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:
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, target enrichment, or with whole-genome bisulfite sequencing (WGBS). 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.
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.
Click on the below to view products for each workflow step.
Generate whole-genome bisulfite sequencing libraries from as little as 50 ng DNA, from any species that uses cytosine methylation.
Create target enrichment-based bisulfite sequencing libraries from as little as 500 ng of human DNA samples.
Flexible benchtop sequencer supporting multiple applications, sequencing 1 DNA sample per 2 flow cells.HiSeq 4000 System
High throughput and low cost to sequence 2-3 samples per flow cell.NovaSeq 6000 System
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.
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.
View example WGBS data generated using Illumina library preparation kits and sequencing instruments (use the “Methyl-Seq” category filter).
Studies of epigenetic alterations in cancer, such as aberrant methylation and altered transcription factor binding, can provide insight into important tumorigenic pathways. Learn more about analyzing epigenetic changes in cancer.
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.
*Data calculations on file. Illumina, Inc., 2015