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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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Whole Genome Methylation Coverage

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
Epigenetic Contributions to Addiction

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

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Methylation and Metastasis
Methylation and Metastasis

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

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Runner
Methylation and Exercise

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

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Methylation Sequencing Workflow

More than 90% of the world’s sequencing data is generated using Illumina NGS technology.*

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

DRAGEN Bio-IT Platform for Methylation Sequencing Data Analysis

The DRAGEN Bio-IT Platform provides accurate, ultra-rapid methylation sequencing data analysis for epigentic studies with high coverage density and flexibility.

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DRAGEN Bio-IT Platform for Methylation Sequencing Data Analysis

Related Solutions

Epigenetics and Cancer

Studies of aberrant methylation, altered transcription factor binding, and other epigenetic alterations can provide insight into important tumorigenic pathways. Learn more about cancer epigenetics research.

Complex Disease Genomics

Genome-wide methylation sequencing can help researchers understand the functional mechanisms at work in complex neurological, immunological, and other diseases. Learn more about complex disease research.

Methods Guide

Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.

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Methods Guide

Featured Publications

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

J Biotechnol 199 38-46 2015

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

Cell Rep 10 1386-97 2015

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

Nat Biotechnol 33 769-74 2015

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Additional Resources

Peter Laird: Epigenetics, DNA Methylation, and Arrays
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.

Whole-Genome Bisulfite Sequencing Library Prep
Whole-Genome Bisulfite Sequencing Library Prep

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

Library Prep for WGBS with Fraz Syed
Library Prep for WGBS with Fraz Syed

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

*Data calculations on file. Illumina, Inc., 2015