ArticleNature protocols2020
Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 36 citations in OpenAlex.
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.Nature communications · 2026Article
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.bioRxiv : the preprint server for biology · 2026Article
- 3D Chromatin Architecture During Early Development: New Methods and New Findings.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Nanoscale dynamics of enhancer-promoter interactions during exit from pluripotency.Nucleic acids research · 2025Article
- Characterization of induced cohesin loop extrusion trajectories in living cells.Nature genetics · 2025Article
- Chromatin insulators in gene regulation and 3D genome organization.Biochemical Society transactions · 2025Review
- Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D.Nature structural & molecular biology · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation.Nucleic acids research · 2024Article
- Three-way contact analysis characterizes the higher order organization of the Tcra locus.Nucleic acids research · 2023Article
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- Capturing Chromosome Conformation Across Length Scales.Journal of visualized experiments : JoVE · 2023Article
- Functional genomic assays to annotate enhancer-promoter interactions genome wide.Human molecular genetics · 2022Review
- Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.Nature protocols · 2022Review
- SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding.Nature protocols · 2022Review
- Application of the 3C Method to Study the Developmental Genes inFrontiers in genetics · 2022Article
- Modification mapping by nanopore sequencing.Frontiers in genetics · 2022Review
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
- Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.Current opinion in structural biology · 2021Review
- Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present the experimental protocol and data analysis toolbox for multi-contact 4C (MC-4C), a new proximity ligation method tailored to study the higher-order chromatin contact patterns of selected genomic sites. Conventional chromatin conformation capture (3C) methods fragment proximity ligation products for efficient analysis of pairwise DNA contacts. By contrast, MC-4C is designed to preserve and collect large concatemers of proximity ligated fragments for long-molecule sequencing on an Oxford Nanopore or Pacific Biosciences platform. Each concatemer of proximity ligation products represents a snapshot topology of a different individual allele, revealing its multi-way chromatin interactions. By inverse PCR with primers specific for a fragment of interest (the viewpoint) and DNA size selection, sequencing is selectively targeted to thousands of different complex interactions containing this viewpoint. A tailored statistical analysis toolbox is able to generate background models and three-way interaction profiles from the same dataset. These profiles can be used to distinguish whether contacts between more than two regulatory sequences are mutually exclusive or, conversely, simultaneously occurring at chromatin hubs. The entire procedure can be completed in 2 w, and requires standard molecular biology and data analysis skills and equipment, plus access to a third-generation sequencing platform.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.