ArticleMolecular systems biology2016
Exploiting native forces to capture chromosome conformation in mammalian cell nuclei.
Article in Molecular systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 61 citations in OpenAlex.
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- Revisiting models of enhancer-promoter communication in gene regulation.Genome research · 2025Review
- Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape.Nature aging · 2025Article
- Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations.Experimental & molecular medicine · 2024Review
- Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.Nature methods · 2023Article
- Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion.Nature genetics · 2023Article
- The Nodewalk assay to quantitate chromatin fiber interactomes in very small cell populations.Nature protocols · 2023Review
- Long range inter-chromosomal interaction of Oct4 distal enhancer loci regulates ESCs pluripotency.Cell death discovery · 2023Article
- Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.Nature protocols · 2022Review
- 3D genome organization links non-coding disease-associated variants to genes.Frontiers in cell and developmental biology · 2022Review
- TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer.Nature cancer · 2021Article
- The macro and micro of chromosome conformation capture.Wiley interdisciplinary reviews. Developmental biology · 2021Review
- RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis.Science advances · 2021Article
- The relationship between genome structure and function.Nature reviews. Genetics · 2021Review
- Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression.Frontiers in cell and developmental biology · 2021Review
- FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains.Frontiers in cell and developmental biology · 2021Review
- The Toolbox for Untangling Chromosome Architecture in Immune Cells.Frontiers in immunology · 2021Review
- Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation.Human molecular genetics · 2020Article
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.Molecular cell · 2020Review
- Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies.Nature protocols · 2020Article
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure-to-function relationship. However, all 3C-based methods rely on chemical cross-linking to stabilize spatial interactions. This step remains a "black box" as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed "i3C", a novel approach for capturing spatial interactions without a need for cross-linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation-based orthogonal validation method, "TALE-iD", we show that native interactions resemble cross-linked ones, but display improved signal-to-noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.
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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.