ArticleNature communications2023
High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Review
- Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.Nature plants · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- Transcription clusters and developmental pathways - nature, nurture, noise.Journal of cell science · 2026Review
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.Nature communications · 2026Article
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Article
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.bioRxiv : the preprint server for biology · 2026Article
- HyperDeepTAD: a topologically associated domains detection method based on multiway chromatin interaction data and deep learning.BMC genomics · 2026Article
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- Structural organization and function of telomeric chromatin.Nature cell biology · 2026Review
- Article
- PHScaffolding: a hypergraph clustering and dual-weight integration strategy for scaffolding with Pore-C reads.Briefings in bioinformatics · 2026Article
- CiFi: accurate long-read chromosome conformation capture with low-input requirements.Nature communications · 2025Article
- SLUR(M)-py: a SLURM powered Pythonic pipeline for parallel processing of 3D (Epi)genomic profiles.Epigenomics · 2025Article
- Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes.Nature communications · 2025Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- From Rabl-like Architecture to Chromosome Territories: A Conserved Developmental Transition in Animal Genomes.Molecular biology and evolution · 2025Article
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
- Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants.PLoS pathogens · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not the single-allele topologies in populations of cells. Recently developed Pore-C can capture multiway chromatin contacts that reflect regional topologies of single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive but regionally restricted clusters of single-allele topologies that aggregate into canonical 3D genome structures in two human cell types. We show that fragments in multi-contact reads generally coexist in the same TAD. In contrast, a concurrent significant proportion of multi-contact reads span multiple compartments of the same chromatin type over megabase distances. Synergistic chromatin looping between multiple sites in multi-contact reads is rare compared to pairwise interactions. Interestingly, the single-allele topology clusters are cell type-specific even inside highly conserved TADs in different types of cells. In summary, HiPore-C enables global characterization of single-allele topologies at an unprecedented depth to reveal elusive genome folding principles.
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