Methylation Sequencing

Benefits of Methylation Sequencing

Cytosine methylation can significantly modify temporal and spatial gene expression and chromatin remodeling. Leveraging the power of next-generation sequencing (NGS), both genome-wide analysis and targeted approaches can provide researchers with insight into methylation patterns at a single nucleotide level.

Advantages of methylation sequencing:

Discover methylation patterns of CpG, CHH, and CHG regions across the human genome
View methylation at practically every cytosine in the genome across most species with whole-genome bisulfite sequencing (WGBS), a genome-wide approach
Capture full sample diversity with small amounts of DNA
Cover emerging regions of interest in the human genome identified by ENCODE, FANTOM5, and the Epigenomics RoadMap Consortium with targeted methylation sequencing

Advancing DNA Methylation Studies with NGS

This eBook discusses gene expression and regulation research. See how scientists use methylation sequencing and array methods to accelerate their research.

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How Does Bisulfite Sequencing Work?

Many approaches leverage the high quality and sensitivity of NGS for methylation analysis. Most methods rely on bisulfite conversion of DNA to detect unmethylated cytosines. Bisulfite conversion changes unmethylated cytosines to uracil during library preparation. Converted bases are identified (after PCR) as thymine in the sequencing data, and read counts are used to determine the % methylated cytosines.

Bisulfite conversion sequencing can be done with targeted methods such as amplicon methyl-seq or target enrichment, or with whole-genome bisulfite sequencing. Additionally, alternative chemistries like OxBS and TAB-Seq can be used with NGS for identification of hydroxymethylation (5-hMc) in conjunction with methylation (5-mc) analysis.

See the Field Guide to DNA Methylation Analysis for a deep dive into methylation analysis methods.

Featured Methylation Research

Epigenetic Contributions to Addiction

Marilee Morgan discusses the use of targeted methylation sequencing to correlate epigenetic signatures with brain image scans of substance abusers.

Read Article

Methylation and Metastasis

Researchers use NGS-based methylation sequencing and microarrays to investigate the epigenetics behind cancer metastasis.

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Methylation and Exercise

Researchers use RNA-Seq and methylation arrays to study exercise-related epigenetic changes.

Read Article

Methylation Sequencing Workflow

Illumina offers a fully supported workflow, from library preparation to data analysis, for methylation sequencing.

TruSeq Methyl Capture EPIC Library Prep Kit

Create target enrichment-based bisulfite sequencing libraries from as little as 500 ng of human DNA samples.

NextSeq 2000 System

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications, with higher efficiency and fewer restraints.

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

MethylSeq App

For WGBS or targeted methylation sequencing. Maps bisulfite-treated sequencing reads to the genome of interest and performs methylation calls using the Bismark algorithm.

MethylKit App

MethylKit analyzes sequencing data from reduced-representation bisulfite sequencing (RRBS) as well as whole-genome bisulfite sequencing.

BaseSpace Data Repository

View examples of methylation sequencing data generated using Illumina library preparation kits and sequencing instruments (use the “Methyl-Seq” category filter).

Featured Publications

The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells.

J Biotechnol 199 38-46 2015

View Summary

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.

Cell Rep 10 1386-97 2015

View Summary

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.

Nat Biotechnol 33 769-74 2015

View Summary

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Additional Resources

Peter Laird: Epigenetics, DNA Methylation, and Arrays

Peter Laird, PhD, discusses his studies of epigenetics and the role DNA methylation may play in contributing to cancer.

View Video

Whole-Genome Bisulfite Sequencing Library Prep

Efficient nanogram-scale library preparation, sequencing, and analysis of DNA methylation.

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Library Prep for WGBS with Fraz Syed

Illumina scientist Fraz Syed explains library preparation for whole-genome bisulfite sequencing.

View Video

Comprehensive exploration of the methylome

NGS enhances epigenetic studies with high coverage density and flexibility

Benefits of Methylation Sequencing

Advancing DNA Methylation Studies with NGS

How Does Bisulfite Sequencing Work?

Featured Methylation Research

Epigenetic Contributions to Addiction

Methylation and Metastasis

Methylation and Exercise

Methylation Sequencing Workflow

TruSeq Methyl Capture EPIC Library Prep Kit

NextSeq 2000 System

NovaSeq 6000 System

Platform Comparison Tool

Sequencing Reagents

MethylSeq App

MethylKit App

BaseSpace Data Repository

Related Solutions

Epigenetics and Cancer

Complex Disease Genomics

Featured Publications

Interested in receiving newsletters, case studies, and information on genomic analysis techniques?

Additional Resources

Peter Laird: Epigenetics, DNA Methylation, and Arrays

Whole-Genome Bisulfite Sequencing Library Prep

Library Prep for WGBS with Fraz Syed

For every lab, everywhere

NextSeq 1000 and NextSeq 2000 Reagents

NGS Workflow Finder

DRAGEN v4.3 now available on-premises and on-cloud

Illumina Proactive Instrument Performance Service

Do more, faster than ever

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

Next-generation sequencing for beginners

This is the Genome Era

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Methylation Sequencing

Comprehensive exploration of the methylome

NGS enhances epigenetic studies with high coverage density and flexibility

Benefits of Methylation Sequencing

Advancing DNA Methylation Studies with NGS

How Does Bisulfite Sequencing Work?

Featured Methylation Research

Epigenetic Contributions to Addiction

Methylation and Metastasis

Methylation and Exercise

Methylation Sequencing Workflow

DRAGEN Bio-IT Platform for Methylation Sequencing Data Analysis

Related Solutions

Epigenetics and Cancer

Complex Disease Genomics

Methods Guide

Featured Publications