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 insight into methylation patterns at a single nucleotide level.
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.
For a deep dive into methylation analysis methods, please see the Field Guide to DNA Methylation Analysis. View Guide.
More than 90% of the world’s sequencing data is generated using Illumina NGS technology.*
In addition to industry-leading 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.
Flexible desktop sequencer supporting multiple applications, sequencing 1 DNA sample per 2 flow cells.HiSeq 2500 System
Power and efficiency to sequence 2 DNA samples per flow cell.HiSeq 3000/HiSeq 4000 Systems
Maximum throughput and lowest cost to sequence 2-3 samples per flow cell.
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.
For WGBS or targeted methylation sequencing. Maps bisulfite-treated sequencing reads to the genome of interest and performs methylation calls using the Bismark algorithm. Bowtie 2, an ultrafast, memory-efficient tool, aligns the reads to long reference sequences.MethylKit App
MethylKit analyzes sequencing data from reduced-representation bisulfite sequencing (RRBS) as well as whole-genome bisulfite sequencing. It calculates methylation statistics and also differential methylation regions.
View example WGBS data generated using the TruSeq DNA Methylation Kit and Illumina 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. As altered methylation often activates or silences genes, changes in the epigenome can affect gene expression and the rate of cancer progression. Learn more about cancer epigenetics.
Genome-wide methylation profiling can help researchers understand the functional mechanisms at work in complex disease cases. Aberrant cytosine methylation can impact gene expression, and has been implicated in many disease processes, such as Alzheimer’s disease and asthma. Learn more about complex disease research.
*Data calculations on file. Illumina, Inc., 2015