Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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An oestrogen-receptor-α-bound human chromatin interactome

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A map of the cis-regulatory sequences in the mouse genome

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HiChIP: efficient and sensitive analysis of protein-directed genome architecture

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Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data

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Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

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Topology of mammalian developmental enhancers and their regulatory landscapes

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Brain cell type–specific enhancer–promoter interactome maps and disease - risk association

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The role of 3D genome organization in development and cell differentiation

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Circular ecDNA promotes accessible chromatin and high oncogene expression

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Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

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The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

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Methods for mapping 3D chromosome architecture

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Towards a comprehensive catalogue of validated and target-linked human enhancers

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Understanding 3D genome organization by multidisciplinary methods

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An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

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The Three-Dimensional Organization of Mammalian Genomes

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Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

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Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies

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Identification of significant chromatin contacts from HiChIP data by FitHiChIP

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Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

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Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

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Mechanisms of Interplay between Transcription Factors and the 3D Genome

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Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

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UTX condensation underlies its tumour-suppressive activity

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CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

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Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases

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The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

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A supervised learning framework for chromatin loop detection in genome-wide contact maps

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The spatial organization of transcriptional control

Hafner, A., & Boettiger, A. N. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00526-0 · Cited by 158

Cell-type-specific 3D epigenomes in the developing human cortex

Song, M., Pebworth, M.-P., Yang, X., Abnousi, A., Fan, C., Wen, J., Rosen, J. D., Choudhary, M. N. K., Cui, X., Jones, I. R., et al. (2020) · Nature · doi:10.1038/s41586-020-2825-4 · Cited by 145

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

Wang, X., Luan, Y., & Yue, F. (2022) · Science Advances · doi:10.1126/sciadv.abn9215 · Cited by 148

Gene Regulatory Elements, Major Drivers of Human Disease

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Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II, and Pol III

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Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

Chandra, V., Bhattacharyya, S., Schmiedel, B. J., Madrigal, A., Gonzalez-Colin, C., Fotsing, S., Crinklaw, A., Seumois, G., Mohammadi, P., Kronenberg, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00745-3 · Cited by 122

Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes

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MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

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A Comparative Overview of Epigenomic Profiling Methods

Mehrmohamadi, M., Sepehri, M. H., Nazer, N., & Norouzi, M. R. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.714687 · Cited by 119

The chromosome folding problem and how cells solve it

Dekker, J., & Mirny, L. A. (2024) · Cell · doi:10.1016/j.cell.2024.10.026 · Cited by 112

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

Petrovic, J., Zhou, Y., Fasolino, M., Goldman, N., Schwartz, G. W., Mumbach, M. R., Nguyen, S. C., Rome, K., Sela, Y., Zapataro, Z., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.01.006 · Cited by 107

Unraveling the 3D Genome Architecture in Plants: Present and Future

Ouyang, W., Xiong, D., Li, G., & Li, X. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.10.002 · Cited by 96

H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation

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Trac-looping measures genome structure and chromatin accessibility

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Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project

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Integrating ChIP-seq with other functional genomics data

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SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity

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Characterization of altered molecular mechanisms in Parkinson’s disease through cell type–resolved multiomics analyses

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Chromatin Architectural Changes during Cellular Senescence and Aging

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Sensory experience remodels genome architecture in neural circuit to drive motor learning

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Nuclei isolation of multiple brain cell types for omics interrogation

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Transcriptional enhancers and their communication with gene promoters

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Deciphering Hi-C: from 3D genome to function

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HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization

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dcHiC detects differential compartments across multiple Hi-C datasets

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Three-dimensional genome architecture and emerging technologies: looping in disease

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OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks

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Understanding the 3D genome: Emerging impacts on human disease

Krumm, A., & Duan, Z. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.004 · Cited by 76

Extrachromosomal circular DNA: a new potential role in cancer progression

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Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features

Yan, K., Andricovich, J., Zeng, Z., Zhu, J., Tzatsos, A., & Peng, W. (2018) · Nature Communications · doi:10.1038/s41467-018-06664-6 · Cited by 73

An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis

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3D chromatin architecture and transcription regulation in cancer

Deng, S., Feng, Y., & Pauklin, S. (2022) · Journal of Hematology & Oncology · doi:10.1186/s13045-022-01271-x · Cited by 79

Transcription factors: building hubs in the 3D space

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Pregnancy, preeclampsia and maternal aging: From epidemiology to functional genomics

Miller, E. C., Wilczek, A., Bello, N. A., Tom, S. E., Wapner, R. J., & Suh, Y. (2021) · Ageing Research Reviews · doi:10.1016/j.arr.2021.101535 · Cited by 78

Gene regulation in the 3D genome

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DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution

Zhang, S., Plummer, D., Lu, L., Cui, J., Xu, W., Wang, M., Liu, X., Prabhakar, N., Shrinet, J., Srinivasan, D., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01116-w · Cited by 63

Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

Kumar, S., Kaur, S., Seem, K., Kumar, S., & Mohapatra, T. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.774719 · Cited by 70

Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

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Determining chromatin architecture with Micro Capture-C

Hamley, J. C., Li, H., Denny, N., Downes, D. J., & Davies, J. O. J. (2023) · Nature Protocols · doi:10.1038/s41596-023-00817-8 · Cited by 62

An integrated view of the structure and function of the human 4D nucleome

Dekker, J., Oksuz, B. A., Zhang, Y., Wang, Y., Minsk, M. K., Kuang, S., Yang, L., Gibcus, J. H., Krietenstein, N., Rando, O. J., et al. (2025) · Nature · doi:10.1038/s41586-025-09890-3 · Cited by 64

Plant and animal chromatin three-dimensional organization: similar structures but different functions

Dong, P., Tu, X., Liang, Z., Kang, B., & Zhong, S. (2020) · Journal of Experimental Botany · doi:10.1093/jxb/eraa220 · Cited by 60

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

Quinodoz, S. A., Bhat, P., Chovanec, P., Jachowicz, J. W., Ollikainen, N., Detmar, E., Soehalim, E., & Guttman, M. (2022) · Nature Protocols · doi:10.1038/s41596-021-00633-y · Cited by 58

3D genome and its disorganization in diseases

Li, R., Liu, Y., Hou, Y., Gan, J., Wu, P., & Cheng, L. (2018) · Cell Biology and Toxicology · doi:10.1007/s10565-018-9430-4 · Cited by 56

Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression

Fasolino, M., Goldman, N., Wang, W., Cattau, B., Zhou, Y., Petrovic, J., Link, V. M., Coté, A., Chandra, A., Silverman, M. A., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.01.003 · Cited by 50

Integrated Analysis of Whole Genome and Epigenome Data Using Machine Learning Technology: Toward the Establishment of Precision Oncology

Asada, K., Kaneko, S., Takasawa, K., Machino, H., Takahashi, S., Shinkai, N., Shimoyama, R., Komatsu, M., & Hamamoto, R. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.666937 · Cited by 54

Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers

Liu, Y., Guo, B., Aguilera-Jimenez, E., Chu, V. S., Zhou, J. R., Wu, Z., Francis, J. M., Yang, X., Choi, P. S., Bailey, S. D., et al. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-1287 · Cited by 53

3D chromatin architecture and epigenetic regulation in cancer stem cells

Feng, Y., Liu, X., & Pauklin, S. (2021) · Protein & Cell · doi:10.1007/s13238-020-00819-2 · Cited by 55

Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy

Feng, Y., Cai, L., Hong, W., Zhang, C., Tan, N., Wang, M., Wang, C., Liu, F., Wang, X., Ma, J., et al. (2022) · Circulation · doi:10.1161/circulationaha.121.055781 · Cited by 56

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

Boninsegna, L., Yıldırım, A., Polles, G., Zhan, Y., Quinodoz, S. A., Finn, E. H., Guttman, M., Zhou, X. J., & Alber, F. (2022) · Nature Methods · doi:10.1038/s41592-022-01527-x · Cited by 48

High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding

Zhong, J., Niu, L., Lin, Z., Bai, X., Chen, Y., Luo, F., Hou, C., & Xiao, C. (2023) · Nature Communications · doi:10.1038/s41467-023-36899-x · Cited by 58

Transcriptional network orchestrating regional patterning of cortical progenitors

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PAX5 is part of a functional transcription factor network targeted in lymphoid leukemia

Okuyama, K., Strid, T., Kuruvilla, J., Somasundaram, R., Cristóbal, S., Smith, E. M. K., Javarappa, M. P. A., Fioretos, T., Lilljebjörn, H., Soneji, S., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008280 · Cited by 50

Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Xu, H., Zhang, S., Yi, X., Plewczyński, D., & Li, M. J. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.02.013 · Cited by 48

A human brain vascular atlas reveals diverse cell mediators of Alzheimer’s disease risk

Yang, A. C., Vest, R. T., Kern, F., Lee, D. P., Maat, C. A., Losada, P. M., Chen, M. B., Agam, M., Schaum, N., Khoury, N., et al. (2021) · doi:10.1101/2021.04.26.441262 · Cited by 48

Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL

Sun, L.-H., Zhou, J.-R., Xu, X., Liu, Y., Ma, N., Liu, Y.-T., Nie, W., Zou, L., Deng, X.-W., & He, H. (2024) · Nature Communications · doi:10.1038/s41467-023-44347-z · Cited by 42

GRID-seq for comprehensive analysis of global RNA–chromatin interactions

Zhou, B., Li, X., Luo, D., Lim, D., Zhou, Y., & Fu, X. (2019) · Nature Protocols · doi:10.1038/s41596-019-0172-4 · Cited by 48

ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization

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H3K27ac HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility

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Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis

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