Zheng, H. & Xie, W. The role of 3D genome organization in development and cell differentiation. Nat. Rev. Mol. Cell Biol. 20, 535–550 (2019).
Chen, Z. & Zhang, Y. Role of mammalian DNA methyltransferases in development. Annu. Rev. Biochem. 89, 135–158 (2020).
Schmitt, A. D., Hu, M. & Ren, B. Genome-wide mapping and analysis of chromosome architecture. Nat. Rev. Mol. Cell Biol. 17, 743–755 (2016).
Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017).
Yu, M. & Ren, B. The three-dimensional organization of mammalian genomes. Annu. Rev. Cell Dev. Biol. 33, 265–289 (2017).
Li, Z. et al. Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements. Nature 623, 643–651 (2023).
Emerson, D. J. et al. Cohesin-mediated loop anchors confine the locations of human replication origins. Nature 606, 812–819 (2022).
Dekker, J. et al. Spatial and temporal organization of the genome: current state and future aims of the 4D nucleome project. Mol. Cell 83, 2624–2640 (2023).
Liu, Y. et al. Fork coupling directs DNA replication elongation and termination. Science 383, 1215–1222 (2024).
Li, D. et al. Chromatin accessibility dynamics during iPSC reprogramming. Cell Stem Cell 21, 819–833.e6 (2017).
Wan, Y. et al. Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell 184, 2878–2895.e20 (2021).
Wen, X. et al. Single-cell multiplex chromatin and RNA interactions in ageing human brain. Nature 628, 648–656 (2024).
Lupianez, D. G. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012–1025 (2015).
Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell 10, 1453–1465 (2002).
Schoenfelder, S. & Fraser, P. Long-range enhancer–promoter contacts in gene expression control. Nat. Rev. Genet. 20, 437–455 (2019).
Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390–394 (2011).
Zhou, Y., Xu, S., Zhang, M. & Wu, Q. Systematic functional characterization of antisense eRNA of protocadherin α composite enhancer. Genes Dev. 35, 1383–1394 (2021).
Li, G. et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 11, R22 (2010).
Beagrie, R. A. et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524 (2017).
Beagrie, R. A. et al. Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. Nat. Methods 20, 1037–1047 (2023).
Mirny, L. A. & Solovei, I. Keeping chromatin in the loop(s). Nat. Rev. Mol. Cell Biol. 22, 439–440 (2021).
Boettiger, A. N. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016).
Su, J. H., Zheng, P., Kinrot, S. S., Bintu, B. & Zhuang, X. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell 182, 1641–1659.e26 (2020).
Takei, Y. et al. Integrated spatial genomics reveals global architecture of single nuclei. Nature 590, 344–350 (2021).
Yang, T. & Wang, S. Image-based 3D genomics through chromatin tracing. Nat. Rev. Methods Primers 4, 76 (2024).
Pownall, M. E. et al. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 381, 92–100 (2023).
Gabriele, M. et al. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science 376, 496–501 (2022).
Yang, J. H. & Hansen, A. S. Enhancer selectivity in space and time: from enhancer−promoter interactions to promoter activation. Nat. Rev. Mol. Cell Biol. 25, 574–591 (2024).
Brückner, D. B., Chen, H. T., Barinov, L., Zoller, B. & Gregor, T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science 380, 1357–1362 (2023).
Alexander, J. M. et al. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8, e41769 (2019).
Chen, H. T. et al. Dynamic interplay between enhancer−promoter topology and gene activity. Nat. Genet. 50, 1296–1303 (2018).
Janicki, S. M. et al. From silencing to gene expression: real-time analysis in single cells. Cell 116, 683–698 (2004).
Masui, O. et al. Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell 145, 447–458 (2011).
Xu, H. et al. TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Res. 48, 13013–13014 (2020).
Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491 (2013).
Wang, H. et al. CRISPR-mediated live imaging of genome editing and transcription. Science 365, 1301–1305 (2019).
Qin, P. et al. Live cell imaging of low- and non-repetitive chromosome loci using CRISPR−Cas9. Nat. Commun. 8, 14725 (2017).
Gu, B. et al. Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 359, 1050–1055 (2018).
Lyu, X. Y. et al. CRISPR FISHer enables high-sensitivity imaging of nonrepetitive DNA in living cells through phase separation-mediated signal amplification. Cell Res. 32, 969–981 (2022).
Yang, L. et al. CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells. Nat. Methods 21, 1646–1657 (2024).
Ma, H. et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat. Biotechnol. 34, 528–530 (2016).
Cheng, A. W. et al. Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling. Cell Res. 26, 254–257 (2016).
Ma, H. et al. CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat. Methods 15, 928–931 (2018).
Mao, S., Ying, Y., Wu, X., Krueger, C. J. & Chen, A. K. CRISPR/dual-FRET molecular beacon for sensitive live-cell imaging of non-repetitive genomic loci. Nucleic Acids Res. 47, e131 (2019).
Peng, Q. et al. Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells. Nat. Commun. 13, 7933 (2022).
Clow, P. A. et al. CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus. Nat. Commun. 13, 1871 (2022).
Geng, Y. T. & Pertsinidis, A. Simple and versatile imaging of genomic loci in live mammalian cells and early pre-implantation embryos using CAS-LiveFISH. Sci. Rep. 11, 12220 (2021).
Zhang, Z. et al. Fluorogenic CRISPR for genomic DNA imaging. Nat. Commun. 15, 934 (2024).
Hong, Y., Lu, G., Duan, J., Liu, W. & Zhang, Y. Comparison and optimization of CRISPR/dCas9/gRNA genome-labeling systems for live cell imaging. Genome Biol. 19, 39 (2018).
Mao, S., Wu, R., Luo, W., Qin, J. & Chen, A. K. Spuriously transcribed RNAs from CRISPR-sgRNA expression plasmids scaffold biomolecular condensate formation and hamper accurate genomic imaging. Nucleic Acids Res. 53, gkaf192 (2025).
Chen, B. et al. Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Res. 44, e75 (2016).
Ge, X. et al. Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation. Nat. Commun. 14, 8101 (2023).
Lv, X. et al. Patterned cPCDH expression regulates the fine organization of the neocortex. Nature 612, 503–511 (2022).
Wu, Q. & Maniatis, T. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell 97, 779–790 (1999).
Wang, Y., Chen, Y., Hu, Y. & Fang, X. Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription. Proc. Natl Acad. Sci. USA 117, 22823–22832 (2020).
Niu, X. et al. Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs. Nat. Commun. 12, 6417 (2021).
Wang, Y. et al. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem. Sci. 11, 9655–9664 (2020).
Li, L. J. et al. Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications. J. Am. Chem. Soc. 136, 826–829 (2014).
Lee, K. H., Hamashima, K., Kimoto, M. & Hirao, I. Genetic alphabet expansion biotechnology by creating unnatural base pairs. Curr. Opin. Biotechnol. 51, 8–15 (2018).
Betz, K. et al. KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry. Nat. Chem. Biol. 8, 612–614 (2012).
Oh, J. et al. Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nat. Chem. Biol. 17, 906–914 (2021).
Korolev, S. & Gagnon, K. SpCas9 with sgRNA and target DNA. RCSB Protein Data Bank. https://doi.org/10.2210/pdb8G1I/pdb (2023).
Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).
Xu, J. Q. et al. Super-resolution imaging of higher-order chromatin structures at different epigenomic states in single mammalian cells. Cell Rep. 24, 873–882 (2018).
Ricci, M. A., Manzo, C., GarcÃa-Parajo, M. F., Lakadamyali, M. & Cosma, M. P. Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 160, 1145–1158 (2015).
Nozaki, T. et al. Condensed but liquid-like domain organization of active chromatin regions in living human cells. Sci. Adv. 9, eadf1488 (2023).
Saxton, M. N., Morisaki, T., Krapf, D., Kimura, H. & Stasevich, T. J. Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. Sci. Adv. 9, eadh4819 (2023).
Nagashima, R. et al. Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II. J. Cell Biol. 218, 1511–1530 (2019).
Feng, Y. et al. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Genome Biol. 21, 296 (2020).
Lasko, L. M. et al. Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. Nature 550, 128–132 (2017).
Vigushin, D. M. et al. Trichostatin A is a histone deacetylase inhibitor with potent antitumor activity against breast cancer. Clin. Cancer Res. 7, 971–976 (2001).
Payer, B. & Lee, J. T. X chromosome dosage compensation: how mammals keep the balance. Annu. Rev. Genet. 42, 733–772 (2008).
Xie, G. J. et al. MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. Nat. Genet. 55, 693–705 (2023).
Alver, B. H. et al. The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers. Nat. Commun. 8, 14648 (2017).
Lex, R. K. et al. GLI transcriptional repression is inert prior to Hedgehog pathway activation. Nat. Commun. 13, 808 (2022).
Kraushaar, D. C. et al. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol. 14, R121 (2013).
Huang, X., Bashkenova, N., Yang, J. H., Li, D. & Wang, J. L. ZFP281 recruits polycomb repressive complex 2 to restrict extraembryonic endoderm potential in safeguarding embryonic stem cell pluripotency. Protein Cell 12, 213–219 (2021); erratum 12, 511–513 (2021).
Xie, W. H. et al. RNF40 regulates gene expression in an epigenetic context-dependent manner. Genome Biol. 18, 32 (2017).
Pham, P. D. et al. Transcriptional network governing extraembryonic endoderm cell fate choice. Dev. Biol. 502, 20–37 (2023).
Kaemena, D. F. et al. B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors. Nat. Commun. 14, 488 (2023).
Raccaud, M. et al. Mitotic chromosome binding predicts transcription factor properties in interphase. Nat. Commun. 10, 487 (2019).
Du, Z. H. et al. Stepwise de novo establishment of inactive X chromosome architecture in early development. Nat. Genet. 56, 2185–2198 (2024).
Cloutier, M., Harris, C., Gayen, S., Maclary, E. & Kalantry, S. Experimental analysis of imprinted mouse X-chromosome inactivation. Methods Mol. Biol. 1861, 177–203 (2018).
Cox, G. & Sheppard, C. J. R. Practical limits of resolution in confocal and non-linear microscopy. Microsc. Res. Tech. 63, 18–22 (2004).
Kehayova, P., Monahan, K., Chen, W. S. & Maniatis, T. Regulatory elements required for the activation and repression of the protocadherin-α gene cluster. Proc. Natl Acad. Sci. USA 108, 17195–17200 (2011).
Guo, Y. et al. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc. Natl Acad. Sci. USA 109, 21081–21086 (2012).
Monahan, K. et al. Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of Protocadherin-α gene expression. Proc. Natl Acad. Sci. USA 109, 9125–9130 (2012).
Wang, T. F. et al. Chemical-induced phase transition and global conformational reorganization of chromatin. Nat. Commun. 14, 5556 (2023).
Ye, C. Y. et al. DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery. Nat. Commun. 9, 4307 (2018).
Tak, Y. E. et al. Augmenting and directing long-range CRISPR-mediated activation in human cells. Nat. Methods 18, 1075–1081 (2021).
Morgan, S. L. et al. Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nat. Commun. 8, 15993 (2017).
Furlan, G. et al. The Ftx noncoding locus controls X chromosome inactivation independently of its RNA products. Mol. Cell 70, 462–472 (2018).
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).
Bal, E. et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 607, 808–815 (2022).
Sabari, B. R. et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958 (2018).
Cho, W. K. et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361, 412–415 (2018).
Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).
Delmore, J. E. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917 (2011).
Linares-Saldana, R. et al. BRD4 orchestrates genome folding to promote neural crest differentiation. Nat. Genet. 53, 1480–1492 (2021).
Crump, N. T. et al. BET inhibition disrupts transcription but retains enhancer-promoter contact. Nat. Commun. 12, 223 (2021).
Xiang, J. et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res. 24, 513–531 (2014).
Cai, Z. K. et al. RIC-seq for global in situ profiling of RNA−RNA spatial interactions. Nature 582, 432–437 (2020).
Zhu, Y. et al. High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH. Cell 188, 3310–3328.e27 (2025).
Wan, X. et al. SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells. Genome Biol. 26, 1 (2025).
Ochiai, H., Sugawara, T. & Yamamoto, T. Simultaneous live imaging of the transcription and nuclear position of specific genes. Nucleic Acids Res. 43, e127 (2015).
Lengner, C. J. et al. Primary mouse embryonic fibroblasts: a model of mesenchymal cartilage formation. J. Cell. Physiol. 200, 327–333 (2004).
Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Beliveau, B. J. et al. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc. Natl Acad. Sci. USA 109, 21301–21306 (2012).
Wang, H. et al. CRISPR-mediated programmable 3D genome positioning and nuclear organization. Cell 175, 1405–1417.e14 (2018).
Zou, Z., Ohta, T., Miura, F. & Oki, S. ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Res. 50, W175–W182 (2022).






