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Chromatin conformation

'Pore-C assesses high-order genome structure with substantially higher efficiency (70–80% of concatemers are high-order) than previous assays ... Pore-C may be the ideal method to study functional high-order 3D interactions at the genome scale'

Deshpande, A.S. et al. Nat. Biotechnol. (2022)

Use long nanopore reads to generate enhanced, multi-way chromatin interaction data
Generate new insights into gene expression, enhance genome assembly contiguity, and investigate modified bases
Utilise the complete, end-to-end Pore-C chromosome conformation capture workflow — from sample to results

A complete, end-to-end workflow for chromosome conformation capture

Chromatin conformation capture (3C) techniques reveal genomic interactions in three dimensions. This can provide key information on the effect of chromatin structure on transcriptional regulation; the data can also be utilised to orient contigs, producing highly contiguous scaffolded assemblies. However, the traditionally used short-read 3C methodology limits the number of contacts available to analyse per read. Combining chromatin conformation capture with long nanopore reads, Pore-C provides long-range contact information, shedding light on higher-order structure. The technique is PCR free, allowing the characterisation of base modifications in the same dataset.

Technology comparison

Oxford Nanopore sequencing

Legacy short-read sequencing

    • 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
    • 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
    • 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
    • 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
    • Lengthy sample prep is required
    • Long sequencing run times
    • Workflow efficiency is reduced, and time to result is increased

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