Pore-C Service | High-Order 3D Genome Mapping with Nanopore
Unlock a more complete view of chromatin architecture with CD Genomics' Pore-C service — the next generation in genome conformation analysis. Unlike traditional Hi-C, which captures only pairwise interactions, Pore-C employs Nanopore long-read sequencing to detect high-order, multi-way chromatin contacts in a single run. In addition, Pore-C preserves native DNA methylation signals, enabling simultaneous structural and epigenetic analysis.
Our streamlined protocol removes the need for biotin labeling, PCR amplification, or intermediate fragmentation — saving time and maintaining data integrity. With as little as 30× coverage, our Pore-C service delivers assembly scaffolding and interaction mapping equivalent to over 100× Hi-C, making it both powerful and cost-effective.
Whether your focus is de novo genome assembly, chromosome scaffolding, enhancer-promoter interaction studies, or cancer structural variation, CD Genomics' Pore-C service offers unmatched resolution, reliability, and insight.
At a glance:
- Why Choose Pore-C?
- How Our Pore-C Analysis Works
- Performance Metrics & Use Cases
- Pore-C Data Analysis Workflow
- Sample Requirements & Submission Guidelines
- Demo Results
- Frequently Asked Questions (FAQ)
Why Choose Pore-C?
Pore-C is CD Genomics' advanced service for 3D genome mapping. By combining proximity ligation with Oxford Nanopore long-read sequencing, our service offers:
- High-order, multi-way contact detection — directly capture three or more genomic regions interacting simultaneously, a leap over pairwise-only methods.
- Simultaneous methylation profiling — non-amplified long reads preserve native DNA methylation for epigenetic insights.
- Streamlined lab workflow — no biotin labeling, PCR, or fragmentation steps, cutting prep time and complexity.
- Efficient data usage — fewer reads and bases deliver Hi-C-equivalent pairwise contact counts, enhancing cost-effectiveness.
- Long-read clarity — accurate mapping across repetitive or GC-rich regions, crucial for genome assembly and structural variant resolution.
Pore-C vs Hi-C
| Feature | Pore-C | Hi-C |
| Contact detection | Multi-way (3+ loci per read) | Pairwise only |
| Epigenetic profiling | Methylation retained via Nanopore signal | Requires separate bisulfite workflow |
| Library prep | Simplified (no biotin/PCR) | Complex with labeling, pull-down, PCR |
| Data efficiency | Comparable contacts with fewer reads | Higher sequencing depth required |
| Resolution in repeats | Long reads enable mapping in complex regions | Challenges in repetitive/GC-rich DNA |
How Our Pore-C Analysis Works
CD Genomics' Pore-C service blends a streamlined wet-lab protocol with a robust bioinformatics pipeline to reveal multi-way chromatin interactions and methylation on long reads.
1. Sample Preparation & Cross-linking
- Cells or tissues are cross-linked using formaldehyde to freeze spatial DNA contacts in place.
- After in situ restriction enzyme digestion, ligation captures interacting DNA fragments into chimeric concatemers.
2. Nanopore Sequencing
- Chimeric Pore-C DNA is purified (phenol–chloroform extraction and ethanol precipitation) and size-selected (>1.5 kb).
- Sequencing is performed on Oxford Nanopore PromethION/MinION platforms, producing long reads containing multi-locus contacts and methylation signatures.
3. "Align-then-Fragment" Bioinformatics Pipeline
A modern pipeline, similar to the HiPore-C approach, significantly optimizes Pore-C data processing:
- Raw FastQ reads are aligned end-to-end to the reference genome using Minimap2 or NGMLR.
- Based on restriction enzyme cut positions, reads are in silico fragmented into mapped fragments.
- Contact assignments are made: multi-way concatemer fragments seeding high-order interactions, and pairwise contacts are extracted for downstream compatibility.
- Outputs include Hi-C–style pairs, cooler/mcool contact matrices, and fragment-level annotation tables.
- This workflow improves data recovery by reducing mis-splitting and multi-position misalignment that hampered earlier "cut-first" methods.
4. Contact Mapping & Methylation Profiling
- High-order contacts (3+ fragments per read) are quantified.
- Pairwise shuffles enable standard contact map and TAD-level analyses.
- Methylation signals are retained across reads for simultaneous epigenetic profiling.
5. Assembly & Structural Insight
- Contact maps support chromosome-scale scaffolding, misassembly correction, and structural variant detection.
- Multi-way data offers deeper insight into enhancer-promoter hubs, especially for complex or rearranged genomes .
Performance Metrics & Use Cases
| Application | Recommended Coverage | Typical Outcome |
| Chromosome-Level Genome Scaffolding | 25–35× | Anchoring rate ≥ 93%; T2T or near-T2T genome assembly |
| High-Order Chromatin Interaction | 30–40× | Multi-way contacts per read: 3–6; improved detection of TADs, compartments |
| Epigenetic Context (5mC Profiling) | Native (no bisulfite) | Methylation patterns retained across interaction loci |
| Cancer Structural Variant Discovery | 35–50× | Long-range SVs revealed in high-copy or rearranged regions (e.g. Tyfonas in breast cancer) |
| Enhancer–Promoter Interaction Mapping | 30×+ | Synergistic multi-locus contacts captured with transcriptional correlation |
| Comparative 3D Genomics | 20–25× | Resolution of tissue-specific or lineage-specific chromatin architecture |
Pore-C Data Analysis Workflow
Pore-C Data Analysis Workflow: From raw Nanopore reads to chromatin interaction mapping and methylation profiling.
Sample Requirements & Submission Guidelines
| Sample Type | Material Accepted | Minimum Amount | Fixation/Preparation | Storage & Shipping |
| Human (PBMCs) | White blood cells (crosslinked PBMCs) | ≥ 1 × 10⁷ cells | Formaldehyde crosslinking following Pore-C protocol | Flash-freeze in liquid nitrogen, store at –80 °C, ship on dry ice |
| Plant Tissue | Young leaves, buds (fresh, disease-free) | ≥ 3 g | Rinse with 75% ethanol + sterile water, blot dry, liquid nitrogen snap-freeze | Use foil + sealed bag + cryobox, ship on dry ice |
| Animal Tissue | Blood, isolated cells, muscle, or organs | Blood: ≥ 7 mL (mammals), ≥ 100 μL (birds, etc.) Cells: ≥ 6 × 10⁷ Muscle: ≥ 3 g Organs: ≥ 0.5 g |
Fixation protocol same as human PBMCs | Flash-freeze, seal in tubes or foil bags, ship on dry ice |
Demo Results
Frequently Asked Questions (FAQ)
What is Pore-C service?
Answer: Pore-C service is a next-generation chromatin conformation capture method. It uses Nanopore long-read sequencing to map multi-way (high-order) interactions among genomic loci and detect native DNA methylation—all in a single experiment.
How does Pore-C differ from Hi-C?
Answer: Although Pore-C and Hi-C share similar wet-lab steps, Pore-C replaces short-read sequencing with long-read Nanopore technology. This enables direct capture of 3+ loci interactions, preserves epigenetic marks, and simplifies library prep by removing biotin-tagging and PCR .
What does your Nanopore-based Pore-C analysis include?
Answer:
- Basecalling & demultiplexing of raw Nanopore reads using Guppy/Megalodon
- Concatemer parsing to identify chimeric DNA
- Genome alignment of full-length reads
- Multi-contact calling and pairwise extraction
- Construction of Hi-C–style contact maps and 3D structure analysis
- Optional methylation calling at CpG sites
- Outputs: BAM/FASTQ, .pairs, .cool, TAD/corner assignments, and visualization-ready data.
What sequencing depth is recommended?
Answer:
- Chromatin structure & scaffolding: 25–35× coverage
- High-order interaction detection: 30–40×
- Structural variant calling (e.g., Tyfonas): 35–50×
These depths yield robust contact maps and multi-way interaction profiles comparable or superior to 100× Hi-C.
Can you detect DNA methylation and interactions simultaneously?
Answer: Yes. Pore-C is PCR-free, so native 5mC methylation remains intact. Studies in Arabidopsis and human cells confirmed high concordance with WGBS, and precise co-localization of methylation and interaction events .
What biological applications suit Pore-C?
Answer:
- Genome scaffolding for high-quality assembly, including T2T genomes
- Chromatin architecture studies: compartments, TADs, enhancer-promoter hubs
- Epigenomic profiling alongside 3D structure
- Cancer research with structural variant analysis (e.g., Tyfonas multi-way hubs)
- Comparative 3D genomics across cell types or conditions
References
- Deshpande A. S. et al. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Nature Biotechnology, 40, 1488–1499 (2022). Demonstrates Pore-C with Chromunity to detect high-order contacts, epigenetic patterns, and cancer-associated structural hubs. https://doi.org/10.1038/s41587-022-01289-z
- Li Z., Long Y., Yu Y., Zhang F., Zhang H., Liu Z., Jia J., Mo W., Tian S. Z., Zheng M., & Zhai J. Pore-C simultaneously captures genome-wide multi-way chromatin interaction and associated DNA methylation status in Arabidopsis. Plant Biotechnology Journal (2022). Confirms multi-site interaction mapping and methylation retention in plant genomes. DOI: 10.1111/pbi.13811
- Ulahannan N. et al. Nanopore sequencing of DNA concatemers reveals higher-order chromatin interactions. bioRxiv (2022). Highlights Pore-C's capability in cancer SV reconstruction and de novo assembly support. doi: https://doi.org/10.1101/833590
- Imieliński M. & team. Team architecture in 3D genomic interactions revealed through nanopore sequencing. Nature Biotechnology commentary (2022). Overview of Pore-C and Chromunity method. https://doi.org/10.1038/s41587-022-01290-6
For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment