Overview of epigenome sequencing

Epigenetics is the reversible regulation of gene expression that occurs independently of DNA sequence. Epigenetic modifications mediated by DNA methylation, histone tail modifications and non-coding RNA interventions predispose the genome to malignant progression. Epigenetic changes represent a layer of heritable information that regulates DNA transcription. In many organisms, these changes are critical for understanding gene regulation and expression. Epigenetic dysregulation, such as methylation of DNA (CpG), histone modifications, binding of microRNAs to prevent translation, post-transcriptional silencing of short interfering RNAs (siRNAs), and modification of chromatin structure by non-coding RNAs (ncRNAs), have been associated with the development of multiple diseases. Epigenetic studies can reveal changes in expression phenotypes, X chromosome inactivation, and transcriptional errors, and their role in a variety of human diseases such as cancer, neurodegenerative diseases, and cardiovascular diseases is well established.

The workflow of epigenome sequencing service

With years of experience and high quality NGS sequencing technology, CD Genomics offers the following common NGS-based methods available for epigenetic analysis.

• Methyl-seq

CD Genomics uses bisulfite treatment to convert cytosine residues to uracil, while methylation residues remain unchanged. Several methyl sequence strategies have been developed, including whole genome bisulfite sequencing (WGBS) and reduced representative bisulfite sequencing (RRBS), which enriches CpG islands.

• ATAC-seq

CD Genomics offers chromatin sequencing analysis for transposases that identifies chromatin accessibility regions and maps DNA binding proteins to identify active promoters, enhancers and other cis-regulatory elements.

• ChIP-seq

CD Genomics combines chromatin immunoprecipitation (ChIP) with NGS to identify binding sites for DNA-associated proteins throughout the genome and are commonly used to map histone modifications and transcription factors. This approach relies on targeted antibody selection to enrich DNA fragments of interest for binding to specific proteins.

• RIP-seq

RIP-seq in combination with NGS can detect a large number of RNA-protein complexes in a single run and is used to study protein-RNA interactions to detect the interaction of RNA with target proteins.

01. Sequencing sample requirements

02. Library construction and NGS

NGS-based Illumina / MGI platform

03. Bioinformatics Analysis

• Mapping to reference genome
• Peak calls
• Theme prediction
• Peak annotation and functional analysis of peak-associated genes
• Differential peak summarization and functional analysis of differential peak-associated genes
• Visualization of Methyl-seq/ ATAC-seq/ChIP-seq/ RIP-seq data

Advantages of our epigenome sequencing service

• Ability to sequence natural DNA and RNA molecules
• Allows detection of multiple types of modifications, such as 5mC, 5hmC and 6mA
• Eliminates the need for additional sample preparation, avoiding DNA degradation and amplification bias
• Compatible with PCR-free, CRISPR-based enrichment technologies to provide efficient targeted genetic and epigenetic analysis

Applications in pharma research

CD Genomics offers epigenomic sequencing analysis that can be used to study heritable changes in gene activity caused by mechanisms other than DNA sequence changes in epigenetics. Epigenetic analysis studies may involve the study of changes in DNA methylation, DNA-protein interactions, chromatin accessibility, histone modifications, etc., with major applications in disease mechanism studies.

CD Genomics is committed to combining professional project protocol guidance and standardized analysis processes to ensure that your project is performed accurately and quickly. If you are interested in CD Genomics' epigenome sequencing service in the field of pharma research, please feel free to contact us now.