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

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The Genome of Drosophila Melanogaster

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

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An integrated map of structural variation in 2,504 human genomes

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Transcription factors: from enhancer binding to developmental control

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A comparison of topologically associating domain callers over mammals at high resolution

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GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

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Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models

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Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3

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Structural variants in the 3D genome as drivers of disease

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The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook

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Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells

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Histone H1 Mutations in Lymphoma: A Link(er) between Chromatin Organization, Developmental Reprogramming, and Cancer

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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

Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions

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Somatic structural variant formation is guided by and influences genome architecturePreprint

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High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis

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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

Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system

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Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila

Kyrchanova, O. V., Bylino, O. V., & Georgiev, P. G. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.1081088 · Cited by 29

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

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Single cell analysis pushes the boundaries of TAD formation and function

Luppino, J. M., & Joyce, E. F. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.03.005 · Cited by 29

Tidying-up the plant nuclear space: domains, functions, and dynamics

Santos, A. P., Gaudin, V., Mozgová, I., Pontvianne, F., Schubert, D. S. P., Tek, A. L., Dvořáčková, M., Liu, C., Fransz, P. F., Rosa, S., et al. (2020) · Journal of Experimental Botany · doi:10.1093/jxb/eraa282 · Cited by 29

Nuclear genome organization in fungi: from gene folding to Rabl chromosomes

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Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer

Du, Y., Gu, Z., Li, Z., Yuan, Z., Zhao, Y., Zheng, X., Bo, X., Chen, H., & Wang, C. (2022) · Advanced Science · doi:10.1002/advs.202200818 · Cited by 28

DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication

Sun, Z., Wang, Y., Song, Z., Zhang, H., Wang, Y., Liu, K., Ma, M., Wang, P., Fang, Y., Cai, D., et al. (2022) · Journal of Advanced Research · doi:10.1016/j.jare.2022.07.007 · Cited by 27

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

Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C

Chi, Y., Shi, J., Xing, D., & Tan, L. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.959688 · Cited by 25

Functional genomic approaches to elucidate the role of enhancers during development

Ryan, G. E., & Farley, E. K. (2019) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1467 · Cited by 22

The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome

Jordan, W. T., & Larschan, E. N. (2020) · bioRxiv · doi:10.1186/s13072-021-00399-3 · Cited by 17

Epistatic selection on a selfish Segregation Distorter supergene – drive, recombination, and genetic load

Navarro-Domínguez, B. M., Chang, C.-H., Brand, C. L., Muirhead, C. A., Presgraves, D. C., & Larracuente, A. M. (2022) · eLife · doi:10.7554/elife.78981 · Cited by 23

Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

Chakraborty, S., Wenzlitschke, N., Anderson, M. J., Eraso, A., Baudic, M., Thompson, J. J., Evans, A. A., Shatford-Adams, L. M., Chari, R., Awasthi, P., et al. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.02.002 · Cited by 22

When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancer

Weischenfeldt, J., & Ibrahim, D. M. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102048 · Cited by 19

POSTRE: a tool to predict the pathological effects of human structural variants

Sánchez-Gaya, V., & Rada-Iglesias, Á. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad225 · Cited by 22

Long-range gene regulation in hormone-dependent cancer

Tettey, T. T., Rinaldi, L., & Hager, G. L. (2023) · Nature reviews. Cancer · doi:10.1038/s41568-023-00603-4 · Cited by 23

Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

Nakato, R., Sakata, T., Wang, J., Nagai, L. A. E., Nagaoka, Y., Oba, G. M., Bando, M., & Shirahige, K. (2023) · Nature Communications · doi:10.1038/s41467-023-41316-4 · Cited by 22

Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All?

Ghavi-Helm, Y. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.09.010 · Cited by 20

The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes

Melnikova, L. S., Georgiev, P. G., & Golovnin, A. K. (2020) · Acta Naturae · doi:10.32607/actanaturae.11144 · Cited by 24

Decoding the organization, dynamics, and function of the 4D genome

Aboelnour, E., & Bonev, B. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.04.023 · Cited by 24

Network models of chromatin structure

Pancaldi, V. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102051 · Cited by 21

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

Torres, D. E., Kramer, H. M., Tracanna, V., Fiorin, G. L., Cook, D. E., Seidl, M. F., & Thomma, B. P. H. J. (2024) · Nature Communications · doi:10.1038/s41467-024-45884-x · Cited by 23

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 25

Reorganization of the 3D Genome Pinpoints Noncoding Drivers of Primary Prostate Tumors

Hawley, J. R., Zhou, S., Arlidge, C., Grillo, G., Kron, K. J., Hugh-White, R., van der Kwast, T. H., Fraser, M. E., Boutros, P. C., Bristow, R. G., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-21-2056 · Cited by 21

Spectrum and Density of Gamma and X-ray Induced Mutations in a Non-Model Rice Cultivar

Jankowicz-Cieślak, J., Hofinger, B. J., Jarc, L., Junttila, S., Gálik, B., Gyenesei, A., Ingelbrecht, I., & Till, B. J. (2022) · Plants · doi:10.3390/plants11233232 · Cited by 20

Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis)

Li, Y., Wang, S., Zhang, Z., Luo, J., Lin, G. L., Deng, W., Guo, Z., Han, F., Wang, L., Li, J., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad006 · Cited by 20

Genome organization via loop extrusion, insights from polymer physics models

Ghosh, S. K., & Jost, D. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz023 · Cited by 24

Centric Fusions behind the Karyotype Evolution of Neotropical Nannostomus Pencilfishes (Characiforme, Lebiasinidae): First Insights from a Molecular Cytogenetic Perspective

Sember, A., de Oliveira, E. A., Ráb, P., Bertollo, L. A. C., de Freitas, N. L., Viana, P. F., Yano, C. F., Hatanaka, T., Marinho, M., de Moraes, R. L. R., et al. (2020) · Genes · doi:10.3390/genes11010091 · Cited by 21

Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans

Stutzman, A. V., Liang, A. S., Beilinson, V., & Ikegami, K. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0325-2 · Cited by 20

Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif

Armstrong, R. L., Das, S., Hill, C. A., Duronio, R. J., & Nordman, J. T. (2020) · Genetics · doi:10.1534/genetics.120.303155 · Cited by 20

Regulation of RNA polymerase II transcription through re-initiation and bursting

Nagel, M., & Taatjes, D. J. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.04.011 · Cited by 17

Transcription bursting and epigenetic plasticity: an updated view

Beckman, W. F., Jiménez, M. Á. L., & Verschure, P. J. (2021) · Epigenetics Communications · doi:10.1186/s43682-021-00007-1 · Cited by 22

The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong!

Chua, E. H. Z., Yasar, S., & Harmston, N. (2022) · Biology Open · doi:10.1242/bio.059091 · Cited by 22

Altering enhancer–promoter linear distance impacts promoter competition in cis and in trans

Bateman, J. R., & Johnson, J. E. (2022) · Genetics · doi:10.1093/genetics/iyac098 · Cited by 19

3D genome organisation in Drosophila

Moretti, C., Stévant, I., & Ghavi-Helm, Y. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz029 · Cited by 19

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Buendía, G. A. R., Leleu, M., Marzetta, F., Vanzan, L., Tan, J. Y., Ythier, V., Randall, E. L., Marques, A. C., Baubec, T., Murr, R., et al. (2020) · Science Advances · doi:10.1126/sciadv.aaz4012 · Cited by 19

Regulation of organelle size and organization during development

Chen, P., & Levy, D. L. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.02.002 · Cited by 20

Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor

Warwick, T., Schulz, M. H., Gilsbach, R., Brandes, R. P., & Seuter, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac178 · Cited by 16

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing

Soto, D. C., Shew, C. J., Mastoras, M., Schmidt, J. M., Sahasrabudhe, R. M., Kaya, G., Andrés, A. M., & Dennis, M. Y. (2020) · Genes · doi:10.3390/genes11030276 · Cited by 18

3D or Not 3D: Shaping the Genome during DevelopmentPreprint

Glaser, J., & Mundlos, S. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040188 · Cited by 18

Regulation of cohesin‐mediated chromosome folding by PDS5 in mammals

Yu, D., Chen, G., Wang, Y., Wang, Y., Lin, R., Liu, N., Zhu, P., Liu, H., Hu, T., Feng, R., et al. (2022) · EMBO Reports · doi:10.15252/embr.202254853 · Cited by 15

Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies

Sánchez-Gaya, V., Mariner-Faulí, M., & Rada-Iglesias, Á. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00688 · Cited by 17

Multi-Scale Organization of the Drosophila melanogaster Genome

Peterson, S. C., Samuelson, K. B., & Hanlon, S. L. (2021) · Genes · doi:10.3390/genes12060817 · Cited by 20

The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology

Rodríguez, S., Scadden, A. W., Reckard, A. T., Shtanko, Y., Hull-Crew, C., & Klocko, A. D. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac053 · Cited by 18

The Arabidopsis condensin CAP‐D subunits arrange interphase chromatin

Municio-Diaz, C., Antosz, W., Grasser, K. D., Kornobis, É., Bel, M. V., Eguinoa, I., Coppens, F., Bräutigam, A., Lermontová, I., Bruckmann, A., et al. (2021) · New Phytologist · doi:10.1111/nph.17221 · Cited by 18

Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units

Liang, J., & Perez-Rathke, A. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.06.017 · Cited by 16

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification

Liu, C., Nagashima, H., Fernando, N., Bass, V., Gopalakrishnan, J., Signorella, S., Montgomery, W., Lim, A. I., Harrison, O. J., Reich, L. N., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.04.007 · Cited by 18

Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics

Pancaldi, V. (2021) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2021.742216 · Cited by 17

Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network

Hunt, G., Vaid, R., Пирогов, С. А., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegård, J., & Mannervik, M. (2024) · Genome biology · doi:10.1186/s13059-023-03135-0 · Cited by 16

The scales, mechanisms, and dynamics of the genome architecture

Lizana, L., & Schwartz, Y. B. (2024) · Science Advances · doi:10.1126/sciadv.adm8167 · Cited by 18

Engineering three-dimensional genome folding

Zhang, D., Lam, J. C., & Blobel, G. A. (2021) · Nature Genetics · doi:10.1038/s41588-021-00860-9 · Cited by 17

Enhancers navigate the three-dimensional genome to direct cell fate decisions

Kim, J., & Dean, A. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.06.005 · Cited by 15

Chromatin Organization and Function in Drosophila

Llorens‐Giralt, P., Camilleri‐Robles, C., Corominas, M., & Climent‐Cantó, P. (2021) · Cells · doi:10.3390/cells10092362 · Cited by 16

β-actin mediated H3K27ac changes demonstrate the link between compartment switching and enhancer-dependent transcriptional regulation

Mahmood, S. R., Said, N. H. E., Gunsalus, K. C., & Percipalle, P. (2023) · Genome biology · doi:10.1186/s13059-023-02853-9 · Cited by 16

Disruption of regulatory domains and novel transcripts as disease‐causing mechanisms

Allou, L., & Mundlos, S. (2023) · BioEssays · doi:10.1002/bies.202300010 · Cited by 15

A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer–promoter communication

Denaud, S., Bardou, M., Papadopoulos, G. L., Grob, S., Stefano, M. D., Sabarís, G., Nöllmann, M., Schuettengruber, B., & Cavalli, G. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01375-7 · Cited by 15

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

High-resolution Hi-C maps highlight multiscale chromatin architecture reorganization during cold stress in Brachypodium distachyon

Zhang, X., Yu, G., Dai, Y., Zhang, H., Wang, K., & Han, J. (2023) · BMC Plant Biology · doi:10.1186/s12870-023-04269-w · Cited by 14

A genome disconnect

Finn, E. H., & Misteli, T. (2019) · Nature Genetics · doi:10.1038/s41588-019-0476-x · Cited by 15

Self-inflicted DNA breaks in cell differentiation and cancer

Benada, J., Alsowaida, D., Megeney, L. A., & Sørensen, C. S. (2023) · Trends in Cell Biology · doi:10.1016/j.tcb.2023.03.002 · Cited by 12

Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster

McBroome, J., Liang, D., & Corbett-Detig, R. B. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa103 · Cited by 14

Identification and Characterization of Breakpoints and Mutations on Drosophila melanogaster Balancer Chromosomes

Miller, D. E., Kahsai, L., Buddika, K., Dixon, M. J., Kim, B. Y., Calvi, B. R., Sokol, N. S., Hawley, R. S., & Cook, K. R. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.120.401559 · Cited by 16

Transcription factor expression is the main determinant of variability in gene co‐activity

van Duin, L., Krautz, R., Rennie, S., & Andersson, R. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211392 · Cited by 11

Eliminating elevated p53 signaling fails to rescue skeletal muscle defects or extend survival in lamin A/C-deficient mice

Kirby, T. J., Zahr, H. C., Fong, E. H. H., & Lammerding, J. (2024) · Cell Death Discovery · doi:10.1038/s41420-024-01998-1 · Cited by 14

Understanding breast cancer heterogeneity through non-genetic heterogeneity

Barough, N. B., Sajjadian, F., Jalilzadeh, N., Shafaei, H., & Velaei, K. (2021) · Breast Cancer · doi:10.1007/s12282-021-01237-w · Cited by 13

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 conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes

Omura, C. S., & Lott, S. E. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008645 · Cited by 14

Reprogramming of three-dimensional chromatin organization in the early embryo

Theis, A., & Harrison, M. M. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102613 · Cited by 12

Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes

Feng, C., Wang, J., & Chu, X. (2023) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjad042 · Cited by 12

Gene structure heterogeneity drives transcription noise within human chromosomesPreprint

Chiang, M., Brackley, C. A., Naughton, C., Nozawa, R., Battaglia, C., Marenduzzo, D., & Gilbert, N. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.09.495447 · Cited by 11

Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements

Zhou, B., Hu, P., Liu, G., Chang, Z., Dong, Z., Li, Z., Yin, Y., Tian, Z., Han, G., Wang, W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50529-0 · Cited by 13

Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping

Foran, G., Hallam, R. D., Megaly, M., Turgambayeva, A., Antfolk, D., Li, Y., Luca, V. C., & Necakov, A. (2024) · Scientific Reports · doi:10.1038/s41598-024-71634-6 · Cited by 11

Engineering structural variants to interrogate genome function

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

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