Long-range enhancer–promoter contacts in gene expression control

An integrated encyclopedia of DNA elements in the human genome

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

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

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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Capturing Chromosome Conformation

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Spatial partitioning of the regulatory landscape of the X-inactivation centre

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Coactivator condensation at super-enhancers links phase separation and gene control

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A unique chromatin signature uncovers early developmental enhancers in humans

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Therapies Targeting Epigenetic Alterations in Acute Kidney Injury-to-Chronic Kidney Disease Transition

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Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

Bonev, B., Castelo‐Branco, G., Chen, F., Codeluppi, S., Corces, M. R., Fan, J., Heiman, M., Harris, K., Inoue, F., Kellis, M., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01806-0 · Cited by 44

SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells

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Identification and analysis of 35 genes associated with vitamin D deficiency: A systematic review to identify genetic variants

Sepúlveda-Villegas, M., Elizondo‐Montemayor, L., & Treviño, V. (2019) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2019.105516 · Cited by 35

Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools

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Selective Xi reactivation and alternative methods to restore MECP2 function in Rett syndrome

Grimm, N.-B., & Lee, J. T. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.01.007 · Cited by 34

Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation

Zhou, P., VanDusen, N. J., Zhang, Y., Cao, Y., Sethi, I., Hu, R., Zhang, S., Wang, G., Ye, L., Mazumdar, N., et al. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.03.020 · Cited by 34

Enhancer RNAs in transcriptional regulation: recent insights

Chen, Q., Zeng, Y., Kang, J., Hu, M., Li, N., Sun, K., & Zhao, Y. F. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1205540 · Cited by 41

Multi-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes

Crespo, M., Damont, A., Blanco, M., Lastrucci, E., Kennani, S. E., Ialy‐Radio, C., Khattabi, L. E., Terrier, S., Louwagie, M., Kieffer‐Jaquinod, S., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa163 · Cited by 43

Chromatin accessibility and regulatory vocabulary across indicine cattle tissues

Alexandre, P. A., Naval-Sánchez, M., Menzies, M., Nguyen, L. T., Porto-Neto, L. R., Fortes, M. R. S., & Reverter, A. (2021) · Genome biology · doi:10.1186/s13059-021-02489-7 · Cited by 34

3D chromatin reprogramming primes human memory T H 2 cells for rapid recall and pathogenic dysfunction

Schoonhoven, A. O.-V., de Bruijn, M. J. W., Stikker, B., Brouwer, R. W. W., Braunstahl, G., van IJcken, W. F. J., Graf, T., Huylebroeck, D., Hendriks, R. W., Stik, G., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.adg3917 · Cited by 35

Evolutionary genetics of skin pigmentation in African populations

Feng, Y., McQuillan, M. A., & Tishkoff, S. A. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab007 · Cited by 34

Capturing large genomic contexts for accurately predicting enhancer-promoter interactions

Chen, K., Zhao, H., & Yang, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbab577 · Cited by 33

Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk

Ying, P., Chen, C., Lu, Z., Chen, S., Zhang, M., Cai, Y., Zhang, F., Huang, J., Fan, L., Ning, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41690-z · Cited by 37

Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression

Chan, B., & Rubinstein, M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2401494121 · Cited by 34

Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan

Chai, H., Huang, X., Xiong, G., Huang, J., Pels, K. K., Meng, L., Han, J., Tang, D., Pan, G., Deng, L., et al. (2025) · Nature Methods · doi:10.1038/s41592-025-02658-7 · Cited by 35

The chicken model organism for epigenomic research

Beacon, T. H., & Davie, J. (2020) · Genome · doi:10.1139/gen-2020-0129 · Cited by 32

Myeloma-specific superenhancers affect genes of biological and clinical relevance in myeloma

Jia, Y.-L., Zhou, J.-B., Tan, T.-K., Chung, T.-H., Wong, R., Chooi, J., Lim, J. S. L., Sanda, T., Ooi, M., de Mel, S., et al. (2021) · Blood Cancer Journal · doi:10.1038/s41408-021-00421-7 · Cited by 29

GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data

Giacopuzzi, E., Popitsch, N. P., & Taylor, J. C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac130 · Cited by 31

RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure

Brown, J. M., Ornellas, S. D., Parisi, E., Schermelleh, L., & Buckle, V. J. (2022) · Nature Protocols · doi:10.1038/s41596-022-00685-8 · Cited by 30

Mechanisms of transcription control by distal enhancers from high-resolution single-gene imaging

Cheng, L., De, C., Li, J., & Pertsinidis, A. (2023) · doi:10.1101/2023.03.19.533190 · Cited by 32

Mouse B2 SINE elements function as IFN-inducible enhancers

Horton, I., Kelly, C. J., Dziulko, A., Simpson, D. M., & Chuong, E. B. (2023) · eLife · doi:10.7554/elife.82617 · Cited by 33

Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction

Liu, S., Cao, Y., Cui, K., Ren, G., Zhao, T., Wang, X., Wei, D., Chen, Z., Gurram, R. K., Liu, C., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.03.018 · Cited by 34

CTCF-mediated genome organization and leukemogenesis

Qiu, Y., & Huang, S. (2020) · Leukemia · doi:10.1038/s41375-020-0906-x · Cited by 32

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

Owens, D. D. G., Anselmi, G., Oudelaar, A. M., Downes, D. J., Cavallo, A., Harman, J. R., Schweßinger, R., Bucakci, A., Greder, L. V., Ornellas, S. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28376-8 · Cited by 33

Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans

Gilbertson, S. E., Walter, H. C., Gardner, K., Wren, S. N., Vahedi, G., & Weinmann, A. S. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110769 · Cited by 31

Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustnessPreprint

Laverré, A., Tannier, É., & Necşulea, A. (2021) · Genome Research · doi:10.1101/gr.275901.121 · Cited by 30

Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

Chen, X. X., Wang, Y., Cappuccio, A., Cheng, W.-S., Ruf-Zamojski, F. M., Nair, V. D., Miller, C. M., Rubenstein, A. B., Nudelman, G., Tadych, A., et al. (2023) · Nature Computational Science · doi:10.1038/s43588-023-00476-5 · Cited by 31

p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response

Serra, F., Nieto-Aliseda, A., Fanlo, L., Rovirosa, L., Cabrera-Pasadas, M., Lazarenkov, A., Urmeneta, B., Alcalde-Merino, A., Nola, E., Okorokov, A. L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46666-1 · Cited by 30

Evolution of Regulated Transcription

Bylino, O. V., Ibragimov, A. N., & Shidlovskii, Y. V. (2020) · Cells · doi:10.3390/cells9071675 · Cited by 31

DNA Methylation and HPV-Associated Head and Neck Cancer

Nakagawa, T., Kurokawa, T., Mima, M., Imamoto, S., Mizokami, H., Kondo, S., Okamoto, Y., Misawa, K., Hanazawa, T., & Kaneda, A. (2021) · Microorganisms · doi:10.3390/microorganisms9040801 · Cited by 32

Multiomics analysis provides insights into musk secretion in muskrat and musk deer

Wang, T., Yang, M., Shi, X., Tian, S., Li, Y., Xie, W., Zou, Z., Leng, D., Zhang, M., Zheng, C., et al. (2025) · GigaScience · doi:10.1093/gigascience/giaf006 · Cited by 29

High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection

Vangala, P., Murphy, R., Quinodoz, S. A., Gellatly, K. J., McDonel, P. E., Guttman, M., & Garber, M. G. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.09.005 · Cited by 29

Genetic insights into immune mechanisms of Alzheimer’s and Parkinson’s disease

Nott, A., & Holtman, I. R. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1168539 · Cited by 33

Diversity, duplication, and genomic organization of homeobox genes in LepidopteraPreprint

Mulhair, P. O., Crowley, L. M., Boyes, D., Harper, A., Lewis, O. T., & Holland, P. W. H. (2022) · Genome Research · doi:10.1101/gr.277118.122 · Cited by 29

Locally acting transcription factors regulate p53-dependent cis-regulatory element activity

Catizone, A. N., Uzunbas, G. K., Celadova, P., Kuang, S., Bose, D. A., & Sammons, M. A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa147 · Cited by 28

Nuclear dynamics and stress responses in Alzheimer’s disease

Iatrou, A., Clark, E. M., & Wang, Y. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00489-6 · Cited by 31

Distinct roles for CKM–Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction

Dimitrova, E., Feldmann, A., van der Weide, R. H., Flach, K. D., Lastuvkova, A., de Wit, E., & Klose, R. J. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00840-5 · Cited by 26

Quantifying transcriptome diversity: a review

Jones, E. F., Haldar, A., Oza, V. H., & Lasseigne, B. N. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad019 · Cited by 28

Spatial promoter–enhancer hubs in cancer: organization, regulation, and function

Zhao, J., & Faryabi, R. B. (2023) · Trends in Cancer · doi:10.1016/j.trecan.2023.07.017 · Cited by 28

Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription

Shaban, H. A., Barth, R., & Bystricky, K. (2020) · Genome biology · doi:10.1186/s13059-020-02185-y · Cited by 28

Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants

Duan, A., Wang, H., Zhu, Y., Wang, Q., Zhang, J., Hou, Q., Xing, Y., Shi, J., Hou, J., Qin, Z. S., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-00977-7 · Cited by 26

Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

Lange, M., Begolli, R., & Giakountis, A. (2021) · Non-Coding RNA · doi:10.3390/ncrna7030047 · Cited by 26

Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on superenhancers

Bansal, K., Michelson, D. A., Ramírez, R. N., Viny, A. D., Levine, R. L., Benoist, C. O., & Mathis, D. J. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2110991118 · Cited by 26

Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver

Chen, L., Li, J., Yuan, R., Wang, Y., Zhang, J., Lin, Y., Wang, L., Zhu, X., Zhu, W., Bai, J., et al. (2022) · Cell Discovery · doi:10.1038/s41421-022-00416-z · Cited by 31

3D genome organization links non-coding disease-associated variants to genes

Orozco, G., Schoenfelder, S., Walker, N. J., Eyre, S., & Fraser, P. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.995388 · Cited by 30

Aneuploidy effects on human gene expression across three cell types

Liu, S., Akula, N., Reardon, P. K., Russ, J. L., Torres, E. N., CLASEN, L. S., Blumenthal, J. D., Lalonde, F., McMahon, F. J., Szele, F. G., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218478120 · Cited by 26

Applications of single-cell genomics and computational strategies to study common disease and population-level variationPreprint

Auerbach, B. J., Hu, J., Reilly, M. P., & Li, M. (2021) · Genome Research · doi:10.1101/gr.275430.121 · Cited by 28

Genetic factors mediating long-range enhancer–promoter communication in mammalian development

Bower, G., & Kvon, E. Z. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102282 · Cited by 30

Regulation of T-cell Receptor Gene Expression by Three-Dimensional Locus Conformation and Enhancer Function

Rodríguez-Caparrós, A., Álvarez-Santiago, J., del Valle-Pastor, M. J., Suñé, C., López-Ros, J., & Hernández-Munaín, C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21228478 · Cited by 30

Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks

Bigness, J., Loinaz, X., Patel, S. S., Larschan, E., & Singh, R. (2022) · Journal of Computational Biology · doi:10.1089/cmb.2021.0316 · Cited by 25

Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures

Nair, S. J., Suter, T., Wang, S. S., Lu, Y., Yang, F., & Rosenfeld, M. G. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.05.015 · Cited by 27

ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs

Chai, H.-X., Tjong, H., Li, P., Liao, W., Wang, P., Wong, C.-H., Ngan, C., Leonard, W., Wei, C.-L., & Ruan, Y. (2023) · Nature Communications · doi:10.1038/s41467-023-35879-5 · Cited by 23

A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest

Kessler, S., Minoux, M., Joshi, O., Zouari, Y. B., Ducret, S., Ross, F., Vilain, N., Salvi, A., Wolff, J., Kohler, H., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38953-0 · Cited by 28

Genetic and epigenetic targets of natural dietary compounds as anti-Alzheimer’s agents

Ordoñez, W. O. C., Cajas‐Salazar, N., & Velasco-Reyes, M. A. (2023) · Neural Regeneration Research · doi:10.4103/1673-5374.382232 · Cited by 26

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function

Narducci, D. N., & Hansen, A. S. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.11.032 · Cited by 25

Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle

Nair, V. D., Vasoya, M., Nair, V., Smith, G. R., Pinças, H., Ge, Y., Douglas, C. M., Esser, K. A., & Sealfon, S. C. (2021) · Genomics · doi:10.1016/j.ygeno.2021.09.013 · Cited by 25

Predict long-range enhancer regulation based on protein–protein interactions between transcription factors

Wang, H., Huang, B., & Wang, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab841 · Cited by 26

Towards precision medicine in lymphoid malignancies

Bühler, M. M., Martín-Subero, J. I., Pan‐Hammarström, Q., Campo, E., & Rosenquist, R. (2021) · Journal of Internal Medicine · doi:10.1111/joim.13423 · Cited by 28

Emerging roles of BET proteins in transcription and co‐transcriptional RNA processing

Eischer, N., Arnold, M., & Mayer, A. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1734 · Cited by 26

Locus-specific induction of gene expression from heterochromatin loci during cellular senescence

Tomimatsu, K., Bihary, D., Olan, I., Parry, A. J., Schoenfelder, S., Chan, A. S. L., Slater, G. S. C., Ito, Y., Rugg-Gunn, P. J., Kirschner, K., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00147-y · Cited by 25

A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth

Wang, C., Liu, X., Liang, J., Narita, Y., Ding, W.-Y., Li, D., Zhang, L., Wang, H.-B., Leong, M., Hou, I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37347-6 · Cited by 20

CEBPA Phase Separation Links Transcriptional Activity and 3D Chromatin Hubs

Christou‐Kent, M., Cuartero, S., Garcia‐Cabau, C., Rühle, J., Naderi, J., Erber, J., Neguembor, M. V., Plana-Carmona, M., Alcoverro-Bertran, M., de Andrés-Aguayo, L., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2023.112897 · Cited by 27

Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans

Ramírez-Colmenero, A., Oktaba, K., & Fernández-Valverde, S. L. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.589697 · Cited by 26

Competition Between Transcription and Loop Extrusion Modulates Promoter and Enhancer DynamicsPreprint

Platania, A., Erb, C., Barbieri, M., Molcrette, B., Grandgirard, E., de Kort, M. A. C., Meaburn, K. J., Taylor, T., Shchuka, V. M., Kocanova, S., et al. (2023) · SSRN Electronic Journal · doi:10.1101/2023.04.25.538222 · Cited by 32

EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction

Ahmed, F. S., Aly, S., & Liu, X. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05784-9 · Cited by 26

Fine-mapping genomic loci refines bipolar disorder risk genes

Koromina, M., Ravi, A., Panagiotaropoulou, G., Schilder, B. M., Humphrey, J., Braun, A., Bidgeli, T., Chatzinakos, C., Coombes, B. J., Kim, J., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-01998-z · Cited by 29

Establishment and function of chromatin modification at enhancers

Tafessu, A., & Banaszynski, L. A. (2020) · Open Biology · doi:10.1098/rsob.200255 · Cited by 24

HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test

Lagler, T. M., Abnousi, A., Hu, M., Yang, Y., & Li, Y. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.01.009 · Cited by 24

Epigenetic Regulations in Mammalian Cells: Roles and Profiling Techniques

Kim, U., & Lee, D.-S. (2023) · Molecules and Cells · doi:10.14348/molcells.2023.0013 · Cited by 27

Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids

Noack, F., Vangelisti, S., Ditzer, N., Chong, F., Albert, M., & Bonev, B. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01296-5 · Cited by 27

Dynamic control of gene expression by ISGF3 and IRF1 during IFNβ and IFNγ signaling

Geetha, A. R. S. J., Fischer, K., Babadei, O., Smesnik, G., Vogt, A., Platanitis, E., Müller, M. M., Farlik, M., & Decker, T. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00092-7 · Cited by 26

Chemical and Light Inducible Epigenome Editing

Zhao, W., Wang, Y., & Liang, F. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21030998 · Cited by 23

The dynamics of chromatin architecture in brain development and function

Harabula, I., & Pombo, A. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.008 · Cited by 26

The activity of human enhancers is modulated by the splicing of their associated lncRNAs

Tan, J. Y., & Marques, A. C. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009722 · Cited by 26

OpenXGR: a web-server update for genomic summary data interpretation

Bao, C., Wang, S., Jiang, L., Fang, Z., Zou, K., Lin, J. C.-J., Chen, S., & Fang, H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad357 · Cited by 22

Large-scale analysis of the integration of enhancer-enhancer signals by promotersPreprint

Martinez-Ara, M., Comoglio, F., & van Steensel, B. (2023) · eLife · doi:10.7554/elife.91994 · Cited by 30

Genome-wide absolute quantification of chromatin looping

Jusuf, J. M., Yang, J. H., Toppen, J., Grosse-Holz, S., Gabriele, M., Mach, P., Flyamer, I. M., Zechner, C., Giorgetti, L., Mirny, L. A., et al. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-026-01819-2 · Cited by 22

Regulation of CTCF loop formation during pancreatic cell differentiation

Lyu, X., Rowley, M. J., Kulik, M. J., Dalton, S., & Corces, V. G. (2023) · Nature Communications · doi:10.1038/s41467-023-41964-6 · Cited by 21

TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk

Hou, Y., Li, Y., Xiang, J., Tilahun, K., Jiang, J., Corces, V. G., & Yao, B. (2024) · Cell Reports · doi:10.1016/j.celrep.2023.113662 · Cited by 25

Mechanism and regulation of class switch recombination by IgH transcriptional control elements

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Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters

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