ReviewWiley interdisciplinary reviews. Developmental biology2021
The macro and micro of chromosome conformation capture.
Review in Wiley interdisciplinary reviews. Developmental biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- Understanding the physical processes behind DNA-DNA proximity ligation assays.Research square · 2025Article
- Dynamics of microcompartment formation at the mitosis-to-G1 transition.Nature structural & molecular biology · 2025Article
- Article
- Understanding the physical processes behind DNA-DNA proximity ligation assays.bioRxiv : the preprint server for biology · 2025Article
- Transcription dynamics and genome organization in the mammalian nucleus: Recent advances.Molecular cell · 2025Review
- Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function.Molecular cell · 2025Article
- Article
- Review
- A 3D genome view of colon cancer initiation.Nature cancer · 2024Article
- Generation of densely labeled oligonucleotides for the detection of small genomic elements.Cell reports methods · 2024Article
- Pairtools: From sequencing data to chromosome contacts.PLoS computational biology · 2024Article
- IntegrativebioRxiv : the preprint server for biology · 2023Article
- DeCOOC Deconvoluted Hi-C Map Characterizes the Chromatin Architecture of Cells in Physiologically Distinctive Tissues.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Analysis of super-enhancer using machine learning and its application to medical biology.Briefings in bioinformatics · 2023Review
- Pairtools: from sequencing data to chromosome contacts.bioRxiv : the preprint server for biology · 2023Article
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- Visualizing the Nucleome Using the CRISPR-Cas9 System: From in vitro to in vivo.Biochemistry. Biokhimiia · 2023Review
- Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis.Frontiers in genetics · 2023Article
- Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase-scale compartments and topologically associating domains (TADs) down to kilobase-scale enhancer-promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C-based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi-C. We also discuss ChIP-based techniques that focus on 3D genome organization mediated by specific proteins, capture-based methods that focus on particular regions or regulatory elements, 3C-orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA-RNA and RNA-RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro-C as an emerging frontier in chromosome conformation capture and discuss recent Micro-C findings uncovering fine-scale chromatin organization in unprecedented detail. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics.
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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.