Epigenetics and methylation analysis
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'For detection of multiple modified bases … most techniques require samples to be split, and different modified bases to be detected separately. In the current study, we took advantage of nanopore sequencing’s ability to determine the 5mCpG and 5hmCpG simultaneously'
Goldsmith, C. et al. J. Immunol. (2024)
Directly detect DNA and RNA methylation
Epigenetics is crucial for regulating gene expression and is linked to various diseases, including cancer. Legacy sequencing methods require PCR, which often removes base modifications and involves complex library preparation steps that damage nucleic acids. However, Oxford Nanopore sequencing preserves these modifications and directly sequences them without extra steps, providing a simple workflow for epigenetic research. Long-range epigenetic modifications, structural variants (SVs), single nucleotide polymorphisms (SNPs), and repeats can be identified and phased in a single dataset. Furthermore, open chromatin regions and base modifications can also be detected.
Using nanopore sequencing, researchers have directly identified DNA and RNA base modifications at single-nucleotide resolution, including m6A in RNA, and 5mC, 5hmC, and 6mA in DNA, and generated comprehensive methylome profiling of all 28 million CpG sites in the human genome. Nanopore technology generates reads of unrestricted length, which preserves the methylation context over large genomic distances and on individual DNA strands. This is particularly useful for identifying differentially methylated regions (DMRs), allowing an overarching view of methylation patterns across entire complex regions.
Featured content
A guide to investigating methylation in the human genome
With Oxford Nanopore sequencing, it is possible to prepare and sequence native DNA, enabling the direct methylation analysis alongside the nucleotide sequence, without additional library preparation steps. This guide provides a complete introduction to the direct sequencing of DNA methylation in human genomes.
Calling methylation and genomic variants in the human genome
In this best-practice workflow, discover how PCR-free nanopore sequencing enables detection of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) methylation alongside SNVs, SVs, and STRs in a single streamlined assay.
Recommended device for epigenetics and methylation analysis
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PromethION 24
Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of ultra-rich sequencing data — ideal for comprehensive epigenomic analysis across large numbers of samples.
Technology comparison
Oxford Nanopore sequencing
Legacy short-read sequencing
Any read length (50 bp to >4 Mb)
Short read length (<300 bp)
- Generate complete, high-quality genomes with fewer contigs and simplify de novo assembly
- Resolve genomic regions inaccessible to short reads, including complex structural variants (SVs) and repeats
- Analyse long-range haplotypes, accurately phase single nucleotide variants (SNVs) and base modifications, and identify parent-of-origin effects
- Sequence short DNA fragments, such as amplicons and cell-free DNA (cfDNA)
- Sequence and quantify full-length transcripts to annotate genomes, fully characterise isoforms, and analyse gene expression — including at single-cell resolution
- Resolve mobile genetic elements — including plasmids and transposons — to generate critical genomic insights
- Enhance taxonomic resolution using full-length reads of informative loci, such as the entire 16S gene
- Assembly contiguity is reduced and complex computational analyses are required to infer results
- Complex genomic regions such as SVs and repeat elements typically cannot be sequenced in single reads (e.g. transposons, gene duplications, and prophage sequences)
- Transcript analysis is limited to gene-level expression data
- Important genetic information is missed
Direct sequencing of native DNA/RNA
Amplification required
- Eliminate amplification- and GC-bias, along with read length limitations, and access genomic regions that are difficult to amplify
- Detect epigenetic modifications, such as methylation, as standard — no additional, time-consuming sample prep required
- Create cost-effective, amplification-free, targeted panels with adaptive sampling to detect SVs, repeats, SNVs, and methylation in a single assay
- Amplification is often required and can introduce bias
- Base modifications are removed, necessitating additional sample prep, sequencing runs, and expense
- Uniformity of coverage is reduced, resulting in assembly gaps
Real-time data streaming
Fixed run time with bulk data delivery
- Analyse data as it is generated for immediate access to actionable results
- Stop sequencing when sufficient data is obtained — wash and reuse flow cell
- Combine real-time data streaming with intuitive, real-time EPI2ME data analysis workflows for deeper insights
- Time to result is increased
- Workflow errors cannot be identified until it is too late
- Additional complexities of handling large volumes of bulk data
Accessible and affordable sequencing
Constrained to centralised labs
- Sequence on demand with flexible end-to-end workflows that suit your throughput needs
- Sequence at sample source, even in the most extreme or remote environments, with the portable MinION device — minimise potential sample degradation caused by storage and shipping
- Scale up with modular GridION and PromethION devices — suitable for high-output, high-throughput sequencing to generate ultra-rich data
- Sequence as and when needed using low-cost, independently addressable flow cells — no sample batching needed
- Use sample barcodes to multiplex samples on a single flow cell
- Bulky, expensive devices that require substantial site infrastructure — use is restricted to well-resourced, centralised locations, limiting global accessibility
- High sample batching is required for optimal efficiency, delaying time to results
Streamlined, automatable workflows
Laborious workflows
- Prepare samples in as little as 10 minutes, including multiplexing
- Use end-to-end whole-genome, metagenomic, targeted (including 16S barcoding), direct RNA and cDNA sequencing workflows
- Scale and automate your workflows to suit your sequencing needs
- Perform real-time enrichment of single targets or panels without additional wet-lab prep by using adaptive sampling
- Lengthy sample prep is required
- Long sequencing run times
- Workflow efficiency is reduced, and time to result is increased
