Chromatin structure dynamics during the mitosis-to-G1 phase transition

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

Formation of chromosomal domains by loop extrusion

Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

Weintraub, A. S., Li, C. H., Zamudio, A. V., Sigova, A. A., Hannett, N. M., Day, D. S., Abraham, B. J., Cohen, M. A., Nabet, B., Buckley, D. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.008 · Cited by 992

Organization of the mitotic chromosome

Naumova, N., Imakaev, M., Fudenberg, G., Zhan, Y., Lajoie, B. R., Mirny, L. A., & Dekker, J. (2013) · Science · doi:10.1126/science.1236083 · Cited by 976

Cell-cycle dynamics of chromosomal organization at single-cell resolution

Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A. (2017) · Nature · doi:10.1038/nature23001 · Cited by 794

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

Zuin, J., Dixon, J. R., van der Reijden, M. I. J. A., Ye, Z., Kolovos, P., Brouwer, R. W. W., van de Corput, M. P. C., van de Werken, H. J. G., Knoch, T. A., van IJcken, W. F. J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317788111 · Cited by 779

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cellsPreprint

Soares, M. A. F., Soares, D. S., Teixeira, V., Heskol, A., Bressan, R. B., Pollard, S. M., Oliveira, R. A., & Castro, D. S. (2021) · Genes & Development · doi:10.1101/gad.348174.120 · Cited by 26

SARS-CoV-2 Restructures the Host Chromatin ArchitecturePreprint

Wang, R.-Y., Lee, J.-H., Xiong, F., Kim, J., Hasani, L. A., Yuan, X.-Y., Shivshankar, P., Krakowiak, J., Qi, C.-Y., Wang, Y.-Y., et al. (2021) · bioRxiv · doi:10.1101/2021.07.20.453146 · Cited by 40

Transcriptional repression across mitosis: mechanisms and functions

Contreras, A., & Perea-Resa, C. (2024) · Biochemical Society Transactions · doi:10.1042/bst20231071 · Cited by 23

Repair of DNA double-strand breaks leaves heritable impairment to genome function

Bantele, S. C. S., Mordini, I., Biran, A., Alcaraz, N., Zonderland, G., Wenger, A., Krietenstein, N., Groth, A., & Lukas, J. (2025) · Science · doi:10.1126/science.adk6662 · Cited by 33

Cell cycle heterogeneity directs spontaneous 2C state entry and exit in mouse embryonic stem cells

Zhu, Y., Cheng, C., Chen, L., Zhang, L., Pan, H., Hou, L., Sun, Z., Zhang, L., Fu, X., Chan, K. Y., et al. (2021) · Stem Cell Reports · doi:10.1016/j.stemcr.2021.09.003 · Cited by 22

The 3D genome and its impacts on human health and disease

Wang, S., Luo, Z., Liu, W., Hu, T., Zhao, Z., Rosenfeld, M. G., & Song, X. (2023) · Life Medicine · doi:10.1093/lifemedi/lnad012 · Cited by 22

Live-cell imaging of chromatin contacts opens a new window into chromatin dynamics

van Staalduinen, J., van Staveren, T., Grosveld, F. G., & Wendt, K. S. (2023) · Epigenetics & Chromatin · doi:10.1186/s13072-023-00503-9 · Cited by 26

Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming

Chu, X., & Wang, J. (2020) · Advanced Science · doi:10.1002/advs.202001572 · Cited by 21

The interplay of DNA damage, epigenetics and tumour heterogeneity in driving cancer cell fitness

Rouault, C. D., Charafe‐Jauffret, E., & Ginestier, C. (2025) · Nature Communications · doi:10.1038/s41467-025-64445-4 · Cited by 23

Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging

Pecori, F., & Torres‐Padilla, M. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.02.018 · Cited by 20

Cellular feedback dynamics and multilevel regulation driven by the hippo pathway

Park, J., & Hansen, C. G. (2021) · Biochemical Society Transactions · doi:10.1042/bst20200253 · Cited by 19

Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales

Miura, H., & Hiratani, I. (2022) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.101898 · Cited by 21

The Impact of Space and Time on the Functional Output of the GenomePreprint

Nollmann, M., Bennabi, I., Götz, M., & Gregor, T. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040378 · Cited by 23

Physics of biomolecular recognition and conformational dynamics

Chu, W., Yan, Z., Chu, X., Zheng, X., Liu, Z., Xu, L., Zhang, K., & Wang, J. (2021) · Reports on Progress in Physics · doi:10.1088/1361-6633/ac3800 · Cited by 22

The second half of mitosis and its implications in cancer biology

Moreno-Andrés, D., Holl, K., & Antonin, W. (2022) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2022.11.013 · Cited by 22

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

Attraction and disruption: how loop extrusion and compartmentalisation shape the nuclear genome

Magnitov, M. D., & de Wit, E. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102194 · Cited by 16

3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data

Fernandez, L. R., Gilgenast, T. G., & Phillips‐Cremins, J. E. (2020) · Genome biology · doi:10.1186/s13059-020-02061-9 · Cited by 17

Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics

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

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

Zsidó, B. Z., & Hetényi, C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21114134 · Cited by 19

Three-dimensional nuclear organisation and the DNA replication timing program

Chen, N., & Buonomo, S. B. C. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102704 · Cited by 15

3D genome remodeling and homologous pairing during meiotic prophase of mouse oogenesis and spermatogenesis.

He, J., Yan, A., Chen, B., Huang, J., & Kee, K. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.10.009 · Cited by 16

Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation

Titus, K. R., Simándi, Z., Chandrashekar, H., Paquet, D., & Phillips‐Cremins, J. E. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100606 · Cited by 17

Evolution of 3D Chromatin Folding

Álvarez-González, L., & Ruiz‐Herrera, A. (2024) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-111523-102233 · 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

Sister chromatid–sensitive Hi-C to map the conformation of replicated genomes

Mitter, M., Takács, Z., Köcher, T., Micura, R., Langer, C. C. H., & Gerlich, D. W. (2022) · Nature Protocols · doi:10.1038/s41596-022-00687-6 · Cited by 16

Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm

Schooley, A., Venev, S. V., Aksenova, V., Lehman, J. W., Navarrete, E., Pai, A. A., Dasso, M., & Dekker, J. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01828-1 · Cited by 20

Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation

Popay, T. M., Pant, A., Munting, F. W., Tastemel, M., Black, M. E., Haghani, N. K., & Dixon, J. R. (2026) · Nature Genetics · doi:10.1038/s41588-026-02516-y · Cited by 19

Warm Cells, Hot Mitochondria: Achievements and Problems of Ultralocal Thermometry

Kruglov, A. G., Romshin, A. M., Nikiforova, A. B., Plotnikova, A., & Vlasov, I. I. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242316955 · Cited by 14

The shifting shape and functional specializations of the cell cycle during lineage development

Hwang, Y., Hidalgo, D., & Socolovsky, M. (2020) · WIREs Mechanisms of Disease · doi:10.1002/wsbm.1504 · Cited by 17

Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption

Shah, R., Tortora, M. M. C., Louafi, N., Rahmaninejad, H., Hansen, K. L., Anderson, E. C., Wen, D., Giorgetti, L., Fudenberg, G., & Nora, E. P. (2025) · doi:10.1101/2025.08.14.667581 · Cited by 15

Three-dimensional chromatin organization in brain function and dysfunction

Dileep, V., & Tsai, L.-H. (2021) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2021.04.006 · Cited by 14

Establishment of chromatin architecture interplays with embryo hypertranscription

Yu, G., Xu, K., Xia, W., Zhang, K., Xu, Q., Li, L., Lin, Z., Liu, L., Liu, B., Du, Z., et al. (2025) · Nature · doi:10.1038/s41586-025-09400-5 · Cited by 16

Chromatin Landscaping At Mitotic Exit Orchestrates Genome Function

Shoaib, M., Nair, N., & Sørensen, C. S. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00103 · Cited by 16

The regulation of totipotency transcription: Perspective from in vitro and in vivo totipotency

Xu, H., & Liang, H. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1024093 · Cited by 15

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosisPreprint

Zhang, S., Übelmesser, N., Josipovic, N., Forte, G., Slotman, J., Chiang, M., Gothe, H., Gusmao, E., Becker, C., Altmuller, J., et al. (2020) · bioRxiv · doi:10.1101/2020.10.27.356915 · Cited by 105

Enhancer–promoter interactions and transcription

Higgs, D. R. (2020) · Nature Genetics · doi:10.1038/s41588-020-0620-7 · Cited by 14

Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription

Kim, M., Wang, P., Clow, P. A., Chien, E., Wang, X., Peng, J., Chai, H., Liu, X., Lee, B., Ngan, C. Y., et al. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01708-0 · 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

Two CTCF motifs impede cohesin-mediated DNA loop extrusion

Barth, R., Janissen, R., Muras, L., van der Torre, J., Litos, G., van der Sluis, E. O., van den Berg, A., Davidson, I. F., Peters, J., & Dekker, C. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.11.001 · Cited by 14

3D genomics and its applications in precision medicine

Chen, M.-J., Liu, X., Liu, Q.-Y., Shi, D., & Li, H. (2023) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-023-00428-x · Cited by 12

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

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

The material properties of mitotic chromosomes

Spicer, M. F. D., & Gerlich, D. W. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102617 · Cited by 10

Genome folding dynamics during the M-to-G1-phase transition

Zhang, H., & Blobel, G. A. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102036 · Cited by 13

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus

Sajid, A., Lalani, E., Chen, B., Hashimoto, T., Griffin, D. K., Bhartiya, A., Thompson, G. E., Robinson, I. K., & Yusuf, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115987 · Cited by 10

Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation

Gong, W., Wee, J., Wu, M.-C., Sun, X., Li, C., & Xia, K. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac168 · Cited by 10

Cis-regulatory chromatin contacts form de novo in the absence of loop extrusionPreprint

Aboreden, N. G., Zhao, H., Shan, F., Liu, F., Zhang, H., & Blobel, G. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.12.632634 · Cited by 10

Human Body Single-Cell Atlas of 3D Genome Organization and DNA MethylationPreprint

Zhou, J., Wu, Y., Liu, H., Tian, W., Castanon, R., Bartlett, A., Zhang, Z., Yao, G., Shi, D., Clock, B., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.23.644697 · Cited by 10

Roles for the 3D genome in the cell cycle, DNA replication, and double strand break repair

Giles, K. A., Taberlay, P. C., Cesare, A. J., & Jones, M. V. (2025) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2025.1548946 · Cited by 11

Keeping intracellular DNA untangled: A new role for condensin?

Roca, J., Dyson, S., Segura, J., Valdés, A., & Martínez-García, B. (2021) · Bioessays · doi:10.1002/bies.202100187 · Cited by 7

A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer’s disease mutationsPreprint

Chandrashekar, H., Simándi, Z., Choi, H., Ryu, H.-S., Waldman, A. J., Nikish, A., Muppidi, S. S., Gong, W., Paquet, D., & Phillips‐Cremins, J. E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.27.582395 · Cited by 10

Single-cell long-read Hi-C, scNanoHi-C2, details 3D genome reorganization in embryonic-stage germ cells

Lu, J., Li, W., & Tang, F. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01604-7 · Cited by 9

Human body single-cell atlas of three-dimensional genome organization and DNA methylation

Zhou, J., Wu, Y., Liu, H., Tian, W., Castanon, R., Bartlett, A., Zhang, Z., Yao, G., Shi, D., Clock, B., et al. (2026) · Science · doi:10.1126/science.adx0673 · Cited by 22

Locus architecture and RAG scanning determine antibody diversity

Kenter, A., Priyadarshi, S., & Drake, E. B. (2023) · Trends in immunology · doi:10.1016/j.it.2022.12.005 · Cited by 7

Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation

Harris, R. J., Heer, M., Levasseur, M. D., Cartwright, T. N., Weston, B., Mitchell, J. L., Coxhead, J., Gaughan, L., Prendergast, L., Rico, D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43115-3 · Cited by 9

Viral infection, APOBEC3 dysregulation, and cancer

Lehle, J. D., Soleimanpour-Moghadam, M., Mokhtari, S., & Ebrahimi, D. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1489324 · Cited by 9

Epigenetic priming as a driver of memory recall and dysfunction in T cells

Metzemaekers, M., Rinzema, N. J., & Stadhouders, R. (2025) · The Journal of Experimental Medicine · doi:10.1084/jem.20241433 · Cited by 8

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption

Shah, R., Tortora, M. M. C., Louafi, N., Rahmaninejad, H., Hansen, K. L., Anderson, E. C., Bonitto, K., Wen, D., Giorgetti, L., Fudenberg, G., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.037 · Cited by 27

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

Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle

Oprescu, S. N., Baumann, N., Chen, X., Sun, Q., Zhao, Y., Yue, F., Wang, H., & Kuang, S. (2023) · Skeletal Muscle · doi:10.1186/s13395-023-00324-0 · Cited by 8

Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology

Golov, A. K., & Gavrilov, A. A. (2024) · Biochemistry (Moscow) · doi:10.1134/s0006297924040023 · Cited by 9

Orchestration of pluripotent stem cell genome reactivation during mitotic exit

Placzek, S., Vanzan, L., Deluz, C., & Suter, D. M. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115486 · Cited by 7

FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data

Patel, R. V., Pham, K., Chandrashekar, H., & Phillips‐Cremins, J. E. (2025) · Nature Methods · doi:10.1038/s41592-025-02688-1 · Cited by 8

Genome Topology Control of Antigen Receptor Gene Assembly

Allyn, B. M., Lee, K. D., & Bassing, C. H. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1901356 · Cited by 6

The Functions and Mechanisms of the Cohesin Complex in Regulating the Fate Determinations of Stem Cells

Xiang, J.-W., Lai, Y., & He, Z. (2025) · Research · doi:10.34133/research.0757 · Cited by 6

Many faces of mammalian NSD methyltransferases

Tiukacheva, E. A., Vassetzky, Y. S., Razin, S. V., Fang, D., & Ulianov, S. V. (2026) · Cellular & Molecular Biology Letters · doi:10.1186/s11658-025-00848-x · Cited by 7

A comprehensive review and benchmark of differential analysis tools for Hi-C data

Jorge, É., Foissac, S., Neuvial, P., Zytnicki, M., & Vialaneix, N. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf074 · Cited by 6

The mitotic STAG3–cohesin complex shapes male germline nucleome

Nagano, M., Hu, B., Ogata, K., Umemura, F., Ishikura, Y., Suzuki, S., Katsifis, C. C., Yoshinaga, M., Litos, G., Nagasaka, K., et al. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01647-w · Cited by 6

Hypothesis-driven probabilistic modelling enables a principled perspective of genomic compartments

Kariti, H., Feld, T., & Kaplan, N. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1258 · Cited by 5

Function and regulation of transcription factors during mitosis-to-G1 transition

Soares, M. A. F., Oliveira, R. A., & Castro, D. S. (2022) · Open Biology · doi:10.1098/rsob.220062 · Cited by 7

Repair of DNA double-strand breaks leaves heritable impairment to genome functionPreprint

Bantele, S. C. S., Mordini, I., Biran, A., Alcaraz, N., Wenger, A., Krietenstein, N., Groth, A., & Lukas, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.29.555258 · Cited by 6

Cohesin and CTCF do not assemble TADs inXenopussperm and male pronucleiPreprint

Jessberger, G., Várnai, C., Stocsits, R. R., Tang, W., Stary, G., & Peters, J. (2023) · Genome Research · doi:10.1101/gr.277865.123 · Cited by 6

Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasmPreprint

Schooley, A., Venev, S. V., Aksenova, V., Navarrete, E., Dasso, M., & Dekker, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.16.613305 · Cited by 6

Molecular mechanisms altering cell identity in cancer

Zippo, A., & Beyes, S. (2025) · Oncogene · doi:10.1038/s41388-025-03314-2 · Cited by 5

A comprehensive benchmark of single-cell Hi-C embedding tools

Plummer, D., Lang, X., Zhang, S., Li, Y., Li, J., & Jin, F. (2025) · Nature Communications · doi:10.1038/s41467-025-64186-4 · Cited by 6

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

Chromosome organization through the cell cycle at a glance

Srinivasan, D., Shisode, T., Shrinet, J., & Fraser, P. (2022) · Journal of Cell Science · doi:10.1242/jcs.244004 · Cited by 6

Differential 3D genome architecture and imprinted gene expression: cause or consequence?

Moindrot, B., Imaizumi, Y., & Feil, R. (2024) · Biochemical Society Transactions · doi:10.1042/bst20230143 · Cited by 6

Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformationPreprint

Oomen, M. E., Fox, A. N., González, I., Molliex, A., Papadopoulou, T., Navarro, P., & Dekker, J. (2025) · Genome Research · doi:10.1101/gr.280648.125 · Cited by 5

Human papillomavirus genomes associate with active host chromatin during persistent viral infection

Warburton, A., Markowitz, T. E., Miranda, J. L., Majumder, K., & McBride, A. A. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013454 · Cited by 3

Motif distribution and DNA methylation underlie distinct Cdx2 binding during development and homeostasis

Lorzadeh, A., Ye, G., Sharma, S., & Jadhav, U. (2025) · Nature Communications · doi:10.1038/s41467-025-56187-0 · Cited by 4

Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex

Wang, X., Aboreden, N. G., Cai, Y., Lam, J. C., Henderson, K. A., Xiang, J., Giardine, B. M., Hardison, R. C., Keller, C. A., Nagarajan, L., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.07.012 · Cited by 4

Telomemore enables single-cell analysis of cell cycle and chromatin condensation

Yakovenko, I., Mihai, I. S., Selinger, M., Rosenbaum, W., Dernstedt, A., Gröning, R., Trygg, J., Carroll, L. M., Forsell, M. N. E., & Henriksson, J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf031 · Cited by 4

A Super Enhancer-Derived Enhancer RNA Acts Together with CTCF/Cohesin in Trans to Regulate Erythropoiesis

Xie, B., & Dean, A. (2025) · Genes · doi:10.3390/genes16040389 · Cited by 4

Causality in transcription and genome folding: Insights from X inactivation

Bauer, M., Payer, B., & Filion, G. J. P. (2022) · BioEssays · doi:10.1002/bies.202200105 · Cited by 4

FAIRE‐MS reveals mitotic retention of transcriptional regulators on a proteome‐wide scale

Ye, B., Shen, W., Li, Y., Wang, D., Zhang, Y., Li, P., Yin, M., Wang, Y., Xie, D., Shi, S., et al. (2022) · The FASEB Journal · doi:10.1096/fj.202201038rrr · Cited by 4

Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle

Chu, X., & Wang, J. (2023) · Open Biology · doi:10.1098/rsob.230175 · Cited by 5

The chromatin conformation landscape of Alzheimer’s diseasePreprint

Nativio, R., Lan, Y., Donahue, G. D., Shcherbakova, O., Barnett, N., Titus, K., Chandrashekar, H., Phillips‐Cremins, J. E., Bonini, N. M., & Berger, S. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.09.588722 · Cited by 5

Identification of Two Subsets of Subcompartment A1 Associated with High Transcriptional Activity and Frequent Loop Extrusion

Yin, Z., Cui, S., Xue, S., Xie, Y., Wang, Y., Zhao, C., Zhang, Z., Wu, T., Hou, G., Wang, W., et al. (2023) · Biology · doi:10.3390/biology12081058 · Cited by 3

PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites

Dimond, A., Gim, D. H., Ing‐Simmons, E., Whilding, C., Kramer, H., Djeghloul, D., Montoya, A., Patel, B., Cheriyamkunnel, S. J., Brown, K. E., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63740-4 · Cited by 5

A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion

Polovnikov, K., & Starkov, D. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2534385123 · Cited by 3

Maintaining transcriptional homeostasis during cell cycle

Ramos-Alonso, L., & Chymkowitch, P. (2023) · Transcription · doi:10.1080/21541264.2023.2246868 · Cited by 3

Deciphering the dynamical chromosome structural reorganizations in human neural development

Chu, X., Feng, C., & Wang, J. (2024) · Physical Review Research · doi:10.1103/physrevresearch.6.023309 · Cited by 3

Loop Extrusion Machinery Impairments in Models and Disease

Ryzhkova, A. S., Maltseva, E., Баттулин, Н. Р., & Kabirova, E. (2024) · Cells · doi:10.3390/cells13221896 · Cited by 2

Noncoding function of super enhancer derived Cpox pre-mRNA in modulating neighbouring gene expression and chromatin interactions

Xie, B., & Dean, A. (2025) · RNA Biology · doi:10.1080/15476286.2025.2475421 · Cited by 3

How chromosome topologies get their shape: views from proximity ligation and microscopy methods

Huang, Y., Neijts, R., & de Laat, W. L. (2020) · FEBS Letters · doi:10.1002/1873-3468.13961 · Cited by 3

Remodeling and compaction of the inactive X is regulated by Xist during female B cell activationPreprint

Sierra, I., Nguyen, S. C., Barnett, R. J., Cook, A. L., Ryu, H.-S., Beethem, Z. T., Phillips‐Cremins, J. E., Joyce, E. F., & Anguera, M. C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.19.512821 · Cited by 3

Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancerPreprint

Faseela, E. E., Notani, D., & Sabarinathan, R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.24.563697 · Cited by 3

Re-configuration of Chromatin Structure During the Mitosis-G1 Phase TransitionPreprint

Zhang, H., Emerson, D. J., Gilgenast, T. G., Titus, K. R., Lan, Y., Huang, P., Zhang, D., Wang, H., Keller, C. A., Giardine, B. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/604355 · Cited by 6

Genome folding dynamics during the M-to-G1-phase transition

Zhang, H., & Blobel, G. A. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102036 · Cited by 13

CTCF and transcription influence chromatin structure re-configuration after mitosis

Zhang, H.-Y., Lam, J. C., Zhang, D., Lan, Y., Vermunt, M., Keller, C. A., Giardine, B., Hardison, R., & Blobel, G. (2021) · Nature Communications · doi:10.1038/s41467-021-25418-5 · Cited by 63

Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis

Brunner, A., Morero, N. R., Zhang, W., Hossain, M. J., Lampe, M., Pflaumer, H., Halavatyi, A. A., Peters, J., Beckwith, K. S., & Ellenberg, J. (2024) · The Journal of Cell Biology · doi:10.1083/jcb.202405169 · Cited by 24

High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structurePreprint

Cheng, G., Pratto, F., Brick, K., Li, X., Alleva, B., Huang, M., Lam, K.-W. G., & Camerini‐Otero, R. D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.25.586627 · Cited by 8