RNA Modifications Sequencing Services for Advanced Epitranscriptomics Analysis

Next-generation sequencing (NGS)-based methods, either relying on antibody enrichment or third-generation sequencing, have been developed to map post-transcriptional RNA modification and explore their functions, CD Genomics provide a full range of epitranscriptomics services to investigate RNA modifications using NGS or long-read sequencing (Oxford nanopore sequencing and PacBio SMRT sequencing). We can help you detect many forms of RNA modifications including m7G, m3C, m1A, 5mC, 5hmC, m6A, m6Am, acetylation, and 2'-O-methylation.

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What are RNA Modifications and Epitranscriptomics

Imagine RNA molecules as freshly written books, and RNA modifications as the editorial process these books undergo. These "editors" add various marks, annotations, and even alter certain words, making the book more comprehensible, engaging, or tailored to specific readers. Scientists have uncovered over 170 different types of RNA modifications, and this number continues to grow. These modifications can occur on various types of RNA, such as mRNA, tRNA, rRNA, and snRNA. They act like "seasonings" for RNA molecules, altering their chemical properties and influencing their interactions with other proteins, thereby regulating various RNA functions. The most common and well-studied mRNA modification is N6-methyladenosine (m6A). Most RNA modifications involve adding a methyl group to certain positions on the RNA, much like highlighting key passages in a book. Sometimes, RNA molecules also undergo acetylation, which is akin to placing special bookmarks in certain sections. These modifications dynamically regulate RNA processing, export, translation, and stability. They function as cellular "switches," influencing cell differentiation, stress responses, and even playing a role in tumor formation.The field studying RNA modifications is called epitranscriptomics. If DNA is the blueprint of life, epitranscriptomics is the science of understanding how this blueprint is interpreted and executed. It's similar to epigenetics, which primarily studies modifications to DNA and histones.In essence, RNA modifications open up a whole new perspective on the complexity of life. They're like a sophisticated regulatory language within cells, helping them better adapt to various environmental changes and physiological demands.

Researchers across the world continue to trust us for over a decade, and we continue to deliver on their trust

Leading universities, research institutions, and pharmaceutical companies across the world continue to trust us for over a decade, and we continue to deliver on their trust

Features Service Portfolio Platforms Workflow Bioinformatic & Demo Sample Requirement Publication FAQ Feedback Download Inquiry

Why Choose Our Epitranscriptomics Service

High-resolution analysis

Single-base resolution and high throughput

Broad RNA Coverage

Cover mRNA, lncRNA, pri-miRNA, tRNA, rRNA and other RNAs

Professional bioinformatics analysis

Identification of differentially modified transcripts
Functional annotation of RNA modifications
Integration with other omics data for comprehensive insights

All-in-One Convenience

One-stop solution, covering everything from library construction and sequencing to sample quality control and data analysis.

Types Of RNA modifications We Can Analyze

NA Methylation Modifications	5-Methylcytosine (m5C)	N1-Methyladenosine (m1A)	N6-Methyladenosine (m6A)	N7-Methylguanosine (m7G)	2'-O-Methylation
NA Methylation Modifications
Role	Implicated in RNA stability, translation efficiency, and gene expression regulation.	Involved in tRNA stability and fidelity during translation.	The most abundant RNA modification in eukaryotic cells, influences mRNA stability, processing, and translation.	Enhances mRNA stability and is associated with translational efficiency.	Implicated in RNA stability and structure, as well as regulation of RNA function.
Significance	A key player in the epitranscriptomic landscape, influencing diverse cellular processes.	Essential for maintaining translation accuracy and preventing errors.	Central to post-transcriptional gene regulation and cellular responses.	A common modification contributing to mRNA function and regulation.	Plays a role in RNA stability, structure, and function.
Methods	m5C profiling (RNA-BS)	m1A sequencing	RNA m6A-Seq (MeRIP-Seq)	m7G MeRIP sequencing	2'-O-methylation sequencing

Service Portfolio

Explore how our epitranscriptomics services help researchers map RNA modifications and explore their pathways.

m7G MeRIP-Seq

N7-methylguanosine (m7G) is an essential modification at the 5' cap of eukaryotic mRNA. We provide m7G-MeRIP sequencing to map m7G and reveal its distribution features.

m7G+m3C Sequencing

We provide a deep sequencing-based service for the simultaneous profiling of 7-methylguanosine (m7G) and 3-methylcytidine (m3C) in RNA at single nucleotide resolution.

m1A-Seq

m1A has been found in total RNA, rRNA, and tRNA. We provide m1A-seq service to reveal the presence and functions of m1A in RNA.

Nanopore Direct RNA Sequencing

By utilizing Oxford Nanopore Technologies (ONT), this service allows for real-time, single-molecule sequencing of RNA, enabling direct detection of methylated bases without the need for reverse transcription or amplification. This unique feature allows for more accurate and comprehensive identification of RNA modifications, such as m6A, m5C, m1A, and other important methylations that regulate gene expression and RNA stability.

m5C Profiling

Cytosines can be methylated in the form of 5mC (m5C) and subsequently oxidized to generate 5hmC. We provide RNA BS-seq, m5C-RIP-seq, and hMeRIP-seq for profiling 5mC, or 5hmC, or both.

m6A Profiling

We provide MeRIP-seq/m6A-seq for mapping N6-methyladenosine (m6A) / N6, 2'-O-dimethyladenosine (m6Am) at single-nucleotide resolution.

acRIP-Seq

acRIP-Seq can be used to depict a transcriptome-wide map of N4-acetylcytidine (ac4C) and reveal its roles in RNA stability, alternative splicing, gene expression regulation, and protein synthesis.

2'-O-Methylation Sequencing

2'-O-methylation is a common RNA modification, mostly found in rRNA, snRNA. 2'-O-methylation sequencing enables a transcriptome-wide mapping of this modification.

Pseudo Sequencing

Pseudouridylation sequencing (PA-Ψ-seq) is a NGS-based method to comprehensively detect global maps of pseudouridylation, a post-transcriptional modification in various molecules.

O8G-Seq

CD Genomics' O8G-Seq service enables the detection of O8G oxidation in various types of RNA, including mRNA, lncRNA, and circRNA. We offer both whole-transcriptome sequencing and specific analysis of O8G oxidation in individual RNA species.

hMeRIP Sequencing

Hydroxyl-methylcytosine RNA immunoprecipitation sequencing (hMeRIP-seq) is a next-generation sequencing (NGS)-based method specifically designed to detect 5-Hydroxymethylcytosine (hm5C) across the transcriptome. This method provides a comprehensive map of hm5C, revealing its distribution, location, and function within the RNA, applicable across diverse species.

Sequencing Platforms

A wide range of efficient sequencing platforms

Illumian HiSeq 2500 / HiSeq 4000 / HiSeq X Ten / NovaSeq 6000 / NextSeq 500 / MiSeq
PacBio RS II / Sequel
Nanopore PromethION
10X Genomics

Learn more about a wide range of efficient sequencing platforms.

Our RNA Sequencing Service Process: From Start to Finish

Sample Preparation

1. Sample Preparation

Quality assessment and quantification.

Library Preparation

2. Library Preparation

Sequencing

3. Sequencing

Illumina HiSeq; PE 50/75/100/150.

Data Analysis

4. Data Analysis

Visualize and preprocess results, and perform custom bioinformatics analysis.

Bioinformatic Analysis & Demo Report

Download Our Demo Report

Methylation Site Identification

Detect and annotate RNA methylation sites in your samples.

Differential Methylation Analysis

Compare methylation profiles between different conditions or samples.

Functional Enrichment Analysis

Gain insights into the biological significance of methylated RNA molecules.

Visualization

We provide interactive visualizations to facilitate data interpretation.

Sample Requirements

Sample Starting Volume: can be reduced to 10-20 μ, with a minimum of 1 μg of total RNA.

Sample Types: is compatible with a diverse range of sample types, including animals, plants, cells, and tissues.

Please make sure that the RNA is not significantly degraded.

Sample storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis.

Sample Guideline

Publication form CD Genomics

More publications

Article	Journal	Published	Tags	Species
Exploiting DNA methylation in cassava under water deficit for crop improvement	PLoS ONE	2024	MethylRAD-Seq	Cassava
A de novo assembly of genomic dataset sequences of the sugar beet root maggot Tetanops myopaeformis, TmSBRM_v1.0	Data in Brief	2024	PacBio SMRT Sequencing	Tetanops myopaeformis
Vaccination with a Protective Ipa Protein-Containing Nanoemulsion Differentially Alters the Transcriptomic Profiles of Young and Elderly Mice following Shigella Infection	Vaccines	2024	RNA sequencing	Mice
StarD5 levels of expression correlate with onset and progression of steatosis and liver fibrosis	Gastrointestinal and Liver Physiology	2024	RNA-Seq	Mice
Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride	Biofilm	2024	16S Amplicon Sequencing	Bacteria

FAQ

- What is RNA Modifications Sequencing?
  - RNA modifications sequencing is a high-throughput method to detect and analyze chemical modifications on RNA molecules across the transcriptome. It provides insights into the epitranscriptome - the collection of RNA modifications that regulate gene expression and cellular functions.
- What types of RNA modifications can be detected?
  - Common RNA modifications that can be detected include:
    N6-methyladenosine (m6A)
    2'-O-methylation
    5-methylcytidine
    Pseudouridine
    Inosine
- What RNA types can be analyzed?
  - RNA modification sequencing can analyze various RNA types, including:
    mRNA
    lncRNA
    pri-miRNA
    tRNA
    rRNA
- What are the main approaches for RNA modification sequencing?
  - The two main approaches are:
    Enrichment and purification of modified RNAs before sequencing
    Modification of bioinformatics pipelines to identify modification peaks from sequencing data.
- What sequencing technologies are used?
  - Common sequencing platforms include:
    Illumina short-read sequencing
    PacBio long-read sequencing
    Oxford Nanopore direct RNA sequencing
- What are the advantages of long-read sequencing for RNA modifications?
  - Long-read sequencing can:
    Sequence full-length transcripts
    Detect multiple modifications on the same RNA molecule
    Provide isoform-specific modification information
- How accurate is nanopore sequencing for detecting RNA modifications?
  - Recent studies have shown up to 90% accuracy in detecting m6A modifications using nanopore direct RNA sequencing.
- What analysis services are typically offered?
  - Common services include:
    Quantitative analysis of RNA modifications
    Profiling of global modification patterns
    Differential modification analysis between conditions
    Integration with gene expression data
- What sample types and amounts are required?
  - Most services accept:
    Total RNA
    Poly(A) enriched RNA
    Specific RNA fractions (e.g. small RNAs)
    Typical input amounts range from 100 ng to 5 μg of RNA, depending on the specific protocol.

More FAQ on RNA-seq

What Our Customers Say About Us

I'm happy to share a few words about our experience working with CD Genomics. We are a busy molecular epidemiology laboratory conducting large-scale, multi-omics studies across diverse populations. We have utilized CD Genomics' RNA sequencing services, along with their methylation assays and bioinformatics analysis. Throughout our collaboration, we have been consistently impressed by the high quality of their services and the promptness of their delivery.

I would like to specifically highlight the exceptional work of Dr. Yang H in providing such outstanding services. Our interactions with Dr. Yang have always been positive, and his expertise in both RNA sequencing and bioinformatics analysis has been invaluable to our research. We greatly appreciate his and his team's dedication and support throughout the entire process.

We look forward to continuing our collaboration with Dr. Yang and the CD Genomics team in the upcoming year!

Emily J. Richardson

PhD, Associate Professor of Molecular Biology

References:

Peer E, Rechavi G, Dominissini D. Epitranscriptomics: regulation of mRNA metabolism through modifications. Current opinion in chemical biology, 2017, 41: 93-98.
Shafik A, Schumann U, Evers M, et al. The emerging epitranscriptomics of long noncoding RNAs. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2016, 1859(1): 59-70.

* For Research Use Only. Not for use in diagnostic procedures.

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