Klemm, S. L., Shipony, Z. & Greenleaf, W. J. Chromatin accessibility and the regulatory epigenome. Nat. Rev. Genet. 20, 207–220 (2019).
Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).
Misteli, T. The self-organizing genome: principles of genome architecture and function. Cell 183, 28–45 (2020).
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).
Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Baysoy, A., Bai, Z., Satija, R. & Fan, R. The technological landscape and applications of single-cell multi-omics. Nat. Rev. Mol. Cell Biol. 24, 695–713 (2023).
Chappell, L., Russell, A. J. C. & Voet, T. Single-cell (multi)omics technologies. Annu. Rev. Genomics Hum. Genet. 19, 15–41 (2018).
Zhu, C., Preissl, S. & Ren, B. Single-cell multimodal omics: the power of many. Nat. Methods 17, 11–14 (2020).
Lee, D. S. et al. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nat. Methods 16, 999–1006 (2019).
Li, G. et al. Joint profiling of DNA methylation and chromatin architecture in single cells. Nat. Methods 16, 991–993 (2019).
Liu, Z. et al. Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq. Science 380, 1070–1076 (2023).
Qu, J. et al. Simultaneous profiling of chromatin architecture and transcription in single cells. Nat. Struct. Mol. Biol. 30, 1393–1402 (2023).
Wen, X. et al. Single-cell multiplex chromatin and RNA interactions in ageing human brain. Nature 628, 648–656 (2024).
Wu, H. et al. Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice. Nat. Methods 21, 974–982 (2024).
Zhou, T. et al. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nat. Genet. 56, 1701–1711 (2024).
Chang, L. et al. Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues. Nat. Biotechnol. 43, 1694–1707 (2025).
Chai, H. et al. Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan. Nat. Methods 22, 994–1007 (2025).
Wu, H., Wang, M., Zheng, Y. & Xie, X. S. Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics. Cell Discov. 11, 8 (2025).
Luecken, M. D. et al. Benchmarking atlas-level data integration in single-cell genomics. Nat. Methods 19, 41–50 (2022).
Hu, Y. et al. Benchmarking algorithms for single-cell multi-omics prediction and integration. Nat. Methods 21, 2182–2194 (2024).
Fu, S. et al. Benchmarking single-cell multi-modal data integrations. Nat. Methods 22, 2437–2448 (2025).
Flynn, E., Almonte-Loya, A. & Fragiadakis, G. K. Single-cell multiomics. Annu. Rev. Biomed. Data Sci. 6, 313–337 (2023).
Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380–1385 (2018).
Chen, S., Lake, B. B. & Zhang, K. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat. Biotechnol. 37, 1452–1457 (2019).
Zhu, C. et al. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat. Struct. Mol. Biol. 26, 1063–1070 (2019).
Ma, S. et al. Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183, 1103–1116.e20 (2020).
Tan, L. et al. Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development. Cell 184, 741–758.e17 (2021).
Xiong, H., Luo, Y., Wang, Q., Yu, X. & He, A. Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions. Nat. Methods 18, 652–660 (2021).
Xu, W. et al. ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells. Nat. Methods 19, 1243–1249 (2022).
Bartosovic, M. & Castelo-Branco, G. Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. Nat. Biotechnol. 41, 794–805 (2023).
Xie, Y. et al. Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nat. Struct. Mol. Biol. 30, 1428–1433 (2023).
Sarkar, A. & Hochedlinger, K. The Sox family of transcription factors: versatile regulators of stem and progenitor cell fate. Cell Stem Cell 12, 15–30 (2013).
Li, Y. et al. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. PLoS ONE 9, e114485 (2014).
Alexamder, J. M. et al. Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8, e41769 (2019).
Di Croce, L. & Helin, K. Transcriptional regulation by Polycomb group proteins. Nat. Struct. Mol. Biol. 20, 1147–1155 (2013).
Wang, M. & Zhang, Y. Tn5 transposase-based epigenomic profiling methods are prone to open chromatin bias. Preprint at bioRxiv https://doi.org/10.1101/2021.07.09.451758 (2021).
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).
Macrae, T. A., Fothergill-Robinson, J. & Ramalho-Santos, M. Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat. Rev. Mol. Cell Biol. 24, 6–26 (2023).
Stewart-Morgan, K. R., Petryk, N. & Groth, A. Chromatin replication and epigenetic cell memory. Nat. Cell Biol. 22, 361–371 (2020).
Nagano, T. et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature 547, 61–67 (2017).
Mahat, D. B. et al. Single-cell nascent RNA sequencing unveils coordinated global transcription. Nature 631, 216–223 (2024).
Pope, B. D. et al. Topologically associating domains are stable units of replication-timing regulation. Nature 515, 402–405 (2014).
Owen, J. A., Osmanovic, D. & Mirny, L. Design principles of 3D epigenetic memory systems. Science 382, eadg3053 (2023).
Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59–64 (2013).
Stevens, T. J. et al. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature 544, 59–64 (2017).
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).
Lafontaine, D. L., Yang, L., Dekker, J. & Gibcus, J. H. Hi-C 3.0: improved protocol for genome-wide chromosome conformation capture. Curr. Protoc. 1, e198 (2021).
Wu, H., Zhang, J., Tan, L. & Xie, X. S. Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs. Nat. Genet. 57, 1777–1786 (2025).
Caetano, F. A. et al. MIiSR: molecular interactions in super-resolution imaging enables the analysis of protein interactions, dynamics and formation of multi-protein structures. PLoS Comput. Biol. 11, e1004634 (2015).
Vieux-Rochas, M., Fabre, P. J., Leleu, M., Duboule, D. & Noordermeer, D. Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. Proc. Natl Acad. Sci. USA 112, 4672–4677 (2015).
Xie, L. et al. 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nat. Methods 17, 430–436 (2020).
Bintu, B. et al. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783 (2018).
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
Cho, W. K. et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science 361, 412–415 (2018).
Sabari, B. R. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958 (2018).
Lim, B. & Levine, M. S. Enhancer-promoter communication: hubs or loops?. Curr. Opin. Genet. Dev. 67, 5–9 (2021).
Uyehara, C. M. & Apostolou, E. 3D enhancer-promoter interactions and multi-connected hubs: organizational principles and functional roles. Cell Rep. 42, 112068 (2023).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
Mitra, S. et al. Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. Nat. Genet. 56, 627–636 (2024).
Fulco, C. P. et al. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Nat. Genet. 51, 1664–1669 (2019).
Savage, J. E. et al. Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence. Nat. Genet. 50, 912–919 (2018).
Whitton, L. et al. Genes regulated by SATB2 during neurodevelopment contribute to schizophrenia and educational attainment. PLoS Genet. 14, e1007515 (2018).
Cera, I. et al. Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human cognitive ability. PLoS Genet. 15, e1007890 (2019).
Zarate, Y. A. et al. Natural history and genotype-phenotype correlations in 72 individuals with SATB2-associated syndrome. Am. J. Med. Genet. A 176, 925–935 (2018).
Jaitner, C. et al. Satb2 determines miRNA expression and long-term memory in the adult central nervous system. eLife 5, e17361 (2016).
Li, Y. et al. Satb2 ablation impairs hippocampus-based long-term spatial memory and short-term working memory and immediate early genes (IEGs)-mediated hippocampal synaptic plasticity. Mol. Neurobiol. 43, 15251–15266 (2025).
Wahl, N. et al. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol. Cell 84, 621–639.e9 (2024).
Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975–978 (2017).
Pampari, A. et al. ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants. Preprint at bioRxiv https://doi.org/10.1101/2024.12.25.630221 (2024).
Reveron-Gomez, N. et al. Accurate recycling of parental histones reproduces the histone modification landscape during DNA replication. Mol. Cell 72, 239–249.e5 (2018).
Fennessy, R. T. & Owen-Hughes, T. Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing. Nucleic Acids Res. 44, 7189–7203 (2016).
Ramachandran, S. & Henikoff, S. Transcriptional regulators compete with nucleosomes post-replication. Cell 165, 580–592 (2016).
Stewart-Morgan, K. R., Reveron-Gomez, N. & Groth, A. Transcription restart establishes chromatin accessibility after DNA replication. Mol. Cell 75, 408–414 (2019).
Blayney, J. W. et al. Super-enhancers include classical enhancers and facilitators to fully activate gene expression. Cell 186, 5826–5839.e18 (2023).
Mazzocca, M., Narducci, D. N., Grosse-Holz, S., Matthias, J. & Hansen, A. S. Chromatin dynamics are highly subdiffusive across seven orders of magnitude. Preprint at bioRxiv https://doi.org/10.1101/2025.05.10.653248 (2025).
Sanyal, A., Lajoie, B. R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).
Tian, W. et al. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 382, eadf5357 (2023).
Liu, H. et al. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature 624, 366–377 (2023).
Heffel, M. G. et al. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature 635, 481–489 (2024).
Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).
Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187–1201 (2015).
Vitak, S. A. et al. Sequencing thousands of single-cell genomes with combinatorial indexing. Nat. Methods 14, 302–308 (2017).
Rosenberg, A. B. et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 360, 176–182 (2018).
Meers, M. P., Llagas, G., Janssens, D. H., Codomo, C. A. & Henikoff, S. Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag. Nat. Biotechnol. 41, 708–716 (2023).
Gopalan, S., Wang, Y., Harper, N. W., Garber, M. & Fazzio, T. G. Simultaneous profiling of multiple chromatin proteins in the same cells. Mol. Cell 81, 4736–4746.e5 (2021).
Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).
Mimitou, E. P. et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat. Biotechnol. 39, 1246–1258 (2021).
Meissner, A., Eminli, S. & Jaenisch, R. Derivation and manipulation of murine embryonic stem cells. Methods Mol. Biol. 482, 3–19 (2009).
Hao, Y. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Biotechnol. 42, 293–304 (2024).
Stuart, T., Srivastava, A., Madad, S., Lareau, C. A. & Satija, R. Single-cell chromatin state analysis with Signac. Nat. Methods 18, 1333–1341 (2021).
Zhou, J. et al. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. Proc. Natl Acad. Sci. USA 116, 14011–14018 (2019).
Bonev, B. et al. Multiscale 3D genome rewiring during mouse neural development. Cell 171, 557–572.e24 (2017).
Cai, Y. et al. H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. Nat. Commun. 12, 719 (2021).
Hinrichs, A. S. et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34, D590–D598 (2006).
Murphy, D. et al. 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Nat. Struct. Mol. Biol. 31, 125–140 (2024).
Agrawal, P. et al. Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment. J. Biol. Chem. 296, 100189 (2021).
Tesar, P. J. et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 448, 196–199 (2007).
Xie, L. et al. A dynamic interplay of enhancer elements regulates Klf4 expression in naive pluripotency. Genes Dev. 31, 1795–1808 (2017).
Engreitz, J. M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539, 452–455 (2016).
Moorthy, S. D. et al. Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. Genome Res. 27, 246–258 (2017).

