Loop extrusion as a mechanism for formation of DNA damage repair foci

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Cohesin Loss Eliminates All Loop Domains

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A compendium of chromatin contact maps reveals spatially active regions in the human genome

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Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins

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DNA loop extrusion by human cohesin

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The cohesin release factor WAPL restricts chromatin loop extension

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Real-time imaging of DNA loop extrusion by condensin

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A dual role of Cohesin in DNA DSB repair

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Genome-wide profiling of DNA repair proteins in single cells

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Recombination-mediated genome rearrangements

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Key molecular DNA damage responses of human cells to radiation

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Cohesin complex oligomerization maintains end-tethering at DNA double-strand breaks

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UV-induced reorganization of 3D genome mediates DNA damage response

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ATM signaling modulates cohesin behavior in meiotic prophase and proliferating cells

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

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Three‐dimensional genome structure and function

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SHMT2 regulates CD8+ T cell senescence via the reactive oxygen species axis in HIV-1 infected patients on antiretroviral therapy

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Impacts of chromatin dynamics and compartmentalization on DNA repair

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Integrative studies of 3D genome organization and chromatin structure

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Chromatin Ubiquitination Guides DNA Double Strand Break Signaling and Repair

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Landscape of Double-Stranded DNA Breaks in Postmortem Brains from Alzheimer’s Disease and Non-Demented Individuals

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DCAF15 control of cohesin dynamics sustains acute myeloid leukemia

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Circadian PERIOD proteins regulate TC-DSB repair through anchoring to the nuclear envelope

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Targeting DNA Repair Response Promotes Immunotherapy in Ovarian Cancer: Rationale and Clinical Application

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Mapping cellular responses to DNA double-strand breaks using CRISPR technologies

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CRISPR screens in sister chromatid cohesion defective cells reveal PAXIP1-PAGR1 as regulator of chromatin association of cohesin

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Subunit-specific analysis of cohesin-mutant myeloid malignancies reveals distinct ontogeny and outcomes

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Recruitment of Scc2/4 to double-strand breaks depends on γH2A and DNA end resection

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3D chromatin structure changes during spermatogenesis and oogenesis

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Organization of replicated chromosomes by DNA loops and sister chromatid cohesion

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Sirt6 promotes DNA damage repair in osteoarthritis chondrocytes by activating the Keap1/Nrf2/HO-1 signaling pathway

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In vitro study to identify ligand‐independent function of estrogen receptor‐α in suppressing DNA damage‐induced chondrocyte senescence

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4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modeling

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DNA End Joining: G0-ing to the Core

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Rewiring cancer: 3D genome determinants of cancer hallmarks

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Cohesin in DNA damage response and double-strand break repair

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Live cell single-molecule imaging to study DNA repair in human cells

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The dynamic role of cohesin in maintaining human genome architecture

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Emerging roles of cohesin-STAG2 in cancer

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The kleisin subunit controls the function of C. elegans meiotic cohesins by determining the mode of DNA binding and differential regulation by SCC-2 and WAPL-1

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Airway epithelial cGAS inhibits LPS-induced acute lung injury through CREB signaling

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RAD21 promotes oncogenesis and lethal progression of prostate cancer

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TRACERx analysis identifies a role for FAT1 in regulating chromosomal instability and whole-genome doubling via Hippo signalling

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The interplay between chromatin remodeling and DNA double-strand break repair: Implications for cancer biology and therapeutics

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Communication between chromatin and homologous recombination

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3D Genome Organization: Causes and Consequences for DNA Damage and Repair

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MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

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PDS5 proteins control genome architecture by limiting the lifetime of cohesin-NIPBL complexes

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DNA break induces rapid transcription repression mediated by proteasome-dependent RNAPII removal

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Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes

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Doxorubicin Changes the Spatial Organization of the Genome around Active Promoters

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New facets in the chromatin-based regulation of genome maintenance

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Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair

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Biomimetic astrocyte cell membrane-fused nanovesicles for protecting neurovascular units in hypoxic ischemic encephalopathy

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

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Effect of iodoacetic acid on the reproductive system of male mice

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Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects

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3D CRISPR screen in prostate cancer cells reveals PARP inhibitor sensitization through TBL1XR1-SMC3 interaction

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The interplay of 3D genome organization with UV-induced DNA damage and repair

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A computational approach to quantifying miscounting of radiation-induced double-strand break immunofluorescent foci

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Cohesin — bridging the gap among gene transcription, genome stability, and human diseases

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Chromatin-centric insights into DNA replication

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Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes

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DNA Damage Response and Repair in Adaptive Immunity

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Nanomedicines enhance minimally invasive therapy of pancreatic cancer

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Locus folding mechanisms determine modes of antigen receptor gene assembly

Allyn, B. M., Hayer, K. E., Oyeniran, C., Nganga, V. K., Lee, K. D., Mishra, B., Saçan, A., Oltz, E. M., & Bassing, C. H. (2023) · The Journal of Experimental Medicine · doi:10.1084/jem.20230985 · Cited by 10

DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity

Raimer, H. M., Hou, P., Bartosik, A. R., Atkin, N. D., Wang, L., Wang, Z., Ratan, A., Zang, C., & Wang, Y. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae164 · Cited by 10

Cells use loop extrusion to weave and tie the genome

Mirny, L. A. (2021) · Nature · doi:10.1038/d41586-021-00351-1 · Cited by 10

Carbon ion radiation and clustered DNA double-strand breaks

Shibata, A. (2022) · The Enzymes · doi:10.1016/bs.enz.2022.08.008 · Cited by 9

Roles of histone post-translational modifications in meiosis

Nie, H., Kong, X., Song, X., Guo, X.-Y., Li, Z., Fan, C., Zhai, B., Yang, X., & Wang, Y. (2024) · Biology of Reproduction · doi:10.1093/biolre/ioae011 · Cited by 9

Transcription‐coupled repair: tangled up in convoluted repair

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Anti-proliferation and apoptosis-inducing effects of dihydroartemisinin on SH-SY5Y cells and metabolomic analysis

Xu, D., Fan, K., Zhang, H., Tang, L.-X., Wang, Y., Xiang, Z., Shi, A.-M., Qu, Y., Su, C., & Pan, J. (2022) · Translational Pediatrics · doi:10.21037/tp-22-331 · Cited by 9

The cohesin complex of yeasts: sister chromatid cohesion and beyond

Choudhary, K., & Kupiec, M. (2022) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuac045 · Cited by 11

Confined Target-Triggered Hot Spots for In Situ SERS Analysis of Intranuclear Genotoxic Markers

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LRRC8A promotes the initial development of oxaliplatin resistance in colon cancer cells

Zhang, H., Jing, Z., Liu, R., Shada, Y., Shria, S., Cui, S., Ren, Y., Wei, Y., Li, L., & Peng, S. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e16872 · Cited by 9

Permeable TAD boundaries and their impact on genome‐associated functions

Chang, L., & Noordermeer, D. (2024) · BioEssays · doi:10.1002/bies.202400137 · Cited by 10

Cohesin positions the epigenetic reader Phf2 within the genome

Tang, W., Costantino, L., Stocsits, R. R., Wutz, G., Ladurner, R., Hudecz, O., Mechtler, K., & Peters, J. (2025) · The EMBO Journal · doi:10.1038/s44318-024-00348-2 · Cited by 9

Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions

Attou, A., Zülske, T., & Wedemann, G. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.10.044 · Cited by 9

Double-strand break repair and mis-repair in 3D

Zagelbaum, J., & Gautier, J. (2022) · DNA repair · doi:10.1016/j.dnarep.2022.103430 · Cited by 9

ATM-dependent formation of a novel chromatin compartment regulates the Response to DNA Double Strand Breaks and the biogenesis of translocationsPreprint

Arnould, C., Rocher, V., Bader, A. S., Lesage, E., Puget, N., Clouaire, T., Mourad, R., Noordermeer, D., Bushell, M., & Legube, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.07.467654 · Cited by 12

Strategies and mechanisms of precision genome engineering: From gene editing to genome writing

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An Expanding Toolkit for Heterochromatin Repair Studies

Rawal, C. C., Butova, N. L., Mitra, A., & Chiolo, I. (2022) · Genes · doi:10.3390/genes13030529 · Cited by 8

ATM Regulation of the Cohesin Complex Is Required for Repression of DNA Replication and Transcription in the Vicinity of DNA Double-Strand Breaks

Bass, T. E., Fleenor, D. E., Burrell, P. E., & Kastan, M. B. (2022) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-22-0399 · Cited by 8

Recipes and ingredients for deep learning models of 3D genome folding

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Multifunctional miR181a nanoparticles promote highly efficient radiotherapy for rectal cancer

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Intrachain Distances in a Crumpled Polymer with Random Loops

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Supercoiled ring polymers under shear flow

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Encounters in Three Dimensions: How Nuclear Topology Shapes Genome Integrity

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Replisomes restrict SMC translocation in vivo

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ATRX cooperates with TOP2B for replication fork stability and DNA damage response through G-quadruplex regulation

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It’s all in the numbers: Cohesin stoichiometry

Matityahu, A., & Onn, I. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1010894 · Cited by 7

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

In vitro dynamics of DNA loop extrusion by structural maintenance of chromosomes complexes

Rutkauskas, M., & Kim, E. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102284 · Cited by 6

Cohesin mutations and chromatin changes in cancer

Swett, A. D., & Tóthová, Z. (2025) · International Journal of Cancer · doi:10.1002/ijc.35378 · Cited by 7

Identification and characterization of eccDNA-driven genes in humans

Gu, Y., Song, Y., & Liu, J. (2025) · PLoS ONE · doi:10.1371/journal.pone.0324438 · Cited by 7

Intranuclear paraspeckle‐circular RNA TACC3 assembly forms RNA‐DNA hybrids to facilitate MASH‐related hepatocellular carcinoma growth in an m 6 A‐dependent manner

Fu, J., Wei, Y., Yang, Y., Yang, X., Ouyang, T., Wang, X., Chen, S., Liu, Z., Su, Y., Fu, J., et al. (2025) · 癌症：英文版 · doi:10.1002/cac2.70061 · Cited by 6

Homologous tumor cell membrane-encapsulated methyl 5-aminolevulinate solid lipid nanoparticles for the precise localization of melanoma and sensitization by radiotherapy

Meng, Y., Chen, S., Li, P., Wang, C., & Ni, X. (2024) · Materials & Design · doi:10.1016/j.matdes.2024.112813 · Cited by 6

Diffusion of activated ATM explains γH2AX and MDC1 spread beyond the DNA damage site

Danovski, G., Panova, G., Keister, B. D., Georgiev, G. S., Atemin, A., Uzunova, S., Stamatov, R., Kanev, P.-B., Aleksandrov, R., Blagoev, K. B., et al. (2024) · iScience · doi:10.1016/j.isci.2024.110826 · Cited by 8

Environmental high temperature affects pre-implantation embryo development by impairing the DNA repair ability

Qu, S.-J., Zhu, S., Wang, E.-Y., Yan, X.-L., Cao, R., Li, H., & Jiang, Z.-L. (2024) · Journal of Thermal Biology · doi:10.1016/j.jtherbio.2024.103968 · Cited by 6

Engineered chromatin readers track damaged chromatin dynamics in live cells and animals

da Silva, R. C., Eleftheriou, K., Recchia, D. C., Portegijs, V., ten Bulte, D., Kupfer, N., Wagenaar, N. P. V.-D., Vergara, X., Ouchene, A., van den Heuvel, S., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65706-y · Cited by 6

Unique territorial and compartmental organization of chromosomes in the holocentric silkworm

Gil, J., Navarrete, E., Hockens, C. B., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Banigan, E. J., Rosin, L. F., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00694-3 · Cited by 7

Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity

Bergis, C., Reji, M., Latrasse, D., Catherine Bergounioux, A., Benhamed, M., & Raynaud, C. (2024) · Nature Plants · doi:10.1038/s41477-024-01678-z · Cited by 6

The organizer of chromatin topology RIF1 ensures cellular resilience to DNA replication stress

Lebdy, R., Patouillard, J., Larroque, M., Urbach, S., Merhi, R. A., Larroque, C., & Ribeyre, C. (2023) · Life Science Alliance · doi:10.26508/lsa.202101186 · Cited by 6

Hypermethylation of Bmp2 and Fgfr2 Promoter Regions in Bone Marrow Mesenchymal Stem Cells Leads to Bone Loss in Prematurely Aged Mice

Wang, Y., Sun, L., Kan, T., Xue, W., Wang, H., Xu, P., Zhang, L., Yan, M., Li, H., & Yu, Z. (2024) · Aging and Disease · doi:10.14336/ad.2024.0324 · Cited by 5

Interplay and Dynamics of Chromatin Architecture and DNA Damage Response: An Overview

Ambrosio, S., Noviello, A., Fusco, G. D., Gorini, F., Piscone, A., Amente, S., & Majello, B. (2025) · Cancers · doi:10.3390/cancers17060949 · Cited by 8

Liquid condensates: a new barrier to loop extrusion?

Selivanovskiy, A. V., Molodova, M. N., Khrameeva, E. E., Ulianov, S. V., & Razin, S. V. (2025) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05559-8 · Cited by 6

Genome stability‑related lncRNA ZFPM2‑AS1 promotes tumor progression via miR‑3065‑5p/XRCC4 in hepatocellular carcinoma

Liu, J., Zhang, H., Xia, P., Zhu, Y., Xu, K., Liu, Z., & Yuan, Y. (2022) · International Journal of Oncology · doi:10.3892/ijo.2022.5467 · Cited by 5

Rôle de l'organisation 3D de la chromatine dans la réparation des cassures double-brin de l'ADN

Arnould, C. (2020) · theses.fr (ABES) · doi:10.70675/4c5bbc73z2562z44a9z8aecz49a1e882e5ef

The complexity of phosphorylated H2AX foci formation and DNA repair assembly at DNA double-strand breaks

Nakamura, A., Rao, V. A., Pommier, Y. G., & Bonner, W. M. (2010) · Cell Cycle · doi:10.4161/cc.9.2.10475 · Cited by 162

The role of 3D genome architecture in double-strand break repair

Marín-González, A., Rybczynski, A. T., Zou, R. S., & Ha, T. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2023.11.1457

ATM-dependent formation of a novel chromatin compartment regulates the Response to DNA Double Strand Breaks and the biogenesis of translocationsPreprint

Arnould, C., Rocher, V., Bader, A. S., Lesage, E., Puget, N., Clouaire, T., Mourad, R., Noordermeer, D., Bushell, M., & Legube, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.07.467654 · Cited by 12

Diffusion of activated ATM explains γH2AX and MDC1 spread beyond the DNA damage site

Danovski, G., Panova, G., Keister, B. D., Georgiev, G. S., Atemin, A., Uzunova, S., Stamatov, R., Kanev, P.-B., Aleksandrov, R., Blagoev, K. B., et al. (2024) · iScience · doi:10.1016/j.isci.2024.110826 · Cited by 8