How subtle changes in 3D structure can create large changes in transcription

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

Molecular Biology of the Cell

Alberts, B., Johnson, A., Lewis, J. H., Morgan, D. O., RAFF, M. C., Roberts, K. J., & Walter, P. (2017) · W.W. Norton eBooks · doi:10.1201/9781315735368 · Cited by 7,937

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

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

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 2,421

Nonlinear Dynamics and Chaos

Strogatz, S. H. (2018) · CRC Press eBooks · doi:10.1201/9780429492563 · Cited by 2,247

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132

Mediator and cohesin connect gene expression and chromatin architecture

Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939

Cohesin Loss Eliminates All Loop Domains

Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Bravo González-Blas, C., De Winter, S., Hulselmans, G., Hecker, N., Matetovici, I., Christiaens, V., Poovathingal, S., Wouters, J., Aibar, S., & Aerts, S. (2023) · Nature Methods · doi:10.1038/s41592-023-01938-4 · Cited by 778

Nonlinear control of transcription through enhancer–promoter interactions

Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04570-y · Cited by 415

Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1

Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Darzacq, X., & Tjian, R. (2022) · Nature Genetics · doi:10.1038/s41588-022-01223-8 · Cited by 406

The Mediator complex as a master regulator of transcription by RNA polymerase II

Richter, W. F., Nayak, S., Iwasa, J., & Taatjes, D. J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00498-3 · Cited by 343

Deciphering the multi-scale, quantitative cis-regulatory code

Kim, S., & Wysocka, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2022.12.032 · Cited by 302

Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability

McArthur, E., & Capra, J. A. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.01.001 · Cited by 207

Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation

Yang, J. H., & Hansen, A. S. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00710-6 · Cited by 191

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Rinzema, N. J., Sofiadis, K., Tjalsma, S. J. D., Verstegen, M. J. A. M., Oz, Y., Valdes-Quezada, C., Felder, A.-K., Filipovska, T., van der Elst, S., de Andrade dos Ramos, Z., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00787-7 · Cited by 166

Topologically associating domain boundaries are required for normal genome function

Rajderkar, S., Barozzi, I., Zhu, Y., Hu, R., Zhang, Y., Li, B., Alcaina‐Caro, A., Fukuda-Yuzawa, Y., Kelman, G., Akeza, A., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-04819-w · Cited by 172

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

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communicationPreprint

Karr, J. P., Ferrie, J. J., Tjian, R., & Darzacq, X. (2021) · Genes & Development · doi:10.1101/gad.349160.121 · Cited by 155

The Mediator complex regulates enhancer-promoter interactions

Ramasamy, S., Aljahani, A., Karpińska, M. A., Cao, T. B. N., Velychko, T., Cruz, J. N., Lidschreiber, M., & Oudelaar, A. M. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01027-2 · Cited by 141

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

Aljahani, A., Hua, P., Karpinska, M. A., Quililan, K., Davies, J. O. J., & Oudelaar, A. M. (2022) · Nature Communications · doi:10.1038/s41467-022-29696-5 · Cited by 121

Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening

Tan, J., Shenker-Tauris, N., Rodriguez-Hernaez, J., Wang, E., Sakellaropoulos, T., Boccalatte, F. E., Thandapani, P., Skok, J. A., Aifantis, I., Fenyö, D., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01612-8 · Cited by 123

Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

Chakraborty, S., Kopitchinski, N., Zuo, Z., Eraso, A., Awasthi, P., Chari, R., Mitra, A., Tobias, I. C., Moorthy, S. D., Dale, R. K., et al. (2023) · Nature Genetics · doi:10.1038/s41588-022-01295-6 · Cited by 120

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

New insights into genome folding by loop extrusion from inducible degron technologies

de Wit, E., & Nora, E. P. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00530-4 · Cited by 91

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Chen, Z., Snetkova, V., Bower, G., Jacinto, S. H., Clock, B., Dizehchi, A., Barozzi, I., Mannion, B. J., Alcaina‐Caro, A., López-Ríos, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01681-2 · Cited by 98

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

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

Pancholi, A., Klingberg, T., Zhang, W., Prizak, R., Mamontova, I., Noa, A., Sobucki, M., Kobitski, A. Y., Nienhaus, G. U., Zaburdaev, V., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110272 · Cited by 85

Functional coordination between transcription factor clustering and gene activity

Kawasaki, K., & Fukaya, T. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.018 · Cited by 80

A cohesin traffic pattern genetically linked to gene regulation

Valton, A.-L., Venev, S. V., Mair, B., Khokhar, E. S., Tong, A. H. Y., Ušaj, M., Chan, K., Pai, A. A., Moffat, J., & Dekker, J. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00890-9 · Cited by 83

BRD2 compartmentalizes the accessible genome

Xie, L., Dong, P., Qi, Y., Hsieh, T.-H. S., English, B. P., Jung, S., Chen, X., Marzio, M. D., Casellas, R. C., Chang, H. Y., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01044-9 · Cited by 66

Nonlinear control of transcription through enhancer-promoter interactions

Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2021) · doi:10.1101/2021.04.22.440891 · Cited by 67

Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development

Hung, T.-C., Kingsley, D. M., & Boettiger, A. N. (2024) · Nature Genetics · doi:10.1038/s41588-023-01641-2 · Cited by 64

Enhancer-gene specificity in development and disease

Pachano, T., Haro, E., & Rada-Iglesias, Á. (2022) · Development · doi:10.1242/dev.186536 · Cited by 58

Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription

Reed, K. S. M., Davis, E. S., Bond, M. L., Cabrera, A., Thulson, E., Quiroga, I. Y., Cassel, S., Woolery, K. T., Hilton, I. B., Won, H., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111567 · Cited by 56

Enhancer cooperativity can compensate for loss of activity over large genomic distances

Thomas, H., Feng, S., Haslhofer, F., Huber, M., Gallardo, M. G., Loubière, V., Vanina, D., Pitasi, M., Stark, A., & Buecker, C. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.008 · Cited by 59

The stochastic nature of genome organization and function

Sood, V., & Misteli, T. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.10.004 · Cited by 53

Genomic environments scale the activities of diverse core promotersPreprint

Hong, C. K., & Cohen, B. A. (2021) · Genome Research · doi:10.1101/gr.276025.121 · Cited by 52

Ultra-long-range interactions between active regulatory elementsPreprint

Friman, E. T., Flyamer, I. M., Marenduzzo, D., Boyle, S., & Bickmore, W. A. (2023) · Genome Research · doi:10.1101/gr.277567.122 · Cited by 53

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

Luo, R., Yan, J., Oh, J. W., Wang, X., Shigaki, D., Wong, W., Cho, H., Murphy, D., Cutler, R. R., Rosen, B. P., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01450-7 · Cited by 50

YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle

Lam, J. C., Aboreden, N. G., Midla, S. C., Wang, S., Huang, A., Keller, C. A., Giardine, B. M., Henderson, K. A., Hardison, R. C., Zhang, H., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01871-y · Cited by 47

Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

Luo, S., Wang, Z., Zhang, Z., Zhou, T., & Zhang, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1204 · Cited by 49

Single-molecule states link transcription factor binding to gene expression

Doughty, B. R., Hinks, M. M., Schaepe, J. M., Marinov, G. K., Thurm, A. R., Rios-Martinez, C., Parks, B. E., Tan, Y., Marklund, E., Dubocanin, D., et al. (2024) · Nature · doi:10.1038/s41586-024-08219-w · Cited by 42

Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Darzacq, X., & Tjian, R. (2021) · doi:10.1101/2021.07.14.452365 · Cited by 42

Size limits the sensitivity of kinetic schemes

Owen, J. A., & Horowitz, J. M. (2023) · Nature Communications · doi:10.1038/s41467-023-36705-8 · Cited by 41

Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation

Kim, K. L., Rahme, G. J., Goel, V. Y., Farran, C. A. E., Hansen, A. S., & Bernstein, B. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.007 · Cited by 42

Long-range regulation of transcription scales with genomic distance in a gene-specific manner

Jensen, C. L., Chen, L.-F., Swigut, T., Crocker, O. J., Yao, D., Bassik, M. C., Ferrell, J. E., Boettiger, A. N., & Wysocka, J. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.10.021 · Cited by 39

Chromatin modules and their implication in genomic organization and gene regulation

van Mierlo, G., Pushkarev, O., Kribelbauer, J. F., & Deplancke, B. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.11.003 · Cited by 35

3D genome folding in epigenetic regulation and cellular memory

Paldi, F., & Cavalli, G. (2025) · Trends in Cell Biology · doi:10.1016/j.tcb.2025.03.001 · Cited by 34

Recent progress and challenges in single-cell imaging of enhancer–promoter interaction

Chen, L., Lee, J., & Boettiger, A. N. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102023 · Cited by 31

Uniform dynamics of cohesin-mediated loop extrusion in living human cells

Sabaté, T., Lelandais, B., Robert, M.-C., Szalay, M., Tinevez, J.-Y., Bertrand, E., & Zimmer, C. (2025) · Nature Genetics · doi:10.1038/s41588-025-02406-9 · Cited by 32

Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegansPreprint

Kim, J., Wang, H., & Ercan, S. (2025) · Genome Research · doi:10.1101/gr.279365.124 · Cited by 31

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation

Karpińska, M. A., Zhu, Y., Ghazvini, Z. F., Ramasamy, S., Barbieri, M., Cao, T. B. N., Varahram, N., Aljahani, A., Lidschreiber, M., Papantonis, A., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01555-z · Cited by 35

Complex small-world regulatory networks emerge from the 3D organisation of the human genome

Brackley, C. A., Gilbert, N., Michieletto, D., Papantonis, A., Pereira, M. C. F., Cook, P. R., & Marenduzzo, D. (2021) · Nature Communications · doi:10.1038/s41467-021-25875-y · Cited by 35

Regulatory landscape of enhancer-mediated transcriptional activation

Kawasaki, K., & Fukaya, T. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.01.008 · Cited by 32

Evolution and function of chromatin domains across the tree of life

Szalay, M.-F., Majchrzycka, B., Jerković, I., Cavalli, G., & Ibrahim, D. M. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01427-y · Cited by 31

What is an enhancer?

Thomas, H., & Buecker, C. (2023) · BioEssays · doi:10.1002/bies.202300044 · Cited by 28

Contributions of 3D chromatin structure to cell-type-specific gene regulation

Schaeffer, M., & Nöllmann, M. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102032 · Cited by 26

Managing the Steady State Chromatin Landscape by Nucleosome Dynamics

Ahmad, K., Henikoff, S., & Ramachandran, S. (2022) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-032620-104508 · Cited by 27

Dynamic interplay between non-coding enhancer transcription and gene activity in development

Hamamoto, K., Umemura, Y., Makino, S., & Fukaya, T. (2023) · Nature Communications · doi:10.1038/s41467-023-36485-1 · Cited by 25

Power-law behavior of transcriptional bursting regulated by enhancer–promoter communicationPreprint

Wang, Z., Zhang, Z., Luo, S., Zhou, T., & Zhang, J. (2024) · Genome Research · doi:10.1101/gr.278631.123 · Cited by 27

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

4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction

Wang, Z., Luo, S., Zhang, Z., Zhou, T., & Zhang, J. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011722 · Cited by 23

Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition

Ealo, T., Sánchez-Gaya, V., Respuela, P., Martín, M. M., Martín-Batista, E., Haro, E., & Rada-Iglesias, Á. (2024) · Nature Communications · doi:10.1038/s41467-024-51602-4 · Cited by 24

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding

Paldi, F., Szalay, M.-F., Dufau, S., Di Stefano, M., Reboul, H., Jost, D., Bantignies, F., & Cavalli, G. (2026) · Nature Genetics · doi:10.1038/s41588-025-02489-4 · Cited by 18

Emerging insights into enhancer biology and function

Arnold, M., & Stengel, K. R. (2023) · Transcription · doi:10.1080/21541264.2023.2222032 · Cited by 20

Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome

Papantonis, A., & Oudelaar, A. M. (2025) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120423-012301 · Cited by 19

Enhancer-Promoter Communication: It’s Not Just About Contact

Wurmser, A., & Basu, S. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.867303 · Cited by 19

Spandrels of the cell nucleus

Solovei, I. V., & Mirny, L. A. (2024) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2024.102421 · Cited by 17

Single-molecule chromatin configurations link transcription factor binding to expression in human cellsPreprint

Doughty, B. R., Hinks, M. M., Schaepe, J. M., Marinov, G., Thurm, A. R., Rios-Martinez, C., Parks, B. E., Tan, Y.-X., Marklund, E., Dubocanin, D., et al. (2024) · bioRxiv · doi:10.1101/2024.02.02.578660 · Cited by 14

Understanding transcription across scales: From base pairs to chromosomes

Vos, S. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.002 · Cited by 18

Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila

Götz, M., Messina, O., Espínola, S., Fiche, J.-B., & Nöllmann, M. (2022) · Nature Communications · doi:10.1038/s41467-022-32973-y · Cited by 16

A Cohesin Traffic Pattern Genetically Linked to Gene Regulation

Valton, A.-L., Dekker, J., Venev, S. V., Mair, B., Khokhar, E. S., Pai, A. A., & Moffat, J. (2021) · HAL · Cited by 18

Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

Wang, R., Xu, Q., Wang, C., Tian, K., Wang, H., & Ji, X. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad401 · Cited by 13

A cohesin traffic pattern genetically linked to gene regulationPreprint

Valton, A.-L., Venev, S. V., Mair, B., Khokhar, E. S., Tong, A. H. Y., Ušaj, M., Chan, K. S. K., Pai, A. A., Moffat, J., & Dekker, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.29.454218 · Cited by 15

Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging

Sabaté, T., Lelandais, B., Bertrand, E., & Zimmer, C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad034 · Cited by 13

Deep-learning microscopy image reconstruction with quality control reveals second-scale rearrangements in RNA polymerase II clusters

Hajiabadi, H., Mamontova, I., Prizak, R., Pancholi, A., Koziolek, A., & Hilbert, L. (2022) · PNAS Nexus · doi:10.1093/pnasnexus/pgac065 · Cited by 15

Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells

Liu, R., Xu, R., Yan, S., Li, P., Jia, C., Sun, H., Sheng, K., Wang, Y., Zhang, Q., Guo, J., et al. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1377238 · Cited by 15

Making connections: enhancers in cellular differentiation

Herrmann, J. C., Beagrie, R. A., & Hughes, J. R. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.10.008 · Cited by 14

The method in the madness: Transcriptional control from stochastic action at the single-molecule scale

Whitney, P. H., & Lionnet, T. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102873 · Cited by 13

Cohesin as an essential disruptor of chromosome organization

Bird, A. P. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.010 · Cited by 13

De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion

Aboreden, N. G., Zhao, H., Yang, J., Shan, F., Liu, F., Hansen, A. S., Zhang, H., & Blobel, G. A. (2026) · Nature Genetics · doi:10.1038/s41588-026-02565-3 · Cited by 21

The Drosophila embryo as a tabula rasa for the epigenome

Ahmad, K., & Henikoff, S. (2022) · Faculty Reviews · doi:10.12703/r/11-40 · Cited by 9

LAST-seq: single-cell RNA sequencing by direct amplification of single-stranded RNA without prior reverse transcription and second-strand synthesis

Lyu, J., & Chen, C. (2023) · Genome biology · doi:10.1186/s13059-023-03025-5 · Cited by 11

Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci

Brandani, G. B., Gu, C., Gopi, S., & Takada, S. (2024) · PNAS Nexus · doi:10.1093/pnasnexus/pgae226 · Cited by 11

Image-based 3D genomics through chromatin tracing

Yang, T., & Wang, S. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00354-y · Cited by 10

Integrative approaches to study enhancer–promoter communication

Mach, P., & Giorgetti, L. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102052 · Cited by 10

Better together: how cooperativity influences transcriptional bursting

Fountas, C., & Lenstra, T. L. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102274 · Cited by 9

The Dance of Promoters and Enhancers in Gene Regulation: Fast or Slow, Entwined or Distant?

Nazarova, M., & Sexton, T. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169223 · Cited by 10

Omics Analyses Uncover Host Networks Defining Virus-Permissive and -Hostile Cellular States

Chen, H., Charles, P. D., Gu, Q., Liberatori, S., Robertson, D. L., Palmarini, M., Wilson, S. J., Mohammed, S., & Castelló, A. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100966 · Cited by 9

Redefining enhancer action: Insights from structural, genomic, and single-molecule perspectives

Llères, D., Gizzi, A. M. C., & Nöllmann, M. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102527 · Cited by 11

RNA gradients can guide condensates toward promoters: Implications for enhancer–promoter contacts and condensate-promoter kissing

Goh, D., Kannan, D., Natarajan, P., Goychuk, A., & Chakraborty, A. K. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0277838 · Cited by 8

Genome-wide tracing to decipher nuclear organization

Flores, V., Farabella, I., & Nir, G. (2023) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2023.102175 · Cited by 8

Building regulatory landscapes: enhancer recruits cohesin to create contact domains, engage CTCF sites and activate distant genes

Rinzema, N. J., Sofiadis, K., Tjalsma, S. J. D., Verstegen, M. J. A. M., Oz, Y., Valdes-Quezada, C., Felder, A.-K., Filipovska, T., van der Elst, S., de Andrade dos Ramos, Z., et al. (2021) · doi:10.1101/2021.10.05.463209 · Cited by 8

Cross-Species BAC Transgenesis Reveals Long-Range Regulation Drives Variation in Brain Oxytocin Receptor Expression and Social BehaviorsPreprint

Tsukamoto, M., Nagai, L. A., Inoue, K., Kandasamy, L. C., Pires, M. F., Shin, M., Nagasawa, Y., Sambuu, T., Nakai, K., Itohara, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.01.518660 · Cited by 9

Kinetic organization of the genome revealed by ultra-resolution, multiscale live imagingPreprint

Lee, J., Chen, L., Gaudin, S., Gupta, K., Spakowitz, A. J., & Boettiger, A. N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.27.645817 · Cited by 8

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional burstsPreprint

Tünnermann, J., Roth, G., Cramard, J., & Giorgetti, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.26.645410 · Cited by 8

Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communicationPreprint

Ubertini, M. A., Louafi, N., Landry, K., Kos, P. I., Roth, G., Marchi, E., Cramard, J., Tiana, G., & Giorgetti, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.24.678119 · Cited by 10

Enhancer cooperativity in the folded genome

Friman, E. T., & Bickmore, W. A. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102416 · Cited by 7

Exploring the interplay between enhancer–promoter interactions and transcription

Kittle, R., & Levo, M. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102303 · Cited by 7

Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer SimulationsPreprint

Fu, Y., Zhao, T., Clark, F., Nomikou, S., Tsirigos, A., & Lionnet, T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.07.566032 · Cited by 8

Predicting gene expression changes from chromatin structure modification

Senapati, S., Irshad, I. U., Sharma, A. K., & Kumar, H. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00510-4 · Cited by 8

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

Nanoscale dynamics of enhancer–promoter interactions during exit from pluripotency

Stumberger, G., Hörl, D., Tsouraki, D., Steinek, C., Oudelaar, A. M., Leonhardt, H., & Harz, H. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1255 · Cited by 6

Organization of transcription and 3D genome as revealed by live-cell imaging

Ochiai, H., Ohishi, H., Sato, Y., & Kimurâ, H. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102615 · Cited by 7

A Scaffolding Element Rewires Local 3D Chromatin Architecture During DifferentiationPreprint

Jerković, I., Stefano, M. D., Reboul, H., Szalay, M.-F., Normanno, D., Papadopoulos, G. L., Bantignies, F., & Cavalli, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.23.595561 · Cited by 6

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

TAD ‐dependent sub‐ TAD is required for enhancer–promoter interaction enabling the β‐globin transcription

Lee, D., Kang, J., & Kim, A. (2024) · The FASEB Journal · doi:10.1096/fj.202401526rr · Cited by 4

TAD boundary architecture and gene activity are uncoupledPreprint

Almansour, F., Fursova, N. A., Keikhosravi, A., Reed, K. S. M., Larson, D. R., Pegoraro, G., & Misteli, T. (2026) · eLife · doi:10.7554/elife.110197.1

Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context

Salnikov, P., Belokopytova, P. S., Yan, A., Viesná, E., Korablev, A. N., Serova, I. A., Lukyanchikova, V., Stepanchuk, Y., Torgunakov, N., Tikhomirov, S., et al. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00618-1 · Cited by 6

TAD boundaries and gene activity are uncoupledPreprint

Almansour, F., Fursova, N. A., Keikhosravi, A., Reed, K. S. M., Larson, D. R., Pegoraro, G., & Misteli, T. (2026) · eLife · doi:10.7554/elife.110197 · Cited by 3

Selective cross-TAD gene regulation by the Tcra enhancer during T cell development

Rodríguez-Caparrós, A., López-Castellanos, L., López-Ros, J., Castro-Ruiz, V., Duarte-Ruiz, M., Jiménez-Lozano, S., Moreno-Castillo, A., Terron-Camero, L. C., Andrés‐León, E., Suñé, C., et al. (2026) · Cellular and Molecular Life Sciences · doi:10.64898/2026.04.27.721065