Epigenomics Sequencing (DNA Methylation Analysis)

CD Genomics is offering five platforms for genome-wide epigenomics analysis, each designed to accommodate a wide range of sample types and suit your specific research needs, allowing researchers to look at epigenetic alterations easily. This information will help us not only understand the role of DNA methylation but also identify targets for therapeutic treatment.

What is Epigenetic modifications

Epigenetic modifications are reversible modifications that affect gene expression without altering the DNA sequence and can be inherited during cell division. Two of the most characterized epigenetic modifications are DNA methylation and chromatin modification. Epigenetic modifications play important roles in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation, development and tumorigenesis. DNA methylation is most frequently observed at the C5 position of cytosine followed by guanine (CpG site) in vertebrates, or non-CpG sites such as CHG and CHH in plants or mammalian embryonic stem cells. DNA methylation is established and maintained by DNA methyltransferases (DNMT1, DNMT3a, and DNMT3b).

DNA Methylation Sequencing Technologies

DNA methylation information may be lost during standard molecular biology manipulations, such as molecular cloning in bacteria and PCR, due to lack of maintenance of DNA methyltransferases. Several techniques include methylated DNA immunoprecipitation (MeDIP), bisulfite sequencing (BS-seq), and reduced representation bisulfite sequencing (RRBS) have been proposed to preserve DNA methylation information and simultaneously transform it into quantitative and measurable signals. By combining with high-throughput sequencing, these techniques have provided comprehensive and reliable genome-wide information regarding DNA methylation. A brief outline and workflow of different NGS-based DNA methylation sequencing technologies is shown in below Figure 1.

Different NGS-based DNA methylation analysis methodsFigure 1. Different NGS-based DNA methylation analysis methods (Jeong et al., 2016).

In terms of the merit and bias of these methods, BS-seq and RRBS can generate a base-resolution DNA methylome, whereas MeDIP-seq can only generate relative enrichment of specific regions across the genome. Chromatin immunoprecipitation (ChIP) offers an advantageous tool for studying the levels of histone methylation associated with a specific gene promoter region between normal and diseased tissues. Identifying the genetic targets of DNA binding proteins and revealing the mechanism of protein-DNA interaction is crucial for understanding cellular processes. Chromatin immunoprecipitation sequencing (ChIP-seq) allows you to make the most of your chromatin studies with minimal sequencing bias.

Our Epigenomic Sequencing solutions include:

  • EpiTYPER DNA Methylation Analysis: EpiTYPER DNA Methylation Analysis is a precision-targeted approach used to quantitatively measure the levels of DNA methylation at specific CpG sites, providing a high degree of accuracy for the evaluation of epigenetic modifications.
  • Whole Genome Bisulfite Sequencing: Whole Genome Bisulfite Sequencing provides a comprehensive view of DNA methylation patterns across the entire genome, allowing for the examination of methylated and unmethylated cytosines.
  • Targeted Bisulfite Sequencing: This sequencing methodology selectively captures and examines defined genomic regions, facilitating the precise and cost-effective analysis of DNA methylation patterns.
  • Reduced Representation Bisulfite Sequencing: Reduced Representation Bisulfite Sequencing is a method that focuses on a subset of the genome, offering a balance between genome coverage and cost-effectiveness for DNA methylation analysis.
  • MeDIP Sequencing: MeDIP Sequencing facilitates the enrichment and analysis of methylated DNA fragments, offering valuable insights into the patterns of DNA methylation and their potential functional implications.
  • MethylRAD-Seq: MethylRAD-Seq is a technique that combines methylation-sensitive restriction enzymes and next-generation sequencing to profile DNA methylation status at the single-nucleotide level.
  • ChIP-Seq: Chromatin Immunoprecipitation Sequencing (ChIP-Seq) is a powerful method for identifying protein-DNA interactions, elucidating transcription factor binding sites, and exploring epigenetic modifications.
  • hMeDIP-seq: Hydroxymethylated DNA Immunoprecipitation Sequencing (hMeDIP-Seq) is employed to specifically study DNA hydroxymethylation, a crucial epigenetic mark involved in gene regulation.
  • MeRIP Sequencing (m6A Analysis): MeRIP Sequencing focuses on RNA modifications, particularly N6-methyladenosine (m6A), and aids in understanding post-transcriptional regulation and RNA modification dynamics.
  • RIP-Seq: RNA Immunoprecipitation Sequencing (RIP-Seq) is employed to explore interactions between RNA and proteins, providing valuable insights into the functions of RNA-binding proteins and their impact on RNA functionality.
  • ATAC-Seq: ATAC-Seq yields data concerning chromatin accessibility, enabling the identification of both open and closed chromatin regions within the genome.
  • NGS-BSP: Next-Generation Sequencing of Bisulfite-Converted DNA (NGS-BSP) is a method used for comprehensive DNA methylation analysis, offering single-base resolution insights.
  • DNA 6mA Sequencing: DNA 6mA Sequencing focuses on the detection and quantification of N6-methyladenine (6mA) in DNA, an emerging epigenetic mark.
  • DAP-Seq Service: DNA Affinity Purification Sequencing (DAP-Seq) is a method employed to unveil interactions between proteins and DNA, thus enhancing our comprehension of DNA-binding proteins and their functions in gene regulation.
  • oxBS-seq: Oxidative Bisulfite Sequencing (oxBS-seq) is a specialized method used to discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA, shedding light on their distinct roles in epigenetic regulation.
  • 5mC/5hmC Sequencing: Our high-throughput 5mC/5hmC sequencing service utilizes multiple mature and stable platforms with high efficiency, simplicity, and accuracy to help your epigenetics research.

Our long-standing experience and advanced platforms allow us to offer a comprehensive service package from project consultation, Immunoprecipitation, library construction, sequencing and bioinformatics analysis.


  1. Jeong H.M., et al. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis. Epigenomics. 2016, 8(8):1061-77.
For Research Use Only. Not for use in diagnostic procedures.
Featured Resources
PDF Download
* Email Address:

CD Genomics needs the contact information you provide to us in order to contact you about our products and services and other content that may be of interest to you. By clicking below, you consent to the storage and processing of the personal information submitted above by CD Genomcis to provide the content you have requested.

Quote Request
! For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment.
Contact CD Genomics
Terms & Conditions | Privacy Policy | Feedback   Copyright © CD Genomics. All rights reserved.