Epigenetics and Methylation Analysis Using Long-Read Sequencing

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Epigenetics and Methylation Analysis Using Long-Read Sequencing

Illustration of Epigenetics.

Epigenetic modifications refer to chemical changes in nucleic acids that do not alter DNA sequence but play a key role in genetics, growth, lifespan, aging, and disease, mainly including DNA methylation and histone modifications. With the explosion of technology and understanding in the last decade, researchers realized that RNA methylation is another dynamically regulated, reversible, and widespread post-transcriptional regulator associated with a variety of basic and disease-related biological processes. Using long-read sequencing technologies (PacBio SMRT and Oxford Nanopore sequencing), researchers can directly detect DNA and RNA methylation modifications, such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and N6-methyladenine (6mA) in DNA, and N6-methyladenosine modification (m6A), 5-methylcytosine modification (m5C), and N1-methyladenosine (m1A) in RNA. With years of experience in epigenetics and methylation analysis, our team of experts is dedicated to providing cost-and sequencing-effective solutions for DNA and RNA methylation detection and analysis in plants and animals.

Introduction of DNA and RNA Methylation with Long-Read Sequencing

Since both PacBio SMRT and Nanopore sequencing technologies sequence native unamplified templates, base modifications of DNA and RNA molecules can be preserved, allowing epigenomic changes to be studied by polymerase kinetics or current changes, respectively. Prior to the application of long-read sequencing, the combination of bisulfite treatment and short-read sequencing, known as bisulfite sequencing (BS-seq), served as a common and powerful tool for detecting base modifications (5mC in DNA). Compared to BS-seq methods, native DNA and RNA sequencing via PacBio and/or Nanopore sequencing technology possess a range of advantages, including,

  • The ability to sequence native DNA and RNA molecules.
  • Allow detection of diverse types of modifications, such as 5mC, 5hmC, and 6mA.
  • No additional sample preparation is required, avoiding DNA degradation as well as amplification biases.
  • Compatible with PCR-free, CRISPR-based enrichment techniques, providing effective targeted genetic and epigenetic assays.

Services Offering at CD Genomics

  • Long-Read Sequencing of DNA Methylation
    DNA methylation, a common epigenetic modification, affects the regulation of gene expression and is involved in a variety of human diseases. DNA methylation is also a common topic in the field of agricultural genomics and can be used to explore responses to drought, extreme temperatures, and other environmental changes. Using advanced long-read sequencing platforms, we are dedicated to providing a comprehensive elucidation of DNA methylation, providing valuable information on gene expression regulation at the chromosomal level.
  • Long-Read Sequencing of RNA Methylation
    RNA methylation is another important post-transcriptional regulation that has been overlooked in the past. With the explosion of technology and understanding, great progress has been made in RNA modification research. Based on the Oxford Nanopore sequencing platform, we are providing low-cost, high-efficiency, and high-accuracy RNA methylation identification and analysis. Our service enables direct identification of natural or synthetic RNA base modifications at nucleotide resolution.
Magnifying lens over background with text DNA Methylation.

CD Genomics is a leading global life sciences company. We specialize in the application of third-generation sequencing technologies, including PacBio SMRT and Oxford Nanopore sequencing. We have years of experience in long-read sequencing and are committed to providing effective and cost-effective contract research and developmental services to the global pharmaceutical, medical technology, crop protection, and chemical industries. If you are interested in our services, please don't hesitate to contact us. We are looking forward to cooperating with you.


  1. Logsdon, G. A., Vollger, M. R., & Eichler, E. E. (2020). "Long-read human genome sequencing and its applications." Nature Reviews Genetics, 21(10), 597-614.
  2. Gouil, Q., & Keniry, A. (2019). "Latest techniques to study DNA methylation." Essays in biochemistry, 63(6), 639-648.
  3. Xue, C., et al. (2020). "Advances in RNA cytosine-5 methylation: detection, regulatory mechanisms, biological functions and links to cancer." Biomarker Research, 8(1), 1-13.
For Research Use Only. Not for use in diagnostic procedures.

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