Epigenome sequencing can help you elucidate the complex role between external environmental factors and gene expression. DNA methylation and DNA–histone interactions are among the most commonly studied epigenetic control mechanisms for gene transcription and these processes can be analyzed effectively with next generation sequencing (NGS).

Whole genome vs targeted epigenome sequencing

As with both genome and RNA sequencing, epigenome sequencing can be done for an entire genome or in a targeted manner. Whole genome bisulfite sequencing (WGBS) is a method of measuring the degree of DNA methylation across the genome. It works by treating DNA with sodium bisulfite, which converts nonmethylated cytosine to uracil, and analyzing the sequence.

Targeted, or methyl-capture, sequencing is a method that focuses on the most relevant sections of the genome from a methylation perspective. These sections include CpG islands – often found in promoter regions – and other known differentially methylated regions (DMRs). DNA from these regions is selectively captured, bisulfite treated and sequenced.

ChIP sequencing

Chromatin immunoprecipitation (ChIP) sequencing specifically analyzes DNA fragments based on their interaction with proteins. It works by fragmenting DNA while keeping the DNA–protein bonds intact, and then isolating relevant DNA fragments by capturing a protein of interest. Sequencing and mapping of the captured fragments provides insights into that protein’s role within the genome.

Library preparation kits

• IDT xGen Methyl-Seq Library Prep (WGBS)
• Agilent SureSelectXT Methyl-Seq (targeted)
• Illumina TruSeq ChIP (ChIP sequencing)

Sequencing platforms

• Illumina: NovaSeq 6000, HiSeq, NextSeq 500, MiSeq

Data analysis

• data QC (HiCUP)
• mapping
• peak calling
• peak annotation
• motif result
• methylation profile (BSMAP, Bismark)
• differentially enriched peaks
• differentially methylated regions
• gene annotation