Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).
Google Scholar
Brant, L. et al. Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol. Syst. Biol. 12, 1–8 (2016).
Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).
Google Scholar
Hughes, J. R. et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat. Genet. 46, 205–212 (2014).
Google Scholar
Davies, J. O. J. et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat. Methods 13, 74–80 (2016).
Google Scholar
Van De Werken, H. J. G. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods 9, 969–972 (2012).
Google Scholar
Mifsud, B. et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat. Genet. 47, 598–606 (2015).
Google Scholar
Madsen, J. G. S. et al. Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells. Nat. Genet. 52, 1227–1238 (2020).
Google Scholar
Oudelaar, A. M., Davies, J. O. J., Downes, D. J., Higgs, D. R. & Hughes, J. R. Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C. Nucleic Acids Res. 45, (2017).
Downes, D. J. et al. High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nat. Commun. 12, 531 (2021).
Google Scholar
Oudelaar, A. M. et al. Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nat. Genet. 50, 1744–1751 (2018).
Google Scholar
Oudelaar, A. M., Hughes, J. & Downes, D. Tri-C. Protoc. Exch. https://doi.org/10.21203/rs.2.1650/v2 (2019).
Oudelaar, A. M. et al. Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nat. Commun. 11, (2020).
Golov, A. K. et al. A modified protocol of Capture-C allows affordable and flexible high-resolution promoter interactome analysis. Sci. Rep. 10, 1–15 (2020).
King, A. J. et al. Reactivation of a developmentally silenced embryonic globin gene. Nat. Commun. https://doi.org/10.1038/s41467-021-24402-3 (2021).
Hay, D. et al. Genetic dissection of the α-globin super-enhancer in vivo. Nat. Genet. 48, 895–903 (2016).
Google Scholar
Simon, C. S. et al. Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo. Development 144, 1249–1260 (2017).
Google Scholar
Schäfer, A. et al. Impaired DNA demethylation of C/EBP sites causes premature aging. Genes Dev. 32, 742–762 (2018).
Google Scholar
Godfrey, L. et al. DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nat. Commun. 10, 2803 (2019).
Oudelaar, A. M. et al. A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nat. Commun. https://doi.org/10.1038/s41467-019-13404-x (2019).
Ghavi-Helm, Y. et al. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat. Genet. 51, 1272–1282 (2019).
Google Scholar
Williams, R. M. et al. Reconstruction of the global neural crest gene regulatory network in vivo. Dev. Cell 51, 255–276.e7 (2019).
Google Scholar
Larke, M. S. C. et al. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol. Cell 81, 983-997.e7 (2021).
Blackledge, N. P. et al. PRC1 catalytic activity is central to polycomb system function. Mol. Cell 77, 857-874.e9 (2020).
Rhodes, J. D. P. et al. Cohesin disrupts polycomb-dependent chromosome interactions in embryonic stem cells. Cell Rep. 30, 820–835 (2020).
Google Scholar
Furlan, G. et al. The Ftx noncoding locus controls X chromosome inactivation independently of its RNA products. Mol. Cell 70, 462–472 (2018).
Google Scholar
van Bemmel, J. G. et al. The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nat. Genet. 51, 1024–1034 (2019).
Hanssen, L. L. P. et al. Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat. Cell Biol. 19, 952–961 (2017).
Google Scholar
Hyle, J. et al. Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping. Nucleic Acids Res. 47, 6699–6713 (2019).
Zhang, D. et al. Alteration of genome folding via contact domain boundary insertion. Nat. Genet. 52, 1076-1087 (2020).
Harrold, C. L. et al. A functional overlap between actively transcribed genes and chromatin boundary elements. Preprint at bioRxiv https://doi.org/10.1101/2020.07.01.182089 (2020).
Downes, D. J. et al. An integrated platform to systematically identify causal variants and genes for polygenic human traits. Preprint at bioRxiv https://doi.org/10.1101/813618 (2019).
Thurner, M. et al. Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 diabetes susceptibility loci. eLife 7, e31977 (2018).
Chesi, A. et al. Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density. Nat. Commun. 10, 1260 (2019).
Badat, M. et al. A remarkable case of HbH disease illustrates the relative contributions of the α-globin enhancers to gene expression. Blood https://doi.org/10.1182/blood.2020006680 (2020).
Long, H. K. et al. Loss of extreme long-range enhancers in human neural crest drives a craniofacial disorder. Cell Stem Cell 27, 765–783.e14 (2020).
Google Scholar
Olijnik, A. A. et al. Genetic and functional insights into CDA-I prevalence and pathogenesis. J. Med. Genet. https://doi.org/10.1136/jmedgenet-2020-106880 (2020).
Bozhilov, Y. K. et al. A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer–blocker. Nat. Commun. 12, 3806 (2021).
Schwessinger, R. et al. DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nat. Methods https://doi.org/10.1038/s41592-020-0960-3 (2020).
Brown, J. M. et al. A tissue-specific self-interacting chromatin domain forms independently of enhancer–promoter interactions. Nat. Commun. 9, 3849 (2018).
Chiariello, A. M. et al. A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells. Cell Rep. 30, 2125–2135.e5 (2020).
Google Scholar
Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341–1347 (2006).
Google Scholar
Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C). Nat. Genet. 38, 1348–1354 (2006).
Google Scholar
Hagege, H. et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722–1733 (2007).
Google Scholar
Schwartzman, O. et al. UMI-4C for quantitative and targeted chromosomal contact profiling. Nat. Methods 13, 685–691 (2016).
Google Scholar
Davies, J. O. J., Oudelaar, A. M., Higgs, D. R. & Hughes, J. R. How best to identify chromosomal interactions: a comparison of approaches. Nat. Methods 14, 125–134 (2017).
Google Scholar
Schoenfelder, S. et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 25, 582–597 (2015).
Hsieh, T. H. S. et al. Mapping nucleosome resolution chromosome folding in yeast by Micro-C. Cell 162, 108–119 (2015).
Google Scholar
Hsieh, T. H. S., Fudenberg, G., Goloborodko, A. & Rando, O. J. Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome. Nat. Methods 13, 1009–1011 (2016).
Google Scholar
Ma, W. et al. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat. Methods 12, 71–78 (2014).
Google Scholar
Hua, P. et al. Defining genome architecture at base-pair resolution. Nature https://doi.org/10.1038/s41586-021-03639-4 (2021).
Li, G. et al. Chromatin interaction analysis with paired-end tag (ChIA-PET) sequencing technology and application. BMC Genomics 15, S11 (2014).
Google Scholar
Fang, R. et al. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 26, 1345–1348 (2016).
Zheng, M. et al. Multiplex chromatin interactions with single-molecule precision. Nature 566, 558–562 (2019).
Google Scholar
Mumbach, M. R. et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13, 919–922 (2016).
Google Scholar
Mumbach, M. R. et al. HiChIRP reveals RNA-associated chromosome conformation. Nat. Methods 16, 489–492 (2019).
Google Scholar
Dostie, J. et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299–1309 (2006).
Kolovos, P. et al. Targeted chromatin capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements. Epigenetics Chromatin 7, 10 (2014).
Dryden, N. H. et al. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res. 24, 1854–1868 (2014).
Sanborn, A. L. et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc. Natl Acad. Sci. USA 112, E6456–E6465 (2015).
Google Scholar
Aljahani, A. et al. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Preprint at bioRxiv https://doi.org/10.1101/2021.08.10.455796 (2021).
Olivares-Chauvet, P. et al. Capturing pairwise and multi-way chromosomal conformations using chromosomal walks. Nature 540, 296–300 (2016).
Google Scholar
Allahyar, A. et al. Enhancer hubs and loop collisions identified from single-allele topologies. Nat. Genet. 50, 1151–1160 (2018).
Google Scholar
Vermeulen, C. et al. Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies. Nat. Protoc. 15, 364–397 (2020).
Google Scholar
Beagrie, R. A. et al. Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. Preprint at bioRxiv https://doi.org/10.1101/2020.07.31.230284 (2020).
Beagrie, R. A. et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524 (2017).
Google Scholar
Quinodoz, S. A. et al. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744–757.e24 (2018).
Google Scholar
Takei, Y. et al. Integrated spatial genomics reveals global architecture of single nuclei. Nature 590, 344–350 (2021).
Tan, L., Xing, D., Chang, C. H., Li, H. & Xie, X. S. Three-dimensional genome structures of single diploid human cells. Science 361, 924–928 (2018).
Google Scholar
Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59–64 (2013).
Google Scholar
Nagano, T. et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547, 61–67 (2017).
Google Scholar
Ramani, V. et al. Massively multiplex single-cell Hi-C. Nat. Methods 14, 263–266 (2017).
Google Scholar
Stevens, T. J. et al. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 544, 59–64 (2017).
Google Scholar
Flyamer, I. M. et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature 544, 110–114 (2017).
Google Scholar
Telenius, J. M. et al. CaptureCompendium: a comprehensive toolkit for 3C analysis. Preprint at bioRxiv https://doi.org/10.1101/2020.02.17.952572 (2020).
Anil, A., Spalinskas, R., Åkerborg, Ö. & Sahlén, P. HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications. Bioinformatics 34, 675–677 (2018).
Google Scholar
Hansen, P. et al. GOPHER: Generator Of probes for capture Hi-C experiments at high resolution. BMC Genomics 20, 40 (2019).
Google Scholar
Kent, W. J. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
Smit, A., Hubley, R. & Green, P. RepeatMasker Open-4.0 (2015).
Eijsbouts, C. Q., Burren, O. S., Newcombe, P. J. & Wallace, C. Fine mapping chromatin contacts in capture Hi-C data. BMC Genomics 20, 77 (2019).
Google Scholar
Geeven, G., Teunissen, H., De Laat, W. & De Wit, E. peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data. Nucleic Acids Res. 46, e91 (2018).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1–21 (2014).
Wang, Y. et al. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol. https://doi.org/10.1101/112268 (2018).
Kerpedjiev, P. et al. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. https://doi.org/10.1101/121889 (2018).
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome https://doi.org/10.1186/s13059-015-0831-x (2015).
Buckle, A., Gilbert, N., Marenduzzo, D. & Brackley, C. A. capC-MAP: software for analysis of Capture-C data. Bioinformatics https://doi.org/10.1093/bioinformatics/btz480 (2019).
Cairns, J. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol. 17, 127 (2016).
Thongjuea, S., Stadhouders, R., Grosveld, F. G., Soler, E. & Lenhard, B. R3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res. 41, e132 (2013).
Klein, F. A. et al. FourCSeq: analysis of 4C sequencing data. Bioinformatics 31, 3085–3091 (2015).
Google Scholar
Freire-Pritchett, P. et al. Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools. Nat. Protoc. 16, 4144–4176 (2021).
Smith, A. L., Rue-Albrecht, K. & Sims, D. CapCruncher. Zenodo https://doi.org/10.5281/zenodo.5113088 (2021).
Brandão, H. B., Gabriele, M. & Hansen, A. S. Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging. Curr. Opin. Cell Biol. 70, 18–26 (2021).
Google Scholar
Lakadamyali, M. & Cosma, M. P. Visualizing the genome in high resolution challenges our textbook understanding. Nat. Methods 17, 371–379 (2020).
Google Scholar
Kempfer, R. & Pombo, A. Methods for mapping 3D chromosome architecture. Nat. Rev. Genet. 21, 207–226 (2020).
Google Scholar
Shaban, H. A. & Seeber, A. Monitoring the spatio-temporal organization and dynamics of the genome. Nucleic Acids Res. 48, 3423–3434 (2020).
Beecham, A. H. et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat. Genet. 45, 1353–1360 (2013).
Google Scholar
Boettiger, A. & Murphy, S. Advances in chromatin imaging at kilobase-scale resolution. Trends Genet 36, 273–287 (2020).
Google Scholar
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
Google Scholar
Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).
Google Scholar
Oudelaar, A. M., Downes, D., Davies, J. & Hughes, J. Low-input Capture-C: a chromosome conformation capture assay to analyze chromatin architecture in small numbers of cells. Bio Protoc. 7, e2645 (2017).
