

Deliverables include:

Raw sequencing files in FASTQ format for both Ribo-seq and RNA-seq
Alignment files (BAM) mapped to the reference genome
Ribo-seq coverage and triplet periodicity plots for translation quality control
Differential expression and translation efficiency tables
Annotated ORFs and predicted peptide lists with coding potential scores
GO/KEGG pathway enrichment analysis highlighting relevant biological functions
Summary report containing detailed methods, parameters, and result interpretation

All reports are formatted for inclusion in manuscripts or grant submissions, ensuring traceability and reproducibility of results.

Why Choose CD Genomics

Proven Expertise in Translational Omics

CD Genomics has established itself as a trusted partner in RNA sequencing and ribosome profiling for research institutions, CROs, and biotechnology companies around the world.

Our scientific and technical teams have completed a wide range of projects, including lncRNA translation, micropeptide profiling, and multi-omics integration, which helps clients transform complex sequencing data into actionable biological insights.

We provide professional support across:

Functional genomics and disease mechanism exploration
Non-coding RNA translation analysis for biomarker or target discovery
Customized bioinformatics solutions optimized for each research objective

To explore our complementary transcriptomics capabilities, visit the RNA Sequencing Service.

Integrated End-to-End Workflow

Every project is managed through a seamlessly coordinated workflow that covers experimental design, sequencing, and data analysis.

This integration ensures data traceability, reproducibility, and consistency across experiments.

Key advantages include:

Dual-omics platform combining Ribo-seq and RNA-seq for codon-level translation mapping
Flexible experimental design for diverse sample types and species
Comprehensive bioinformatics reporting with interpretation support
Rigorous quality management ensuring accuracy and reproducibility

Technical Precision and Analytical Depth

CD Genomics applies industry-leading algorithms for ribosome footprint alignment, translation efficiency quantification, and micropeptide prediction.

Through deep sequencing coverage and strict quality controls, our analyses capture even subtle lncRNA-derived translation events that standard methods overlook.

Each dataset is validated for triplet periodicity, ribosome occupancy, and ORF annotation accuracy, guaranteeing data reliability and scientific validity.

Global Collaboration and Data Security

We collaborate with academic and industrial partners worldwide to support cutting-edge research in gene expression and translational control.

Client confidentiality is protected under formal agreements, and all projects are handled through secure data pipelines compliant with research and pharma standards.

Our approach emphasizes transparency, professional communication, and result-driven collaboration that ensures research continuity and trust.

FAQs — lncRNA Translation & Micropeptide Profiling Service

- What is lncRNA translation, and why is it important?
  - lncRNA translation refers to the process by which long non-coding RNAs (lncRNAs) produce small functional peptides, known as micropeptides. These short peptides can regulate cell signalling, metabolism, and disease progression. Studying lncRNA translation helps researchers uncover previously hidden protein-coding potential within the non-coding genome, providing new insights into gene regulation, cancer biology, and therapeutic target discovery.
- How does Ribo-seq differ from RNA-seq in identifying translated regions?
  - RNA-seq measures overall gene expression by sequencing all RNA molecules, while Ribo-seq captures only RNA fragments protected by ribosomes during translation. This difference allows Ribo-seq to reveal which transcripts are actively translated into proteins or peptides. Combining both technologies provides a dual-omics view of gene regulation, distinguishing between transcriptional activity and translational output.
- Can Ribo-seq detect novel peptides encoded by lncRNAs?
  - Yes. Ribo-seq detects ribosome occupancy at codon-level resolution, enabling the identification of small open reading frames (sORFs) and non-canonical translation events that are often missed by standard RNA-seq. This makes it a powerful tool for discovering new micropeptides encoded by lncRNAs and characterizing their functional roles.
- What kind of samples can be used for lncRNA translation analysis?
  - Most biological materials suitable for RNA extraction can be used, including cell lines, animal tissues, and clinical specimens. The key requirement is maintaining RNA integrity and ribosome-mRNA complexes during sample preparation. CD Genomics provides detailed guidance on sample quality assessment and library construction to ensure accurate detection of translation signals.
- How reliable are the results of lncRNA translation profiling?
  - All experiments undergo rigorous quality control and data validation, including triplet periodicity checks, read alignment accuracy, and functional enrichment verification. Advanced bioinformatics pipelines distinguish genuine translation signals from background noise, ensuring that identified lncRNA-derived peptides are statistically supported and biologically relevant.
- What are the applications of micropeptide profiling?
  - Micropeptide profiling can reveal peptides involved in cancer growth, immune activation, and metabolic regulation. It supports drug target discovery, biomarker identification, and translational research in various disease models. By mapping lncRNA translation, researchers can explore new layers of gene expression regulation and uncover potential therapeutic peptides.
- Can lncRNA translation analysis be integrated with other omics studies?
  - Yes. Data from Ribo-seq and RNA-seq can be combined with proteomics, metabolomics, or epigenomics for a more complete view of cellular regulation. Integration with proteomic validation or third-generation RNA sequencing further enhances accuracy and biological interpretation, allowing comprehensive exploration of functional non-coding elements.
- How does CD Genomics ensure data confidentiality and reproducibility?
  - All client data is handled through secure, access-controlled systems under strict confidentiality agreements. Every project follows standardized, traceable workflows from sequencing to reporting. Reproducibility is ensured through internal controls, consistent QC checkpoints, and transparent reporting formats suitable for peer-reviewed publication or regulatory submission.
- How do I start a lncRNA translation or micropeptide profiling project?
  - Clients can contact CD Genomics through the online inquiry form to discuss study design and sample requirements. Our technical specialists assist in project planning, from experimental setup to data interpretation. After sequencing and analysis, clients receive publication-ready reports, annotated datasets, and expert consultation to support further research or collaboration.