ReviewGenes & development2016
The second decade of 3C technologies: detailed insights into nuclear organization.
Review in Genes & development, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 183 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
183 citing papers in PubMed, 369 citations in OpenAlex.
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- Condensin accelerates long-range intra-chromosomal interactions.Nature communications · 2026Article
- Conserved 3D genome reorganization during DNA repair.Life science alliance · 2026Review
- Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A comprehensive benchmark of single-cell Hi-C embedding tools.Nature communications · 2025Article
- Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- Condensin Accelerates Long-Range Intra-Chromosomal Interactions.bioRxiv : the preprint server for biology · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Review
- Crosslinking intensity modulates the reliability and sensitivity of chromatin conformation detection at different structural levels.Communications biology · 2024Article
- Article
- Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.Briefings in bioinformatics · 2024Article
- DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions.Nature communications · 2024Article
- Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs.Nature communications · 2024Article
- MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops.Nucleic acids research · 2024Article
- Article
- Chromatin activity identifies differential gene regulation across human ancestries.Genome biology · 2024Article
123 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The relevance of three-dimensional (3D) genome organization for transcriptional regulation and thereby for cellular fate at large is now widely accepted. Our understanding of the fascinating architecture underlying this function is based on microscopy studies as well as the chromosome conformation capture (3C) methods, which entered the stage at the beginning of the millennium. The first decade of 3C methods rendered unprecedented insights into genome topology. Here, we provide an update of developments and discoveries made over the more recent years. As we discuss, established and newly developed experimental and computational methods enabled identification of novel, functionally important chromosome structures. Regulatory and architectural chromatin loops throughout the genome are being cataloged and compared between cell types, revealing tissue invariant and developmentally dynamic loops. Architectural proteins shaping the genome were disclosed, and their mode of action is being uncovered. We explain how more detailed insights into the 3D genome increase our understanding of transcriptional regulation in development and misregulation in disease. Finally, to help researchers in choosing the approach best tailored for their specific research question, we explain the differences and commonalities between the various 3C-derived methods.
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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.