Long-range enhancer–promoter contacts in gene expression control

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072

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

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652

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

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895

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

Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., Abraham, B. J., Hannett, N. M., Zamudio, A. V., Manteiga, J. C., et al. (2018) · Science · doi:10.1126/science.aar3958 · Cited by 2,595

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233

RNA, Genome Output and Input

Morf, J., Basu, S., & Amaral, P. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.589413 · Cited by 10

Epigenetic aspects of DC development and differentiation

Chauvistré, H., & Seré, K. (2020) · Molecular Immunology · doi:10.1016/j.molimm.2020.10.011 · Cited by 10

Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropyPreprint

Radke, D. W., Sul, J. H., Balick, D. J., Akle, S., Initiative, A. D. N., Green, R. C., & Sunyaev, S. R. (2021) · Genome Research · doi:10.1101/gr.275263.121 · Cited by 9

Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers

Heer, M., Giudice, L., Mengoni, C., Giugno, R., & Rico, D. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad229 · Cited by 8

Myeloid leukemia vulnerabilities embedded in long noncoding RNA locus MYNRL15

Ng, M. S. W., Verboon, L., Issa, H., Bhayadia, R., Vermunt, M. W., Winkler, R., Schüler, L., Alejo-Valle, O., Schuschel, K., Regényi, E., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107844 · Cited by 9

Towards functional maps of non-coding variants in cancer

Wang, Y., & Hon, G. C. (2024) · Frontiers in Genome Editing · doi:10.3389/fgeed.2024.1481443 · Cited by 8

Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation

Cadefau-Fabregat, M., Martínez-Cebrián, G., Lorenzi, L., Weiss, F. D., Frank, A.-K., Castelló-García, J. M., Julià-Vilella, E., Gámez-García, A., Yera, L., de Castro, C. P. M., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58712-7 · Cited by 8

Microfluidic Fluorescence-Activated Cell Sorting of Convolutional Neural Network-Designed Synthetic Yeast Promoter.

Cheng, Z., Wu, W., Zhou, X., Xu, T., Zhang, G.-B., & Chen, H.-W. (2025) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00025 · Cited by 8

DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape

Gehrs, S., Gu, Z., Hey, J., Weichenhan, D., Buckwalter, N., Jakab, M., Hotz‐Wagenblatt, A., Breuer, K., Prada, M. L., Hübschmann, D., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf435 · Cited by 8

DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers

Doyle, C., Herka, K., Flynn, S. M., Melidis, L., Dhir, S., Schoenfelder, S., Tannahill, D., & Balasubramanian, S. (2025) · Genome biology · doi:10.1186/s13059-025-03627-1 · Cited by 10

EAP-LSTM: A Bi-LSTM-Based Deep Learning Framework for Quantitatively Predicting Enhancer Activity in Drosophila and Human Cell Lines

Zhang, Y., Dai, L., Dou, Y., Li, X., Lu, C. F., & Wu, H. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3620986 · Cited by 8

Transcriptional condensates encode a “golden mean” to optimize enhancer–promoter communication across genomic distances

Zhu, T., Li, C., & Chu, X. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2513371122 · Cited by 10

CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci

Liu, M., Huang, K., Zhang, J., Li, Q., Wang, X., Gu, B.-M., Tang, H., Du, Z., Hu, L., Qi, S., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02887-3 · Cited by 13

Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation

Zhou, Y., Jay, A., Burget, N. G., Friedrich, T., Yoon, S., Alsing, J., Nir, G., Grosschedl, R., Vahedi, G., & Faryabi, R. B. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01827-2 · Cited by 8

Enhancer–promoter entanglement explains their transcriptional interdependence

Panigrahi, A. K., Lonard, D. M., & O’Malley, B. W. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2216436120 · Cited by 10

3D genome organization and its study in livestock breeding

Cheng, J., Cao, X., Wang, S., Zhang, J., Yue, B., Zhang, X., Huang, Y., Lan, X., Ren, G., & Chen, H. (2023) · Journal of Integrative Agriculture · doi:10.1016/j.jia.2023.04.007 · Cited by 9

Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube

Afzal, Z., Lange, J. J., Nolte, C., McKinney, S., Wood, C., Paulson, A., Kumar, B. D., Unruh, J. R., Slaughter, B. D., & Krumlauf, R. K. (2023) · Development · doi:10.1242/dev.201259 · Cited by 8

LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data

Liu, J., Li, P., Sun, J., & Guo, J. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad165 · Cited by 8

Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays

Brovkina, M. V., Chapman, M. A., Holding, M. L., & Clowney, E. J. (2023) · BMC Biology · doi:10.1186/s12915-023-01673-4 · Cited by 9

Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns

Wu, C., & Huang, J. (2024) · BMC Genomics · doi:10.1186/s12864-024-10408-w · Cited by 8

Single-Cell Multiomics Analysis of Early Wound Response Programs in the Mouse Corneal Epithelium

Lu, Z., Ye, J.-G., Li, J.-N., Liang, J.-B., Zhou, M., Hu, Q., Zhang, Q., Lin, Y., & Zheng, Y. (2025) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.66.3.9 · Cited by 8

Gene dysregulation analysis builds a mechanistic signature for prognosis and therapeutic benefit in colorectal cancer

Li, Q., Dai, W., Liu, J., Sang, Q., Li, Y., & Li, Y. (2020) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjaa041 · Cited by 8

Integrative analysis identifies potential causal methylation-mRNA regulation chains for rheumatoid arthritis

Mo, X., Zhang, Y.-H., & Lei, S. (2020) · Molecular Immunology · doi:10.1016/j.molimm.2020.12.021 · Cited by 8

Genetic modifiers regulating DNA replication and double-strand break repair are associated with differences in mammary tumors in mouse models of Li-Fraumeni syndrome

Majhi, P. D., Griner, N. B., Mayfield, J. A., Compton, S. L., Kane, J. J., Baptiste, T. A., Dunphy, K. A., Roberts, A. L., Schneider, S. S., Savage, E. M., et al. (2021) · Oncogene · doi:10.1038/s41388-021-01892-5 · Cited by 8

AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators

Meiler, A., Marchianò, F., Haering, M., Weitkunat, M., Schnorrer, F., & Habermann, B. H. (2021) · Scientific Reports · doi:10.1038/s41598-021-94805-1 · Cited by 8

Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

Holm, I., Nardini, L., Pain, A., Bischoff, E., Anderson, C. E., Zongo, S., Guelbeogo, M. W., Sagnon, N., Gohl, D. M., Nowling, R. J., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.785934 · Cited by 8

G-Quadruplex Matters in Tissue-Specific Tumorigenesis by BRCA1 Deficiency

Kim, S., & Hwang, S. (2022) · Genes · doi:10.3390/genes13030391 · Cited by 8

Ectopic Expression of the Rice Grain-Size-Affecting Gene GS5 in Maize Affects Kernel Size by Regulating Endosperm Starch Synthesis

Dong, G., Xiong, H., Zeng, W., et al. (2022) · Genes · doi:10.3390/genes13091542 · Cited by 8

Consequential Innovations in Nature-Inspired Intelligent Computing Techniques for Biomarkers and Potential Therapeutics Identification

Sheikh, K., Sayeed, S., Asif, A., Siddiqui, M. F., Rafeeq, M. M., Sahu, A., & Ahmad, S. (2022) · Studies in computational intelligence · doi:10.1007/978-981-19-6379-7_13 · Cited by 8

Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity

Schofield, J. A., & Hahn, S. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112387 · Cited by 9

Association analysis and functional follow-up identified common variants of JAG1 accounting for risk to biliary atresia

Bai, M.-R., Pei, H.-Y., Zhou, Y., Song, H.-L., Pan, W., Gong, Y., Wu, W., Yu, W., Cui, M., Gu, B.-L., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1186882 · Cited by 8

Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in ‘lactating’ pigeon

Wang, Y., Wang, X., Luo, Y., Zhang, J., Lin, Y., Wu, J. J., Zeng, B., Liu, L., Yan, P., Liang, J.-Y., et al. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010746 · Cited by 8

Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture

Zhu, Y., Rosenfeld, M. G., & Suh, Y. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2313285120 · Cited by 8

A regulatory element associated to NAFLD in the promoter of DIO1 controls LDL-C, HDL-C and triglycerides in hepatic cells

Castillejo-López, C., Barcenas-Walls, J. R., Cavalli, M., Larsson, A. O., & Wadelius, C. (2024) · Lipids in Health and Disease · doi:10.1186/s12944-024-02029-9 · Cited by 9

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Golov, A. K., Gavrilov, A. A., Kaplan, N., & Razin, S. V. (2024) · eLife · doi:10.7554/elife.91596.3 · Cited by 10

B‐cell lymphoma 2 family genes show a molecular pattern of spatiotemporal heterogeneity in gynaecologic and breast cancer

Wang, J., Li, S., Lin, S., Fu, S., Qiu, L., Ding, K., Liang, K., & Du, H. (2020) · Cell Proliferation · doi:10.1111/cpr.12826 · Cited by 7

CTCF Point Mutation at R567 Disrupts Mouse Heart Development via 3D Genome Rearrangement and Transcription Dysregulation

Ren, H., Zhong, H., Zhang, J., Lu, Y., Hu, G., Duan, W., Ma, N., & Yao, H. (2024) · Cell Proliferation · doi:10.1111/cpr.13783 · Cited by 7

PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines

Chyr, J., Zhang, Z., Chen, X. X., & Zhou, X. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.05.013 · Cited by 7

The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis

Li, Y., Gao, J., Zhao, D., et al. (2022) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2023.01.031 · Cited by 7

Enhancer/gene relationships: Need for more reliable genome-wide reference sets

Hoellinger, T., Mestre, C., Aschard, H., Goff, W. L., Foissac, S., Faraut, T., & Djebali, S. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2023.1092853 · Cited by 8

KLF5 regulates actin remodeling to enhance the metastasis of nasopharyngeal carcinoma

Yang, Z., Peng, Y., Wang, Y., Yang, P., Huang, Z.-H., Quan, T.-Q., Xu, X., Sun, P., Sun, Y. H., Lv, J., et al. (2024) · Oncogene · doi:10.1038/s41388-024-03033-0 · Cited by 9

Regulation of 3 D genome organization during T cell activation

Wang, B., & Bian, Q. (2024) · FEBS Journal · doi:10.1111/febs.17211 · Cited by 7

Enhancer‐mediated reporter gene expression in Arabidopsis thaliana: a forward genetic screen

Lin, Y. Y., Zhao, H., Kotlarz, M., et al. (2021) · The Plant Journal · doi:10.1111/tpj.15189 · Cited by 7

An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping

de Llobet, L., Vona, C. D., Morselli, M., Vezzoli, M., Montanini, B., Teichmann, M., de la Luna, S., & Ferrari, R. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042260 · Cited by 7

Analysis of the landscape of human enhancer sequences in biological databases

Mulero-Hernández, J., & Fernández‐Breis, J. T. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.045 · Cited by 9

Convergence of the dysregulated regulome in schizophrenia with polygenic risk and evolutionarily constrained enhancers

Dong, P., Voloudakis, G., Fullard, J. F., Hoffman, G. E., & Roussos, P. (2023) · Molecular Psychiatry · doi:10.1038/s41380-023-02370-y · Cited by 7

SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks

Pan, J.-H., & Du, P.-F. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad494 · Cited by 7

Local Epigenomic Data are more Informative than Local Genome Sequence Data in Predicting Enhancer-Promoter Interactions Using Neural Networks

Xiao, M., Zhuang, Z., & Pan, W. (2019) · Genes · doi:10.3390/genes11010041 · Cited by 7

The loopometer: a quantitative in vivo assay for DNA-looping proteins

Hao, N., Sullivan, A. E., Shearwin, K. E., & Dodd, I. B. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1284 · Cited by 6

Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infectionPreprint

Zhao, S., Li, Y., Chen, G., Wang, X., Chen, N., & Wu, X. (2023) · Genome Research · doi:10.1101/gr.277931.123 · Cited by 7

Transcription factor condensates, 3D clustering, and gene expression enhancement of the MET regulon

Lee, J., Simpson, L., Li, Y., Becker, S., Zou, F., Zhang, X., & Bai, L. (2024) · eLife · doi:10.7554/elife.96028 · Cited by 6

Runx3, Brn3a and Isl1 interplay orchestrates the transcriptional program in the early stages of proprioceptive neuron development

Orlovsky, K., Appel, E., Hantisteanu, S., Olender, T., Lotem, J., Levanon, D., & Groner, Y. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011401 · Cited by 6

BmNPV interacts with super-enhancer regions of the host chromatin to hijack cellular transcription machinery

Zhao, S., Wang, X., Yang, T., Zhu, X., & Wu, X. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf188 · Cited by 6

Nearly telomere-to-telomere genome assembly of the L. edodes diploid genome

Yoshitake, K., Shirasawa, K., Kojima, K. K., Asakawa, S., Tanaka, N., & Kurokochi, H. (2025) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2025.104005 · Cited by 8

Improving polygenic prediction from whole-genome sequencing data by leveraging predicted epigenomic features

Zeng, W., Guo, H., Liu, Q., & Wong, W. H. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2419202122 · Cited by 8

JMJD2 regulates enhancer–promoter interactions via biomolecular condensate formation

Jiang, S., Liu, X., Zhang, Z., Yang, M., Zhu, X. Q., Ma, L., Zhao, L., Ling, X., Zhou, Z., Wu, Z., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02415-8 · Cited by 8

High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

Chovanec, P., Ridgley, T., & Yin, Y. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag119 · Cited by 10

Alu repeat-containing RNAs spatially organize actively transcribed genomic regions around nuclear speckles

Liu, S., Zhongyang, C., Shen, X., Gao, J., Guo, J., Rong, Y., Li, T., Zhou, F., Si, Y., Zhao, H., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.031 · Cited by 7

The Mafb cleft‐associated variant H131Q is not required for palatogenesis in the mouse

Paul, B. J., Palmer, K. J., Rhea, L., et al. (2021) · Developmental Dynamics · doi:10.1002/dvdy.327 · Cited by 6

Divergence of Tbx4 hindlimb enhancer HLEA underlies the hindlimb loss during cetacean evolution

Liang, N., Deme, L., Kong, Q., Sun, L., Cao, Y., Wu, T., Huang, X., Xu, S., & Yang, G. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110292 · Cited by 8

Selection on the promoter regions plays an important role in complex traits during duck domestication

Yin, Z., Li, X., Sun, Y.-X., Smith, J., Hincke, M. T., Yang, N., & Hou, Z. (2023) · BMC Biology · doi:10.1186/s12915-023-01801-0 · Cited by 6

The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis

Yang, K., Zhu, T., Yin, J., Zhang, Q., Li, J. Y., Fan, H., Han, G., Xu, W., Liu, N., & Lv, X. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.02.003 · Cited by 6

A Unified-Field Theory of Genome Organization and Gene Regulation

Negro, G., Semeraro, M., Cook, P. R., & Marenduzzo, D. (2022) · iScience · doi:10.1016/j.isci.2024.111218 · Cited by 8

Structural framework to address variant-gene relationship in primary open-angle glaucoma

Singh, N., Kizhatil, K., Duraikkannu, D., Choquet, H., & Nair, K. S. (2024) · Vision Research · doi:10.1016/j.visres.2024.108505 · Cited by 7

GATv2EPI: Predicting Enhancer–Promoter Interactions with a Dynamic Graph Attention Network

Zhang, T., Zhao, X., Sun, H., Gao, B., & Liu, X. (2024) · Genes · doi:10.3390/genes15121511 · Cited by 6

Developmental Insights into Lung Cancer

Desai, T. (2021) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-070820-032858 · Cited by 6

Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data

Turunen, T., de Sande, A. H., Pölönen, P., & Heinäniemi, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.03.035 · Cited by 6

Promoter DNA Methylation in GWAS-Identified Genes as Potential Functional Elements for Blood Pressure: An Observational and Mendelian Randomization Study

Zhang, H., Wang, A., Xu, T., Mo, X., & Zhang, Y. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.791146 · Cited by 7

Be-1DCNN: a neural network model for chromatin loop prediction based on bagging ensemble learning

Wu, H., Zhou, B., Zhou, H., Zhang, P., & Wang, M. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad015 · Cited by 7

A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1

Xiang, J., Fan, C., Dong, H., Ma, Y., & Xu, P. (2023) · eLife · doi:10.7554/elife.85412 · Cited by 5

Identification of ancestral gnathostome Gli3 enhancers with activity in mammals

Ali, S., Abrar, M. M., Hussain, I., Batool, F., Raza, R. Z., Khatoon, H., Zoia, M., Visel, A., Shubin, N. H., Osterwalder, M., et al. (2023) · Development Growth & Differentiation · doi:10.1111/dgd.12901 · Cited by 6

Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions

Wang, M., He, B., Hao, Y., Srinivasan, D., Shrinet, J., & Fraser, P. (2023) · BMC Biology · doi:10.1186/s12915-023-01766-0 · Cited by 5

Transcription factor condensates, 3D clustering, and gene expression enhancement of the MET regulon

Lee, J., Simpson, L., Li, Y., Becker, S., Zou, F., Zhang, X., & Bai, L. (2024) · eLife · doi:10.7554/elife.96028.3 · Cited by 6

Decrypting DC development

Guilliams, M., & Tamura, T. (2019) · Nature Immunology · doi:10.1038/s41590-019-0457-3 · Cited by 6

Mutations in gene regulatory elements linked to human limb malformations

Nowosad, K., Hordyjewska‐Kowalczyk, E., & Tylżanowski, P. (2019) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2019-106369 · Cited by 6

Liver gene regulatory networks: Contributing factors to nonalcoholic fatty liver disease

Cebola, I. (2020) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1480 · Cited by 5

Molecular cloning of the goose GnRH gene and identification of GnRH polymorphisms associated with laying traits

Gao, G., Zhang, K., Zhao, X., et al. (2020) · British Poultry Science · doi:10.1080/00071668.2020.1758298 · Cited by 6

Enhancing Gonadotrope Gene Expression Through Regulatory lncRNAs

Refael, T., & Melamed, P. (2021) · Endocrinology · doi:10.1210/endocr/bqab116 · Cited by 6

Prioritisation of Candidate Genes Underpinning COVID-19 Host Genetic Traits Based on High-Resolution 3D Chromosomal Topology

Thiecke, M. J., Yang, E. J., Burren, O. S., Ray-Jones, H. F., & Spivakov, M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.745672 · Cited by 7

CpG Site-Specific Methylation-Modulated Divergent Expression of PRSS3 Transcript Variants Facilitates Nongenetic Intratumor Heterogeneity in Human Hepatocellular Carcinoma

Lin, S., Xu, H., Pang, M., Zhou, X., Pan, Y., Zhang, L., Guan, X., Wang, X., Lin, B., Tian, R., et al. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.831268 · Cited by 6

Non‐coding genetic variation in regulatory elements determines thrombosis and hemostasis phenotypes

Stefanucci, L., & Frontini, M. (2022) · Journal of Thrombosis and Haemostasis · doi:10.1111/jth.15754 · Cited by 5

Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution?

Noon, E. P., & Frankel, N. (2022) · Essays in Biochemistry · doi:10.1042/ebc20220057 · Cited by 6

Enhancers as regulators of antigen receptor loci three-dimensional chromatin structure

Barajas-Mora, E. M., & Feeney, A. J. (2019) · Transcription · doi:10.1080/21541264.2019.1699383 · Cited by 7

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strandsPreprint

Roberts, B. S., Partridge, E. C., Moyers, B. A., Agarwal, V., Newberry, K. M., Martin, B., Shendure, J., Myers, R., & Cooper, G. M. (2021) · Genome Research · doi:10.1101/gr.270751.120 · Cited by 6

Glucocorticoid receptor collaborates with pioneer factors and AP-1 to execute genome-wide regulationPreprint

Wissink, E. M., Martinez, D. M., Ehmsen, K. T., Yamamoto, K. R., & Lis, J. T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.01.444518 · Cited by 6

Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specificationPreprint

Parry, A., Krueger, C., Lohoff, T., Wingett, S., Schoenfelder, S., & Reik, W. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.11.523441 · Cited by 7

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer OrganizationPreprint

Cerda-Smith, C. G., Hutchinson, H. M., Liu, A., Goel, V. Y., Sept, C., Kim, H., Casaní-Galdón, S., Burkman, K. G., Bassil, C. F., Hansen, A. S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.20.558459 · Cited by 6

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping modelPreprint

Golov, A. K., Gavrilov, A. A., Kaplan, N., & Razin, S. V. (2023) · eLife · doi:10.7554/elife.91596 · Cited by 5

Fine-mapping genomic loci refines bipolar disorder risk genesPreprint

Koromina, M., Ravi, A., Panagiotaropoulou, G., Schilder, B. M., Humphrey, J., Braun, A., Bidgeli, T., Chatzinakos, C., Coombes, B. J., Kim, J., et al. (2024) · medRxiv · doi:10.1101/2024.02.12.24302716 · Cited by 6

Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression

Lee, J., Simpson, L., Li, Y., Becker, S., Zou, F., Zhang, X., & Bai, L. (2024) · doi:10.1101/2024.02.06.579062 · Cited by 6

Transitions in chromatin conformation shaped by fatty acids and the circadian clock underlie hepatic transcriptional reorganization in obese mice

Pacheco-Bernal, I., Becerril-Pérez, F., Bustamante-Zepeda, M., González-Suárez, M., Olmedo-Suárez, M. Á., Hernández-Barrientos, L. R., del Carmen, A. A., Escalante‐Covarrubias, Q., Mendoza-Viveros, L., Lemus, E. H., et al. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05364-3 · Cited by 6

EBNA leader protein orchestrates chromatin architecture remodeling during Epstein-Barr virus-induced B cell transformation

Maestri, D., Caruso, L. B., Cable, J. M., Sklutuis, R., Preston‐Alp, S., White, R. E., Luftig, M. A., & Tempera, I. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf629 · Cited by 5

Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription

Chiang, M., Battaglia, C., Forte, G., Brackley, C. A., Gilbert, N., & Marenduzzo, D. (2025) · Physical Review Letters · doi:10.1103/bjq4-xnsy · Cited by 9

Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion

Lee, U., Laguillo-Diego, A., Magliulo, D., Wong, W., Kasliwal, K., Ni, Z., Cheng, L., Li, J., Pelham‐Webb, B., Pertsinidis, A., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02556-4 · Cited by 10

Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis

Liu, P., Li, D., Zhang, J., He, M., Gao, D., Wang, Y., Lin, Y., Pan, D., Li, P., Wang, T., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.104757 · Cited by 5

Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

Lyu, R., Gao, Y., Wu, T., Ye, C., Wang, P., & He, C. (2024) · Nature Communications · doi:10.1038/s41467-024-50680-8 · Cited by 7

Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation

DeGroat, W., Inoue, F., Ashuach, T., Yosef, N., Ahituv, N., & Kreimer, A. (2024) · Genome biology · doi:10.1186/s13059-024-03365-w · Cited by 4

Fluctuating Chromatin Facilitates Enhancer–Promoter Communication by Regulating Transcriptional Clustering Dynamics

Zhu, T., Li, C., & Chu, X. (2024) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.4c02453 · Cited by 5

Organization and Dynamics of Chromosomes

Thirumalai, D., Shi, G., Shin, S., & Hyeon, C. (2025) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-082423-024123 · Cited by 5

Systematic decoding of functional enhancer connectomes and risk variants in human glioma

Bi, J., Mo, W., Liu, M., Song, Y., Xiao, Q., Fan, S., Wang, W., Shi, T., Zheng, Y., Lian, J., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01737-3 · Cited by 5

A model of active transcription hubs that unifies the roles of active promoters and enhancers

Zhu, I., Song, W., Ovcharenko, I., & Landsman, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab235 · Cited by 55

Regeneration and Developmental Enhancers are Differentially Compatible with Minimal Promoters

Begeman, I. J., Emery, B. F., Kurth, A., & Kang, J. (2022) · Developmental Biology · doi:10.1016/j.ydbio.2022.09.007 · Cited by 7

Compatibility logic of human enhancer and promoter sequencesPreprint

Bergman, D. T., Jones, T., Liu, V., Siraj, L., Kang, H., Nasser, J., Kane, M., Nguyen, T. H., Grossman, S. R., Fulco, C. P., et al. (2021) · bioRxiv · doi:10.1101/2021.10.23.462170 · Cited by 5

Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers

Bardales, J. A., Wieser, E., Kawaji, H., Murakawa, Y., & Darzacq, X. (2018) · Genes · doi:10.3390/genes9060270 · Cited by 5

Compatibility rules of human enhancer and promoter sequences

Bergman, D. T., Jones, T. R., Liu, V., Ray, J., Jagoda, E., Siraj, L., Kang, H. Y., Nasser, J., Kane, M., Rios, A., et al. (2022) · Nature · doi:10.1038/s41586-022-04877-w · Cited by 169