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

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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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Histone post-translational modifications - cause and consequence of genome function

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Metabolic regulation of homologous recombination repair by MRE11 lactylation

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Genome folding through loop extrusion by SMC complexes

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Human topoisomerases and their roles in genome stability and organization

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Cohesin and CTCF control the dynamics of chromosome folding

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Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases

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Transcription shapes 3D chromatin organization by interacting with loop extrusion

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Chromatin compartmentalization regulates the response to DNA damage

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Meiosis: Dances Between Homologs

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Genome control by SMC complexes

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Radiation-induced DNA damage and repair effects on 3D genome organization

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Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

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ATM’s Role in the Repair of DNA Double-Strand Breaks

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Cohesin regulates homology search during recombinational DNA repair

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The chromosome folding problem and how cells solve it

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The role of chromatin loop extrusion in antibody diversification

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Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open QuestionsPreprint

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Biomolecular condensates at sites of DNA damage: More than just a phase

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Looping the Genome with SMC Complexes

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Chromosome Organization in Early Meiotic Prophase

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DNA Damage Clustering after Ionizing Radiation and Consequences in the Processing of Chromatin Breaks

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Computational methods for analysing multiscale 3D genome organization

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DNA-loop-extruding SMC complexes can traverse one another in vivo

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

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TADs: Dynamic structures to create stable regulatory functions

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Meiotic sex chromosome inactivation and the XY body: a phase separation hypothesis

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Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks

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Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops

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A walk through the SMC cycle: From catching DNAs to shaping the genome

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Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization

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DNA double-strand break–capturing nuclear envelope tubules drive DNA repair

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Chromatin jets define the properties of cohesin-driven in vivo loop extrusion.

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Nuclear and genome dynamics underlying DNA double-strand break repair

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Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience

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ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response

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Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review)

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Histone H2A variants: Diversifying chromatin to ensure genome integrity

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Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

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Determining chromatin architecture with Micro Capture-C

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The multifaceted roles of cohesin in cancer

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Histone Variants: Guardians of Genome Integrity

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NIPBL and cohesin: new take on a classic tale

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Full circle: a brief history of cohesin and the regulation of gene expression

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Multifunctional histone variants in genome function

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Spatial Features and Functional Implications of Plant 3D Genome Organization

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DNA damage and its links to neuronal aging and degeneration

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Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair

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The DNA damage response in the chromatin context: A coordinated process

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Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites

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Role of condensates in modulating DNA repair pathways and its implication for chemoresistance

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Cellular senescence in cancer: molecular mechanisms and therapeutic targets

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Untangling the crosstalk between BRCA1 and R-loops during DNA repair

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Yeast ATM and ATR kinases use different mechanisms to spread histone H2A phosphorylation around a DNA double-strand break

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MYC-Induced Replicative Stress: A Double-Edged Sword for Cancer Development and Treatment

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Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs

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SMC motor proteins extrude DNA asymmetrically and can switch directions

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Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function

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Structural variants in the 3D genome as drivers of disease

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A Paradigm Revolution or Just Better Resolution—Will Newly Emerging Superresolution Techniques Identify Chromatin Architecture as a Key Factor in Radiation-Induced DNA Damage and Repair Regulation?

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ATM–ESCO2–SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex

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DNA double-strand break end synapsis by DNA loop extrusion

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Dynamic histone modification patterns coordinating DNA processes

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Changes in DNA repair compartments and cohesin loss promote DNA damage accumulation in aged oocytes

Sharma, N., Coticchio, G., Borini, A., Tachibana, K.-E. K., Nasmyth, K., & Schuh, M. (2024) · Current Biology · doi:10.1016/j.cub.2024.09.040 · Cited by 41

DNA Repair in Space and Time: Safeguarding the Genome with the Cohesin Complex

Phipps, J., & Dubrana, K. (2022) · Genes · doi:10.3390/genes13020198 · Cited by 36

Cohesin maintains replication timing to suppress DNA damage on cancer genes

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DNA methylation and histone variants in aging and cancer

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The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks

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Protective effect of total flavonoids of Engelhardia roxburghiana Wall. leaves against radiation-induced intestinal injury in mice and its mechanism

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

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Principles of chromosome organization for meiotic recombination

Biot, M., Tóth, A., Brun, C., Guichard, L., de Massy, B., & Grey, C. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.04.001 · Cited by 32

Histone and Chromatin Dynamics Facilitating DNA repair

Mohan, C., Das, C., & Tyler, J. K. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103183 · Cited by 35

Double-strand break toxicity is chromatin context independent

Friskes, A., Koob, L., Krenning, L., Severson, T., Koeleman, E. S., Vergara, X., Schubert, M., van den Berg, J., Evers, B., Manjón, A. G., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac758 · Cited by 32

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

A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH

Jia, B. B., Jussila, A., Kern, C., Zhu, Q., & Ren, B. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01568-9 · Cited by 30

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

A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress

Moeglin, É., Desplancq, D., Stoessel, A., Massute, C., Ranniger, J., McEwen, A. G., Zeder‐Lutz, G., Oulad‐Abdelghani, M., Chiper, M., Lafaye, P. J., et al. (2021) · Cancers · doi:10.3390/cancers13133317 · Cited by 31

DNA Double-Strand Break Repair: All Roads Lead to HeterochROMAtin Marks

Caron, P., Pobega, E., & Polo, S. E. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.730696 · Cited by 34

CTCF: A misguided jack-of-all-trades in cancer cells

Segueni, J., & Noordermeer, D. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.05.044 · Cited by 31

Compartmentalization of the DNA damage response: Mechanisms and functions

Alghoul, E., Basbous, J., & Constantinou, A. (2023) · DNA repair · doi:10.1016/j.dnarep.2023.103524 · Cited by 30

CircCDYL2 bolsters radiotherapy resistance in nasopharyngeal carcinoma by promoting RAD51 translation initiation for enhanced homologous recombination repair

Qu, H., Wang, Y., Yan, Q., Fan, C., Zhang, X., Wang, D., Guo, C., Chen, P., Shi, L., Liao, Q., et al. (2024) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-024-03049-0 · Cited by 28

Sister chromatid cohesion halts DNA loop expansion

Bastié, N., Chapard, C., Cournac, A., Nejmi, S., Mboumba, H., Gadal, O., Thierry, A., Beckouët, F., & Koszul, R. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.004 · Cited by 27

Nucleotide excision repair of aflatoxin-induced DNA damage within the 3D human genome organization

Wu, Y., Adeel, M. M., Xia, D., Sancar, A., & Li, W. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae755 · Cited by 28

D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogramming

Lang, F., Kaur, K., Fu, H., Zaheer, J., Ribeiro, D. L., Aladjem, M. I., & Yang, C. (2025) · Nature Communications · doi:10.1038/s41467-025-56781-2 · Cited by 27

Integration of DNA damage responses with dynamic spatial genome organization

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Cohesin drives chromatin scanning during the RAD51-mediated homology search

Marín-González, A., Rybczynski, A. T., Nilavar, N. M., Nguyen, D., Karwacki-Neisius, V., Li, A. G., Zou, R. S., Avilés-Vázquez, F. J., Kanemaki, M. T., Scully, R., et al. (2025) · Science · doi:10.1126/science.adw1928 · Cited by 34

Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory

Abdulla, A. Z., Vaillant, C., & Jost, D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac702 · Cited by 26

Cohesin guides homology search during DNA repair using loops and sister chromatid linkages

Teloni, F., Takács, Z., Mitter, M., Langer, C. C. H., Prlesi, I., Steinacker, T. L., Reuter, V. P., Mylarshchikov, D. E., & Gerlich, D. W. (2025) · Science · doi:10.1126/science.adw0566 · Cited by 28

The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination

Libri, A., Marton, T., & Deriano, L. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.823943 · Cited by 28

Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome

Fernández, F. G., Almayrac, E., Simon, À. C., Batrin, R., Khalil, Y., Boissac, M., & Fabre, E. (2022) · eLife · doi:10.7554/elife.78015 · Cited by 27

Function and Evolution of the Loop Extrusion Machinery in Animals

Kabirova, E., Nurislamov, A. R., Shadskiy, A., Smirnov, A. V., Popov, A., Salnikov, P., Баттулин, Н. Р., & Fishman, V. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24055017 · Cited by 27

DNA-PKcs suppresses illegitimate chromosome rearrangements

Wang, J., Sadeghi, C., & Frock, R. L. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae140 · Cited by 26

The SMC5/6 complex: folding chromosomes back into shape when genomes take a break

Roy, S., Adhikary, H., & D’Amours, D. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae103 · Cited by 24

Chromatin remodeling and spatial concerns in DNA double-strand break repair

Downs, J. A., & Gasser, S. M. (2024) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2024.102405 · Cited by 23

Mechanism for local attenuation of DNA replication at double-strand breaks

Sebastian, R., Sun, E. G., Fedkenheuer, M., Fu, H., Jung, S., Thakur, B. L., Redon, C. E., Pegoraro, G., Tran, A. D., Gross, J., et al. (2025) · Nature · doi:10.1038/s41586-024-08557-9 · Cited by 22

Multi-scale dynamics of heterochromatin repair

Merigliano, C., & Chiolo, I. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.09.007 · Cited by 22

FLASH-RT does not affect chromosome translocations and junction structures beyond that of CONV-RT dose-rates

Barghouth, P. G., Melemenidis, S., Montay‐Gruel, P., Ollivier, J., Viswanathan, V., Jorge, P. G., Soto, L. A. C., Lau, B. C., Sadeghi, C., Edlabadkar, A., et al. (2023) · Radiotherapy and Oncology · doi:10.1016/j.radonc.2023.109906 · Cited by 23

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

Focused Ion Microbeam Irradiation Induces Clustering of DNA Double-Strand Breaks in Heterochromatin Visualized by Nanoscale-Resolution Electron Microscopy

Lorat, Y., Reindl, J., Isermann, A., Rübe, C., Friedl, A. A., & Rübe, C. E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147638 · Cited by 21

A graph neural network-based interpretable framework reveals a novel DNA fragility–associated chromatin structural unit

Sun, Y., Xu, X., Lin, L., Xu, K., Zheng, Y., Ren, C., Tao, H., Wang, X., Zhao, H., Tu, W.-W., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02916-x · Cited by 21

Transcription induces context-dependent remodeling of chromatin architecture during differentiation

Chahar, S., Zouari, Y. B., Salari, H., Molitor, A. M., Kobi, D., Maroquenne, M., Erb, C., Mossler, A., Karasu, N., Jost, D., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002424 · Cited by 19

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