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

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works

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

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works

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

Durand, N. C., Robinson, J., Shamim, M. S., Machol, I., Mesirov, J. P., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2015.07.012 · Cited by 2,335 · see citing works

An oestrogen-receptor-α-bound human chromatin interactome

Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,728 · see citing works

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

Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361 · see citing works

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

Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016) · Nature Methods · doi:10.1038/nmeth.3999 · Cited by 1,139 · see citing works

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

Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works

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

Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990 · see citing works

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

Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.024 · Cited by 982 · see citing works

Topology of mammalian developmental enhancers and their regulatory landscapes

de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521 · see citing works

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contactsPreprint

Ay, F., Bailey, T. L., & Noble, W. S. (2014) · Genome Research · doi:10.1101/gr.160374.113 · Cited by 479 · see citing works

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

Zhang, Y., Wong, C., Birnbaum, R. Y., Li, G., Favaro, R., Ngan, C. Y., Lim, J., Tai, E., Poh, H. M., Wong, E., et al. (2013) · Nature · doi:10.1038/nature12716 · Cited by 470 · see citing works

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460 · see citing works

The Role of Chromosome Domains in Shaping the Functional Genome

Sexton, T., & Cavalli, G. (2015) · Cell · doi:10.1016/j.cell.2015.02.040 · Cited by 400 · see citing works

The 3D genome in transcriptional regulation and pluripotency

Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391 · see citing works

Robust 4C-seq data analysis to screen for regulatory DNA interactions

van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes‐Quezada, C., Öz, Y., Bouwman, B. A. M., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2173 · Cited by 376 · see citing works

The second decade of 3C technologies: detailed insights into nuclear organizationPreprint

Denker, A., & de Laat, W. L. (2016) · Genes & Development · doi:10.1101/gad.281964.116 · Cited by 346 · see citing works

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

Selvaraj, S., Dixon, J. R., Bansal, V., & Ren, B. (2013) · Nature Biotechnology · doi:10.1038/nbt.2728 · Cited by 286 · see citing works

4C Technology: Protocols and Data Analysis

van de Werken, H. J. G., de Vree, P. J. P., Splinter, E., Holwerda, S. J. B., Klous, P., de Wit, E., & de Laat, W. L. (2012) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-391938-0.00004-5 · Cited by 240 · see citing works

Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum

Wang, F., Zhong, J., Zhao, Y., Xiao, J., Liu, J., Dai, M., Zheng, G., Zhang, L., Yu, J. M., Wu, J., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s1-s11 · Cited by 141 · see citing works

Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization.Preprint

Gribnau, J., Hochedlinger, K., Hata, K., Li, E., & Jaenisch, R. (2003) · Genes & Development · doi:10.1101/gad.1059603 · Cited by 128 · see citing works

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

Li, G., Cai, L., Chang, H., Hong, P., Zhou, Q., Kulakova, E. V., Kolchanov, N. A., & Ruan, Y. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s12-s11 · Cited by 125 · see citing works

3D genome organization in health and disease: emerging opportunities in cancer translational medicine

Babu, D., & Fullwood, M. J. (2015) · Nucleus · doi:10.1080/19491034.2015.1106676 · Cited by 57 · see citing works

Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association

Nott, A., Holtman, I. R., Coufal, N. G., Schlachetzki, J. C. M., Yu, M., Hu, R., Han, C. Z., Pena, M., Xiao, J., Wu, Y., et al. (2019) · Science · doi:10.1126/science.aay0793 · Cited by 823 · see citing works

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

Zheng, H., & Xie, W. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0132-4 · Cited by 711 · see citing works

Circular ecDNA promotes accessible chromatin and high oncogene expression

Wu, S., Turner, K. M., Nguyen, N., Raviram, R., Erb, M. L., Santini, J., Luebeck, J., Rajkumar, U., Diao, Y., Li, B., et al. (2019) · Nature · doi:10.1038/s41586-019-1763-5 · Cited by 651 · see citing works

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

Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562 · see citing works

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

Wang, Y., Song, F., Zhang, B., Zhang, L., Xu, J., Kuang, D., Li, D., Choudhary, M. N. K., Li, Y., Hu, M., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1519-9 · Cited by 552 · see citing works

Methods for mapping 3D chromosome architecture

Kempfer, R., & Pombo, A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0195-2 · Cited by 502 · see citing works

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

Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works

Understanding 3D genome organization by multidisciplinary methods

Jerković, I., & Cavalli, G. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00362-w · Cited by 389 · see citing works

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

Zhu, C., Yu, M., Huang, H., Juric, I., Abnousi, A., Hu, R., Lucero, J., Behrens, M. M., Hu, M., & Ren, B. (2019) · Nature Structural &amp; Molecular Biology · doi:10.1038/s41594-019-0323-x · Cited by 344 · see citing works

The Three-Dimensional Organization of Mammalian Genomes

Yu, M., & Ren, B. (2017) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100616-060531 · Cited by 366 · see citing works

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

Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J. D., Conte, M., Gorkin, D., Yu, M., et al. (2021) · Nature Structural &amp; Molecular Biology · doi:10.1038/s41594-020-00539-5 · Cited by 289 · see citing works

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

Lopes, K. D. P., Snijders, G. J. L., Humphrey, J., Allan, A., Sneeboer, M. A. M., Navarro, E., Schilder, B. M., Vialle, R. A., Parks, M., Missall, R., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00976-y · Cited by 273 · see citing works

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Bhattacharyya, S., Chandra, V., Vijayanand, P., & Ay, F. (2019) · Nature Communications · doi:10.1038/s41467-019-11950-y · Cited by 238 · see citing works

Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

Xu, Q., & Xie, W. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.10.008 · Cited by 214 · see citing works

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

Link, V. M., Duttke, S. H., Chun, H. B., Holtman, I. R., Westin, E., Hoeksema, M. A., Abe, Y., Skola, D., Romanoski, C. E., Tao, J., et al. (2018) · Cell · doi:10.1016/j.cell.2018.04.018 · Cited by 182 · see citing works

Mechanisms of Interplay between Transcription Factors and the 3D Genome

Kim, S., & Shendure, J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.010 · Cited by 204 · see citing works

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

Giuffra, E., & Tuggle, C. K. (2018) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-114913 · Cited by 201 · see citing works

UTX condensation underlies its tumor-suppressive activity

Shi, B.-W., Li, W., Song, Y.-S., Wang, Z., Ju, R., Ulman, A., Hu, J., Palomba, F., Zhao, Y.-F., Le, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03903-7 · Cited by 179 · see citing works

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

Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00863-6 · Cited by 187 · see citing works

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

Lu, L., Liu, X., Huang, W., Giusti‐Rodríguez, P., Cui, J., Zhang, S., Xu, W., Wen, Z., Ma, S., Rosen, J. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.007 · Cited by 170 · see citing works

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

Reiff, S. B., Schroeder, A. J., Kırlı, K., Cosolo, A., Bakker, C., Mercado, L., Lee, S., Veit, A. D., Balashov, A. K., Vitzthum, C. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29697-4 · Cited by 173 · see citing works

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

Salameh, T. J., Wang, X., Song, F., Zhang, B., Wright, S. M., Khunsriraksakul, C., Ruan, Y., & Yue, F. (2020) · Nature Communications · doi:10.1038/s41467-020-17239-9 · Cited by 165 · see citing works

The spatial organization of transcriptional control

Hafner, A., & Boettiger, A. N. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00526-0 · Cited by 150 · see citing works

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 143 · see citing works

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 · see citing works

Gene Regulatory Elements, Major Drivers of Human Disease

Chatterjee, S., & Ahituv, N. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091416-035537 · Cited by 136 · see citing works

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

Jiang, Y., Huang, J. S., Lun, K., Li, B., Zheng, H., Li, Y., Zhou, R., Duan, W., Wang, C., Feng, Y., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02067-3 · Cited by 136 · see citing works

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 123 · see citing works

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

Wolf, B. K., Zhao, Y., McCray, A. D., Hawk, W. H., Deary, L. T., Sugiarto, N. W., LaCroix, I. S., Gerber, S. A., Cheng, C., & Wang, X. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00880-x · Cited by 124 · see citing works

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

Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006982 · Cited by 121 · see citing works

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 112 · see citing works

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 · see citing works

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 102 · see citing works

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 95 · see citing works

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

Kubo, N., Chen, P. B., Hu, R., Ye, Z., Sasaki, H., & Ren, B. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.030 · Cited by 99 · see citing works

Trac-looping measures genome structure and chromatin accessibility

Lai, B., Tang, Q., Jin, W., Hu, G., Wangsa, D., Cui, K., Stanton, B. Z., Ren, G., Ding, Y., Zhao, M., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0107-y · Cited by 85 · see citing works

Spatial and temporal organization of the genome: current state and future aims of the 4D Nucleome Project

Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B. J., Bruneau, B. G., Belmont, A., Bintu, L., Boettiger, A., Calandrelli, R., Disteche, C., et al. (2023) · Molecules and Cells · doi:10.1016/j.molcel.2023.06.018 · Cited by 85 · see citing works

Integrating ChIP-seq with other functional genomics data

Jiang, S., & Mortazavi, A. (2018) · Briefings in Functional Genomics · doi:10.1093/bfgp/ely002 · Cited by 88 · see citing works

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

Fixsen, B. R., Han, C. Z., Zhou, Y., Spann, N. J., Saisan, P., Shen, Z., Balak, C., Sakai, M., Cobo, I., Holtman, I. R., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01528-8 · Cited by 87 · see citing works

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

Lee, A., Kim, C., Park, S.-W., Joo, J., Choi, B., Yang, D., Jun, K., Eom, J., Lee, S., Chung, S. J., et al. (2023) · Science Advances · doi:10.1126/sciadv.abo2467 · Cited by 88 · see citing works

Chromatin Architectural Changes during Cellular Senescence and Aging

Sun, L., Yu, R., & Dang, W. (2018) · Genes · doi:10.3390/genes9040211 · Cited by 83 · see citing works

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

Yamada, T., Yang, Y., Valnegri, P., Juric, I., Abnousi, A., Markwalter, K. H., Guthrie, A. N., Godec, A., Oldenborg, A., Hu, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1190-7 · Cited by 83 · see citing works

Nuclei isolation of multiple brain cell types for omics interrogation

Nott, A., Schlachetzki, J. C. M., Fixsen, B. R., & Glass, C. K. (2021) · Nature Protocols · doi:10.1038/s41596-020-00472-3 · Cited by 79 · see citing works

Transcriptional enhancers and their communication with gene promoters

Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works

Deciphering Hi-C: from 3D genome to function

Kong, S.-Y., & Zhang, Y. (2019) · Cell Biology and Toxicology · doi:10.1007/s10565-018-09456-2 · Cited by 72 · see citing works

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

Wei, X., Yu, X., Peters, D., Marius, C., Sun, T., Shan, R., Ou, J., Lin, X., Yue, F., Li, W., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.01.023 · Cited by 83 · see citing works

dcHiC detects differential compartments across multiple Hi-C datasets

Chakraborty, A., Wang, J., & Ay, F. (2022) · Nature Communications · doi:10.1038/s41467-022-34626-6 · Cited by 75 · see citing works

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

Mishra, A., & Hawkins, R. D. (2017) · Genome Medicine · doi:10.1186/s13073-017-0477-2 · Cited by 77 · see citing works

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

Li, T., Jia, L., Cao, Y., Chen, Q., & Li, C. (2018) · Genome biology · doi:10.1186/s13059-018-1430-4 · Cited by 77 · see citing works

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 75 · see citing works

Extrachromosomal circular DNA: a new potential role in cancer progression

Wang, T., Zhang, H., Zhou, Y.-L., & Shi, J.-H. (2021) · Journal of Translational Medicine · doi:10.1186/s12967-021-02927-x · Cited by 61 · see citing works

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 · see citing works

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

Li, J., Huang, K., Hu, G., Babarinde, I. A., Li, Y., Dong, X., Chen, Y., Shang, L., Guo, W., Wang, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08949-w · Cited by 70 · see citing works

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 75 · see citing works

Transcription factors: building hubs in the 3D space

Giammartino, D. C. D., Polyzos, A., & Apostolou, E. (2020) · Cell Cycle · doi:10.1080/15384101.2020.1805238 · Cited by 66 · see citing works

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 74 · see citing works

Gene regulation in the 3D genome

Li, Y., Hu, M., & Shen, Y. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy164 · Cited by 66 · see citing works

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 · see citing works

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 66 · see citing works

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

Downes, D. J., Smith, A., Karpińska, M. A., Velychko, T., Rue-Albrecht, K., Sims, D., Milne, T. A., Davies, J. O. J., Oudelaar, A. M., & Hughes, J. R. (2022) · Nature Protocols · doi:10.1038/s41596-021-00651-w · Cited by 59 · see citing works

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 59 · see citing works

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 62 · see citing works

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 59 · see citing works

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 55 · see citing works

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 · see citing works

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 51 · see citing works

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 · see citing works

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 51 · see citing works

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 52 · see citing works

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 53 · see citing works

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 49 · see citing works

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 57 · see citing works

Transcriptional network orchestrating regional patterning of cortical progenitors

Ypsilanti, A. R., Pattabiraman, K., Catta-Preta, R., Golonzhka, O., Lindtner, S., Tang, K., Jones, I. R., Abnousi, A., Jurić, I., Hu, M., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024795118 · Cited by 46 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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

Sun, L., Zhou, J., Xu, X. H., Liu, Y., Ma, N., Liu, Y., Nie, W., Zou, L., Deng, X. W., & He, H. (2024) · Nature Communications · doi:10.1038/s41467-023-44347-z · Cited by 50 · see citing works

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 · see citing works

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

Lee, B., Wang, J., Cai, L., Kim, M., Namburi, S., Tjong, H., Feng, Y., Wang, P., Tang, Z., Abbas, A., et al. (2020) · Science Advances · doi:10.1126/sciadv.aay2078 · Cited by 48 · see citing works

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

Giambartolomei, C., Seo, J.-H., Schwarz, T., Freund, M. K., Johnson, R., Spisák, S., Baca, S. C., Gusev, A., Mancuso, N., Paşaniuc, B., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.11.007 · Cited by 48 · see citing works

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

Qi, Q., Li, C., Tang, X., He, Y., Li, Y., Yee, T., Shrestha, D., Feng, R., Xu, P., Zhou, X., et al. (2020) · Blood · doi:10.1182/blood.2020005780 · Cited by 44 · see citing works

Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules

Xie, S., Armendariz, D. A., Zhou, P., Duan, J., & Hon, G. C. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.073 · Cited by 46 · see citing works

Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

You, Q., Cheng, A. Y., Gu, X., Harada, B. T., Yu, M., Wu, T., Ren, B., Ouyang, Z., & He, C. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0643-8 · Cited by 46 · see citing works

The 3D Genome: From Structure to Function

Mohanta, T. K., Mishra, A. K., & Al‐Harrasi, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222111585 · Cited by 45 · see citing works

EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma

Möller, E., Praz, V., Rajendran, S., Dong, R., Cauderay, A., Xing, Y., Lee, L., Fusco, C., Broye, L. C., Cironi, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29910-4 · Cited by 45 · see citing works

The role of 3D genome organization in disease: From compartments to single nucleotides

Chakraborty, A., & Ay, F. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.005 · Cited by 39 · see citing works

Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms

Schilder, B. M., Navarro, E., & Raj, T. (2021) · Neurobiology of Disease · doi:10.1016/j.nbd.2021.105580 · Cited by 42 · see citing works

Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity

Sanalkumar, R., Dong, R., Lee, L., Xing, Y., Iyer, S., Letovanec, I., Rosa, S. L., Finzi, G., Musolino, E., Papait, R., et al. (2023) · Science Advances · doi:10.1126/sciadv.abo3789 · Cited by 45 · see citing works

3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

Kim, K., Jang, I., Kim, M., Choi, J., Kim, M.-S., Lee, B.-W., & Jung, I. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1078 · Cited by 39 · see citing works

Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions

Hu, G., Dong, X., Gong, S., Song, Y., Hutchins, A. P., & Yao, H. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa705 · Cited by 40 · see citing works

cLoops2: a full-stack comprehensive analytical tool for chromatin interactions

Cao, Y., Liu, S., Ren, G., Tang, Q., & Zhao, K. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1233 · Cited by 41 · see citing works

Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity

Liu, Z., Lee, D.-S., Liang, Y., Zheng, Y., & Dixon, J. R. (2023) · Nature Communications · doi:10.1038/s41467-023-42647-y · Cited by 40 · see citing works

Understanding astrocyte differentiation: Clinical relevance, technical challenges, and new opportunities in the omics era

Lattke, M., & Guillemot, F. (2022) · WIREs Mechanisms of Disease · doi:10.1002/wsbm.1557 · Cited by 41 · see citing works

3D organization of regulatory elements for transcriptional regulation in Arabidopsis

Deng, L., Zhou, Q., Zhou, J. R., Zhang, Q., Jia, Z., Zhu, G., Sheng, C., Cheng, L., Yin, C., Yang, C., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03018-4 · Cited by 36 · see citing works

Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation

Chen, P.-S. B., Fiaux, P. C., Zhang, K., Li, B., Kubo, N., Jiang, S., Hu, R., Rooholfada, E., Wu, S.-H., Wang, M.-C., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111630 · Cited by 31 · see citing works

DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell

Li, X., Zeng, G., Li, A., & Zhang, Z. (2021) · Genome biology · doi:10.1186/s13059-021-02435-7 · Cited by 37 · see citing works

Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation

Chandra, A., Yoon, S., Michieletto, M. F., Goldman, N., Ferrari, E. K., Abedi, M., Johnson, I., Fasolino, M., Pham, K., Joannas, L. D., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.05.004 · Cited by 36 · see citing works

Revisiting 3D chromatin architecture in cancer development and progression

Feng, Y., & Pauklin, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa747 · Cited by 36 · see citing works

Unravelling the molecular basis for regulatory T‐cell plasticity and loss of function in disease

Sadlon, T. J., Brown, C. Y., Bandara, V., Hope, C. M., Schjenken, J. E., Pederson, S., Breen, J., Forrest, A. R. R., Beyer, M., Robertson, S. A., et al. (2018) · Clinical & Translational Immunology · doi:10.1002/cti2.1011 · Cited by 37 · see citing works

Computational methods for analyzing and modeling genome structure and organization

Lin, D., Bonora, G., Yardımcı, G. G., & Noble, W. S. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1435 · Cited by 35 · see citing works

Hi-Tag: a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

Qi, X., Zhang, L., Zhao, Q., Zhou, P., Zhang, S., Li, J., Zheng, Z., Xiang, Y., Dai, X., Jin, Z., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-023-2441-0 · Cited by 3 · see citing works

ChromE-seq: Chromatin and Expression Co-assay with Sequencing v1Preprint

Liao, Z., & Ma, S. (2025) · doi:10.17504/protocols.io.e6nvwbq4wvmk/v1

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

Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006982 · Cited by 121 · see citing works

Deciphering the effects of proximity ligation in chromatin contact maps to understand single molecule interactions data

Kim, M., Zheng, M., Tian, S. Z., Lee, B., Capurso, D., Chuang, J. H., & Ruan, Y. (2018) · Research in Computational Molecular Biology

ChIP‐based methods for the identification of long‐range chromatin interactions

Fullwood, M. J., & Ruan, Y. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22116 · Cited by 242 · see citing works