4D Genome Rewiring during Oncogene-Induced and Replicative Senescence
Open accessAbstract
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replicative senescence (RS) or upon oncogene-induced senescence (OIS). We identify senescence-associated heterochromatin domains (SAHDs). Differential intra- versus inter-SAHD interactions lead to the formation of senescence-associated heterochromatin foci (SAHFs) in OIS but not in RS. This OIS-specific configuration brings active genes located in genomic regions adjacent to SAHDs in close spatial proximity and favors their expression. We also identify DNMT1 as a factor that induces SAHFs by promoting HMGA2 expression. Upon DNMT1 depletion, OIS cells transition to a 3D genome conformation akin to that of cells in replicative senescence. These data show how multi-omics and imaging can identify critical features of RS and OIS and discover determinants of acute senescence and SAHF formation.
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Recent advances in 3D DNA FISH such as OligoSTORM can be used to study local changes in the 3D structure of senescent chromosomes in individual cells identified by genomic techniques such as Hi-C.
“Recent advances in 3D DNA FISH such as OligoSTORM can also be used to study, in more detail, local changes in the 3D structure of senescent chromosomes in individual cells that have been identified by genomic techniques such as high-throughput chromosome conformation capture (Hi-C)40,41.”
From Spatial mapping of cellular senescence: emerging challenges and opportunities (2023) · cites this paper as [41]
The Introduction and Results describe using oligopaint-based 3D DNA FISH alongside Hi-C to examine chromosome organization in senescent cells. The paper does not identify its method as OligoSTORM: the Methods describe confocal imaging, so it supports the combined approach but not that specific example. (LLM, conf=0.85)
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Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890 · see citing works
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108 · see citing works
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 · see citing works
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 · see citing works
The serial cultivation of human diploid cell strains
Hayflick, L., & Moorhead, P. S. (1961) · Experimental Cell Research · doi:10.1016/0014-4827(61)90192-6 · Cited by 8,508 · see citing works
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 · see citing works
The limited in vitro lifetime of human diploid cell strains
Hayflick, L. (1965) · Experimental Cell Research · doi:10.1016/0014-4827(65)90211-9 · Cited by 5,876 · see citing works
Oncogenic ras provokes premature cell senescence associated with accumulation of p53 and p16INK4a
Serrano, M., Lin, A. W., McCurrach, M. E., Beach, D., & Lowe, S. W. (1997) · Cell · doi:10.1016/s0092-8674(00)81902-9 · Cited by 5,178 · cited 1× · see citing works
“Subsequently, it was observed in primary cells in response to oncogene activation, and, in that case, it was named oncogene-induced senescence (OIS) (Serrano et al., 1997).”
BackgroundCellular senescence: when bad things happen to good cells
Campisi, J., & d'Adda di Fagagna, F. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2233 · Cited by 4,441 · see citing works
Cellular Senescence: Defining a Path Forward
Gorgoulis, V., Adams, P. D., Alimonti, A., Bennett, D. C., Bischof, O., Bishop, C., Campisi, J., Collado, M., Evangelou, K., Ferbeyre, G., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.005 · Cited by 3,225 · cited 4× · see citing works
“Since most of the SASP genes fall in the immune response pathways and play a vital role in senescence, we mapped their expression profiles 534 Molecular Cell 78, 522–538, May 7, 2020 across all samples.”
BackgroundInfluentialAging, Cellular Senescence, and Cancer
Campisi, J. (2013) · Annual Review of Physiology · doi:10.1146/annurev-physiol-030212-183653 · Cited by 2,954 · cited 4× · see citing works
“Since most of the SASP genes fall in the immune response pathways and play a vital role in senescence, we mapped their expression profiles 534 Molecular Cell 78, 522–538, May 7, 2020 across all samples.”
BackgroundInfluentialSpatial 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 · see citing works
Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence
Narita, M., Nuñez, S., Heard, E., Narita, M., Lin, A. W., Hearn, S. A., Spector, D. L., Hannon, G. J., & Lowe, S. W. (2003) · Cell · doi:10.1016/s0092-8674(03)00401-x · Cited by 2,278 · see citing works
Oncogene-Induced Senescence Relayed by an Interleukin-Dependent Inflammatory Network
Kuilman, T., Michaloglou, C., Vredeveld, L. C. W., Douma, S., van Doorn, R., Desmet, C. J., Aarden, L. A., Mooi, W. J., & Peeper, D. S. (2008) · Cell · doi:10.1016/j.cell.2008.03.039 · Cited by 2,086 · see citing works
Three-dimensional folding and functional organization principles of the Drosophila genome
Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012) · Cell · doi:10.1016/j.cell.2012.01.010 · Cited by 1,983 · see citing works
Self-citationPhase separation drives heterochromatin domain formation
Strom, A. R., Emelyanov, A. V., Mir, M., Fyodorov, D. V., Darzacq, X., & Karpen, G. H. (2017) · Nature · doi:10.1038/nature22989 · Cited by 1,813 · see citing works
Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin
Larson, A. G., Elnatan, D., Keenen, M. M., Trnka, M., Johnston, J. B., Burlingame, A., Agard, D., Redding, S., & Narlikar, G. J. (2017) · Nature · doi:10.1038/nature22822 · Cited by 1,554 · see citing works
Programmed cell senescence during mammalian embryonic development
Muñoz-Espín, D., Cañamero, M., Maraver, A., Gómez-López, G., Contreras, J., Murillo-Cuesta, S., Rodríguez-Baeza, A., Varela-Nieto, I., Ruberte, J., Collado, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.019 · Cited by 1,428 · see citing works
Multiscale 3D Genome Rewiring during Mouse Neural Development
Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.043 · Cited by 1,338 · cited 5× · see citing works
“Identification of A and B Compartments TADs were assigned to either the A or the B compartment as described (Bonev et al., 2017; Nagano et al., 2017).”
BackgroundMethodInfluentialSelf-citationSenescence is a developmental mechanism that contributes to embryonic growth and patterning
Storer, M., Mas, A., Robert-Moreno, A., Pecoraro, M., Ortells, M. C., Di Giacomo, V., Yosef, R., Pilpel, N., Krizhanovsky, V., Sharpe, J., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.041 · Cited by 1,186 · see citing works
Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174 · see citing works
Self-citationA Senescence Program Controlled by p53 and p16INK4a Contributes to the Outcome of Cancer Therapy
Schmitt, C. A., Fridman, J. S., Yang, M., Lee, S., Baranov, E., Hoffman, R. M., & Lowe, S. W. (2002) · Cell · doi:10.1016/s0092-8674(02)00734-1 · Cited by 1,050 · see citing works
Unmasking Transcriptional Heterogeneity in Senescent Cells
Hernandez-Segura, A., de Jong, T. V., Melov, S., Guryev, V., Campisi, J., & Demaria, M. (2017) · Current Biology · doi:10.1016/j.cub.2017.07.033 · Cited by 972 · cited 1× · see citing works
“, which are concordant with previously published GO analysis (Table S5) (Hernandez-Segura et al., 2017).”
ResultCell-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 · see citing works
Single-Cell Dynamics of Genome-Nuclear Lamina Interactions
Kind, J., Pagie, L., Ortabozkoyun, H., Boyle, S., de Vries, S., Janssen, H., Amendola, M., Nolen, L. D., Bickmore, W. A., & van Steensel, B. (2013) · Cell · doi:10.1016/j.cell.2013.02.028 · Cited by 716 · see citing works
A novel role for high-mobility group A proteins in cellular senescence and heterochromatin formation
Narita, M., Narita, M., Krizhanovsky, V., Nuñez, S., Chicas, A., Hearn, S. A., Myers, M. P., & Lowe, S. W. (2006) · Cell · doi:10.1016/j.cell.2006.05.052 · Cited by 629 · see citing works
Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state
Lapasset, L., Milhavet, O., Prieur, A., Besnard, E., Babled, A., Aït-Hamou, N., Leschik, J., Pellestor, F., Ramirez, J.-M., De Vos, J., et al. (2011) · Genes & Development · doi:10.1101/gad.173922.111 · Cited by 570 · see citing works
Self-citationShah, P. P., Donahue, G., Otte, G. L., Capell, B. C., Nelson, D. M., Cao, K., Aggarwala, V., Cruickshanks, H. A., Rai, T. S., McBryan, T., et al. (2013) · Genes & Development · doi:10.1101/gad.223834.113 · Cited by 550 · see citing works
Sun, Y., Zheng, Y., Wang, C., & Liu, Y. (2018) · Cell Death and Disease · doi:10.1038/s41419-018-0794-4 · Cited by 550 · see citing works
De Cecco, M., Criscione, S. W., Peckham, E. J., Hillenmeyer, S., Hamm, E. A., Manivannan, J., Peterson, A. L., Kreiling, J. A., Neretti, N., & Sedivy, J. M. (2013) · Aging Cell · doi:10.1111/acel.12047 · Cited by 459 · see citing works
Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
Bantignies, F., Roure, V., Comet, I., Leblanc, B., Schuettengruber, B., Bonnet, J., Tixier, V., Mas, A., & Cavalli, G. (2011) · Cell · doi:10.1016/j.cell.2010.12.026 · Cited by 429 · see citing works
Self-citationModeling epigenome folding: formation and dynamics of topologically associated chromatin domains
Jost, D., Carrivain, P., Cavalli, G., & Vaillant, C. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku698 · Cited by 425 · see citing works
Self-citationRecurrent turnover of senescent cells during regeneration of a complex structure
Yun, M. H., Davaapil, H., & Brockes, J. P. (2015) · eLife · doi:10.7554/elife.05505 · Cited by 385 · see citing works
Beliveau, B. J., Boettiger, A. N., Avendaño, M. S., Jungmann, R., McCole, R. B., Joyce, E. F., Kim-Kiselak, C., Bantignies, F., Fonseka, C. Y., Erceg, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms8147 · Cited by 384 · see citing works
Self-citationInterplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer
Di Micco, R., Sulli, G., Dobreva, M., Liontos, M., Botrugno, O. A., Gargiulo, G., dal Zuffo, R., Matti, V., d'Ario, G., Montani, E., et al. (2011) · Nature Cell Biology · doi:10.1038/ncb2170 · Cited by 382 · see citing works
Senescent cells harbour features of the cancer epigenome
Cruickshanks, H. A., McBryan, T., Nelson, D. M., VanderKraats, N. D., Shah, P. P., van Tuyn, J., Singh Rai, T., Brock, C., Donahue, G., Dunican, D. S., et al. (2013) · Nature Cell Biology · doi:10.1038/ncb2879 · Cited by 358 · see citing works
Global reorganization of the nuclear landscape in senescent cells
Chandra, T., Ewels, P. A., Schoenfelder, S., Furlan-Magaril, M., Wingett, S. W., Kirschner, K., Thuret, J.-Y., Andrews, S., Fraser, P., & Reik, W. (2015) · Cell Reports · doi:10.1016/j.celrep.2014.12.055 · Cited by 348 · see citing works
Sadaie, M., Salama, R., Carroll, T., Tomimatsu, K., Chandra, T., Young, A. R. J., Narita, M., Pérez-Mancera, P. A., Bennett, D. C., Chong, H., et al. (2013) · Genes & Development · doi:10.1101/gad.217281.113 · Cited by 323 · see citing works
The Human Epigenome Browser at Washington University
Zhou, X., Maricque, B. B., Xie, M., Li, D., Sundaram, V., Martin, E. A., Koebbe, B. C., Nielsen, C. B., Hirst, M., Farnham, P., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1772 · Cited by 309 · see citing works
Chandra, T., Kirschner, K., Thuret, J.-Y., Pope, B. D., Ryba, T., Newman, S., Ahmed, K., Samarajiwa, S. A., Salama, R., Carroll, T., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.010 · Cited by 308 · see citing works
Self-citationSerra, F., Baù, D., Goodstadt, M. N., Castillo, D., Filion, G. J. P., & Martı́-Renom, M. A. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005665 · Cited by 295 · see citing works
Self-citationThe three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules
Baù, D., Sanyal, A., Lajoie, B. R., Capriotti, E., Byron, M., Lawrence, J. B., Dekker, J., & Martı́-Renom, M. A. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1936 · Cited by 267 · see citing works
Robust, universal biomarker assay to detect senescent cells in biological specimens
Evangelou, K., Lougiakis, N., Rizou, S. V., Kotsinas, A., Kletsas, D., Muñoz‐Espín, D., Kastrinakis, N. G., Pouli, N., Marakos, P., Townsend, P., et al. (2017) · Aging Cell · doi:10.1111/acel.12545 · Cited by 259 · cited 1× · see citing works
“Since senescence has been described in vivo in certain physiological conditions, it will be interesting to study in vivo cell senescence (Evangelou et al., 2017) and to compare them with our results.”
ResultSwanson, E. C., Manning, B., Zhang, H., & Lawrence, J. B. (2013) · Journal of Cell Biology · doi:10.1083/jcb.201306073 · Cited by 251 · cited 1× · see citing works
“RS nuclei on the other hand are enlarged and display a variety of features, ranging from compaction of individual chromosome arms to distension of peri-centromeric regions (Cruickshanks et al., 2013; De Cecco et al., 2013; Swanson et al., 2013).”
BackgroundCremer, T., Cremer, M., Hübner, B., Strickfaden, H., Smeets, D., Popken, J., Sterr, M., Markaki, Y., Rippe, K., & Cremer, C. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.05.037 · Cited by 246 · see citing works
Lucas, J., Zhang, Y., Dudko, O. K., & Murre, C. (2014) · Cell · doi:10.1016/j.cell.2014.05.036 · Cited by 239 · see citing works
Lamins Organize the Global Three-Dimensional Genome from the Nuclear Periphery
Zheng, X., Hu, J., Yue, S., Kristiani, L., Kim, M., Sauria, M. E. G., Taylor, J., Kim, Y., & Zheng, Y. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.017 · Cited by 238 · see citing works
Zirkel, A., Nikolic, M., Sofiadis, K., Mallm, J.-P., Brackley, C. A., Gothe, H., Drechsel, O., Becker, C., Altmüller, J., Josipovic, N., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.030 · Cited by 226 · see citing works
Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II
Nagashima, R., Hibino, K., Ashwin, S. S., Babokhov, M., Fujishiro, S., Imai, R., Nozaki, T., Tamura, S., Tani, T., Kimurâ, H., et al. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201811090 · Cited by 219 · see citing works
Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes
Becker, J. S., McCarthy, R. L., Sidoli, S., Donahue, G., Kaeding, K. E., He, Z., Lin, S., Garcia, B. A., & Zaret, K. S. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.030 · Cited by 210 · see citing works
Exploring long-range genome interactions using the WashU Epigenome Browser
Zhou, X., Lowdon, R. F., Li, D., Lawson, H. A., Madden, P. A. F., Costello, J., & Wang, T. (2013) · Nature Methods · doi:10.1038/nmeth.2440 · Cited by 209 · see citing works
Stabilization of chromatin topology safeguards genome integrity
Ochs, F., Karemore, G., Miron, E., Brown, J. M., Polášek-Sedláčková, H., Rask, M., Lampe, M., Buckle, V. J., Schermelleh, L., Lukas, J., et al. (2019) · Nature · doi:10.1038/s41586-019-1659-4 · Cited by 202 · see citing works
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Lun, A. T. L., & Smyth, G. K. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0683-0 · Cited by 199 · see citing works
Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq
Marchal, C., Sasaki, T., Vera, D. L., Wilson, K. A., Sima, J., Rivera‐Mulia, J. C., Trevilla‐García, C., Nogues, C., Nafie, E. H. O., & Gilbert, D. M. (2018) · Nature Protocols · doi:10.1038/nprot.2017.148 · Cited by 190 · see citing works
Self-citationNuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program
Foti, R., Gnan, S., Cornacchia, D., Dileep, V., Bulut-Karslıoğlu, A., Diehl, S., Buneß, A., Klein, F. A., Huber, W. K., Johnstone, E. R., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.12.001 · Cited by 189 · see citing works
Self-citationChromosome conformation capture technologies and their impact in understanding genome function
Sati, S., & Cavalli, G. (2016) · Chromosoma · doi:10.1007/s00412-016-0593-6 · Cited by 181 · see citing works
Self-citationReorganization of chromosome architecture in replicative cellular senescence
Criscione, S. W., De Cecco, M., Siranosian, B., Zhang, Y., Kreiling, J. A., Sedivy, J. M., & Neretti, N. (2016) · Science Advances · doi:10.1126/sciadv.1500882 · Cited by 164 · see citing works
Determinants of histone H1 mobility and chromatin binding in living cells
Catez, F., Ueda, T., & Bustin, M. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1077 · Cited by 153 · see citing works
HMGA proteins as modulators of chromatin structure during transcriptional activation
Öztürk, N., Singh, I., Mehta, A., Braun, T. W., & Barreto, G. (2014) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2014.00005 · Cited by 153 · see citing works
A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly
Canzio, D., Liao, M., Naber, N. I., Pate, E., Larson, A. G., Wu, S., Marina, D. B., Garcia, J. F., Madhani, H. D., Cooke, R., et al. (2013) · Nature · doi:10.1038/nature12032 · Cited by 149 · see citing works
Promoter bivalency favors an open chromatin architecture in embryonic stem cells
Martín, G. M., Blanco, E., Ballaré, C., Sansó, M., Spill, Y. G., Hu, D., Aoi, Y., Dily, F. L., Shilatifard, A., Martı́-Renom, M. A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0218-5 · Cited by 148 · see citing works
Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
Olivares‐Chauvet, P., Mukamel, Z., Lifshitz, A., Schwartzman, O., Elkayam, N. O., Lubling, Y., Deikus, G. Y., Sebra, R., & Tanay, A. (2016) · Nature · doi:10.1038/nature20158 · Cited by 141 · see citing works
Nelson, D. M., Jaber‐Hijazi, F., Cole, J. J., Robertson, N., Pawlikowski, J. S., Norris, K., Criscione, S. W., Pchelintsev, N. A., Piscitello, D., Stong, N., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1017-x · Cited by 106 · see citing works
Ryba, T., Battaglia, D., Chang, B. H., Shirley, J. W., Buckley, Q., Pope, B. D., Devidas, M., Druker, B. J., & Gilbert, D. M. (2012) · Genome Research · doi:10.1101/gr.138511.112 · Cited by 99 · see citing works
Self-citationGenome structure determination via 3C-based data integration by the Integrative Modeling Platform
Baù, D., & Martı́-Renom, M. A. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.004 · Cited by 95 · see citing works
Ghosh, S. K., & Jost, D. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006159 · Cited by 91 · see citing works
Self-citationMassive reshaping of genome-nuclear lamina interactions during oncogene-induced senescence.
Lenain, C., de Graaf, C. A., Pagie, L., Visser, N. L., de Haas, M., de Vries, S. S., Peric-Hupkes, D., van Steensel, B., & Peeper, D. S. (2017) · Genome Research · doi:10.1101/gr.225763.117 · Cited by 89 · see citing works
Polymer Modeling Predicts Chromosome Reorganization in Senescence
Chiang, M., Michieletto, D., Brackley, C. A., Rattanavirotkul, N., Mohammed, H., Marenduzzo, D., & Chandra, T. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.08.045 · Cited by 77 · see citing works
Parallel pathways in RAF-induced senescence and conditions for its reversion
Jeanblanc, M., Ragu, S., Gey, C., Contrepois, K., Courbeyrette, R., Thuret, J., & Mann, C. (2011) · Oncogene · doi:10.1038/onc.2011.481 · Cited by 69 · see citing works
Giri, S., Aggarwal, V., Pontis, J., Shen, Z., Chakraborty, A., Khan, A. A., Mizzen, C. A., Prasanth, K. V., Ait‐Si‐Ali, S., Ha, T., et al. (2015) · eLife · doi:10.7554/elife.06496 · Cited by 50 · see citing works
Deacetylation of H4-K16Ac and heterochromatin assembly in senescence
Contrepois, K., Thuret, J., Courbeyrette, R., Fenaille, F., & Mann, C. (2012) · Epigenetics & Chromatin · doi:10.1186/1756-8935-5-15 · Cited by 49 · see citing works
Ito, S., Magalska, A., Alcaraz-Iborra, M., López-Atalaya, J., Rovira, V., Contreras-Moreira, B., Lipiński, M., Olivares, R., Martínez-Hernández, J., Ruszczycki, B., et al. (2014) · Nature Communications · doi:10.1038/ncomms5450 · Cited by 40 · see citing works
Inactivation of AKT Induces Cellular Senescence in Uterine Leiomyoma
Xu, X., Lu, Z., Qiang, W., Vidimar, V., Kong, B., Kim, J. J., & Wei, J. (2014) · Endocrinology · doi:10.1210/en.2013-1929 · Cited by 39 · see citing works
The folding landscape of the epigenome
Olarte-Plata, J. D., Haddad, N., Vaillant, C., & Jost, D. (2016) · Physical Biology · doi:10.1088/1478-3975/13/2/026001 · Cited by 38 · see citing works
Self-citationThe Dimerization State of the Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2)
Frost, L., Baez, M. A. M., Harrilal, C., Garabedian, A., Fernandez-Lima, F. A., & Leng, F. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130478 · Cited by 28 · see citing works
Glucocorticoids delay RAF-induced senescence promoted by EGR1
Carvalho, C., L'hôte, V., Courbeyrette, R., Kratassiouk, G., Pinna, G., Cintrat, J., Denby-Wilkes, C., Derbois, C., Olaso, R., Deleuze, J., et al. (2019) · Journal of Cell Science · doi:10.1242/jcs.230748 · Cited by 24 · see citing works
Remodeling of nuclear architecture by the thiodioxoxpiperazine metabolite chaetocin
Illner, D., Zinner, R., Handtke, V., Rouquette, J., Strickfaden, H., Lanctôt, C., Conrad, M., Seiler, A., Imhof, A., Cremer, T., et al. (2010) · Experimental Cell Research · doi:10.1016/j.yexcr.2010.03.008 · Cited by 23 · see citing works
HMGA2 is regulated by LIN28 and BRCA1 in human placental cells†
West, R. C., McWhorter, E. S., Ali, A., Goetzmann, L. N., Russ, J. E., Gonzalez-Berrios, C. L., Anthony, R. V., Bouma, G. J., & Winger, Q. A. (2018) · Biology of Reproduction · doi:10.1093/biolre/ioy183 · Cited by 17 · see citing works
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Hallmarks of aging: An expanding universe
López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M., & Kroemer, G. (2023) · Cell · doi:10.1016/j.cell.2022.11.001 · Cited by 6,549 · see citing works
The Self-Organizing Genome: Principles of Genome Architecture and Function
Misteli, T. (2020) · Cell · doi:10.1016/j.cell.2020.09.014 · Cited by 706 · see citing works
Bao, H., Cao, J., Chen, M., Min, C., Chen, W., Chen, X., Chen, Y., Chen, Y., Chen, Y., Chen, Z., et al. (2023) · Science China Life Sciences · doi:10.1007/s11427-023-2305-0 · Cited by 389 · see citing works
Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
Johnstone, S. E., Reyes, A., Qi, Y., Adriaens, C., Hegazi, E., Pelka, K., Chen, J. H., Zou, L. S., Drier, Y., Hecht, V. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.07.030 · Cited by 215 · see citing works
Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators
Tao, W., Yu, Z., & Han, J.-D. J. (2024) · Cell Metabolism · doi:10.1016/j.cmet.2024.03.009 · Cited by 147 · see citing works
Spatial mapping of cellular senescence: emerging challenges and opportunities
Gurkar, A. U., Gerencser, A. A., Mora, A. L., Nelson, A. C., Zhang, A. R., Lagnado, A. B., Enninful, A., Benz, C., Furman, D., Beaulieu, D., et al. (2023) · Nature Aging · doi:10.1038/s43587-023-00446-6 · Cited by 139 · see citing works
Stress, epigenetics, and aging: Unraveling the intricate crosstalk
Wu, Z., Qu, J. T., Zhang, W., & Liu, G. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.006 · Cited by 142 · see citing works
Wu, Z., Qu, J., & Liu, G.-H. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00775-3 · Cited by 118 · see citing works
A common signature of cellular senescence; does it exist?
Sikora, E., Bielak-Żmijewska, A., & Mosieniak, G. (2021) · Ageing Research Reviews · doi:10.1016/j.arr.2021.101458 · Cited by 120 · see citing works
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis
Zhang, S., Übelmesser, N., Josipović, N., Forte, G., Slotman, J. A., Chiang, M., Gothe, H. J., Gusmao, E. G., Becker, C., Altmüller, J., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg8205 · Cited by 114 · see citing works
Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging
Liu, Z., Ji, Q., Ren, J., Yan, P., Wu, Z., Wang, S., Sun, L., Wang, Z., Li, J., Sun, G., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.05.004 · Cited by 109 · see citing works
CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism
Hansen, A. S. (2020) · Nucleus · doi:10.1080/19491034.2020.1782024 · Cited by 101 · see citing works
A stem cell aging framework, from mechanisms to interventions
Liu, B., Qu, J. T., Zhang, W., Belmonte, J. C. I., & Liu, G. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111451 · Cited by 107 · see citing works
Down-syndrome-induced senescence disrupts the nuclear architecture of neural progenitors
Meharena, H. S., Marco, A., Dileep, V., Lockshin, E. R., Akatsu, G. Y., Mullahoo, J., Watson, L. A., Ko, T., Guerin, L. N., Abdurrob, F., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2021.12.002 · Cited by 92 · see citing works
Chromatin basis of the senescence-associated secretory phenotype
Hao, X., Wang, C., & Zhang, R. (2022) · Trends in Cell Biology · doi:10.1016/j.tcb.2021.12.003 · Cited by 94 · see citing works
Zhang, X., Liu, X., Du, Z., Wei, L., Fang, H., Dong, Q., Niu, J., Li, Y., Gao, J. T., Zhang, M. Q., et al. (2021) · Genome Research · doi:10.1101/gr.275235.121 · Cited by 100 · see citing works
Cell division drives DNA methylation loss in late-replicating domains in primary human cells
Endicott, J. L., Nolte, P. A., Shen, H., & Laird, P. W. (2022) · Nature Communications · doi:10.1038/s41467-022-34268-8 · Cited by 91 · see citing works
Liu, F., Yuan, L., Li, L., Yang, J., Liu, J., Chen, Y., Zhang, J., Lu, Y., Yuan, Y., & Cheng, J. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106788 · Cited by 88 · see citing works
Heterochromatin as an Important Driver of Genome Organization
Penagos‐Puig, A., & Furlan-Magaril, M. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.579137 · Cited by 80 · see citing works
Liu, B., Peng, Z., Zhang, H., Zhang, N., Liu, Z., Xia, Z., Huang, S., Luo, P., & Cheng, Q. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02284-z · Cited by 82 · see citing works
Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer
Tan, S. Y. X., Zhang, J., & Tee, W. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.931493 · Cited by 83 · see citing works
The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression
Dasgupta, N., Arnold, R., Equey, A., Gandhi, A., & Adams, P. D. (2024) · npj Aging · doi:10.1038/s41514-024-00172-2 · Cited by 86 · see citing works
Mesoscale phase separation of chromatin in the nucleus
Bajpai, G., Pavlov, D. A., Lorber, D., Volk, T., & Safran, S. A. (2021) · eLife · doi:10.7554/elife.63976 · Cited by 77 · see citing works
Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence
Olan, I., Parry, A. J., Schoenfelder, S., Narita, M., Ito, Y., Chan, A. S. L., Slater, G. S. C., Bihary, D., Bando, M., Shirahige, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19878-4 · Cited by 76 · see citing works
The p53 family member p73 in the regulation of cell stress response
Rozenberg, J. M., Zvereva, S. D., Dalina, A. A., Blatov, I., Zubarev, I. V., Luppov, D. V., Bessmertnyi, A., Romanishin, A. O., Alsoulaiman, L., Kumeiko, V. V., et al. (2021) · Biology Direct · doi:10.1186/s13062-021-00307-5 · Cited by 79 · see citing works
Guan, Y., Zhang, C., Lyu, G., Zhang, X., Zhuang, T., Zhuang, T., Jia, L., Zhang, C., Zhang, C., Li, C., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa858 · Cited by 77 · see citing works
Tortora, M. M. C., Brennan, L. D., Karpen, G., & Jost, D. (2023) · bioRxiv · doi:10.1073/pnas.2211855120 · Cited by 62 · see citing works
Self-citationDu, Q., Smith, G. C., Luu, P., Ferguson, J. M., Armstrong, N. J., Caldon, C. E., Campbell, E. M., Nair, S. S., Zotenko, E., Gould, C. M., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109722 · Cited by 65 · see citing works
Khalil, R., Diab‐Assaf, M., & Lemaı̂tre, J.-M. (2023) · Cells · doi:10.3390/cells12060915 · Cited by 66 · see citing works
Senescence in the Development and Response to Cancer with Immunotherapy: A Double-Edged Sword
Battram, A. M., Bachiller, M., & Martín-Antonio, B. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21124346 · Cited by 63 · see citing works
How can same-gene mutations promote both cancer and developmental disorders?
Nussinov, R., Tsai, C., & Jang, H. (2022) · Science Advances · doi:10.1126/sciadv.abm2059 · Cited by 55 · see citing works
Integrated Stress Response (ISR) Pathway: Unraveling Its Role in Cellular Senescence
Kalinin, A., Zubkova, E., & Menshikov, M. Y. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242417423 · Cited by 58 · see citing works
Dynamic 3D genome reorganization during senescence: defining cell states through chromatin
Shaban, H. A., & Gasser, S. M. (2023) · Cell Death and Differentiation · doi:10.1038/s41418-023-01197-y · Cited by 55 · see citing works
Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
Zhao, Y. F., Ding, Y., He, L., Zhou, Q., Chen, X., Li, Y., Alfonsi, M. V., Wu, Z., Sun, H., & Wang, H. (2023) · Science Advances · doi:10.1126/sciadv.abo1360 · Cited by 52 · see citing works
The aging proteostasis decline: From nematode to human
Meller, A., & Shalgi, R. (2021) · Experimental Cell Research · doi:10.1016/j.yexcr.2021.112474 · Cited by 50 · see citing works
Stefano, M. D., Nützmann, H., Martı́-Renom, M. A., & Jost, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1275 · Cited by 48 · see citing works
Self-citationThe macro and micro of chromosome conformation capture
Goel, V. Y., & Hansen, A. S. (2020) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.395 · Cited by 46 · see citing works
Stefano, M. D., Paulsen, J., Jost, D., & Martí-Renom, M. (2020) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2020.10.004 · Cited by 38 · see citing works
Self-citationLiang, C., Ke, Q., Liu, Z., Ren, J., Zhang, W., Hu, J., Wang, Z., Chen, H., Xia, K., Lai, X., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac146 · Cited by 49 · see citing works
Three-dimensional chromatin reorganization regulates B cell development during ageing
Ma, F., Cao, Y., Du, H., Braikia, F.-Z., Zong, L., Ollikainen, N., Bayer, M., Qiu, X., Park, B., Roy, R., et al. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01424-9 · Cited by 45 · see citing works
Integrated multi-omics approach revealed cellular senescence landscape
Song, Q., Hou, Y., Zhang, Y., Liu, J., Wang, Y., Fu, J., Zhang, C., Cao, M., Cui, Y., Zhang, X., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac885 · Cited by 42 · see citing works
The functional impact of nuclear reorganization in cellular senescence
Rocha, A., Dalgarno, A., & Neretti, N. (2022) · Briefings in Functional Genomics · doi:10.1093/bfgp/elab012 · Cited by 38 · see citing works
Beyond SAHF: An integrative view of chromatin compartmentalization during senescence
Olan, I., Handa, T., & Narita, M. (2023) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2023.102206 · Cited by 38 · see citing works
Liu, Y., Hrit, J. A., Chomiak, A. A., Stransky, S., Hoffman, J. R., Tiedemann, R. L., Wiseman, A. K., Kariapper, L. S., Dickson, B. M., Worden, E. J., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.009 · Cited by 38 · see citing works
Hong, X., Wang, L., Zhang, K., Liu, J., & Liu, J. (2022) · Cells · doi:10.3390/cells11050877 · Cited by 35 · see citing works
Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence
Han, X., Xing, L., Hong, Y., Zhang, X., Hao, B., Lu, J. Y., Huang, M., Wang, Z., Ma, S., Zhan, G., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.03.015 · Cited by 36 · see citing works
Reprogramming: Emerging Strategies to Rejuvenate Aging Cells and Tissues
Alle, Q., Borgne, E. L., Milhavet, O., & Lemaı̂tre, J.-M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22083990 · Cited by 33 · see citing works
Phase Separation and Correlated Motions in Motorized Genome
Jiang, Z., Qi, Y., Kamat, K. D., & Zhang, B. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c03238 · Cited by 29 · see citing works
HiCuT: An efficient and low input method to identify protein-directed chromatin interactions
Sati, S., Jones, P., Kim, H. S., Zhou, L., Rapp-Reyes, E., & Leung, T. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010121 · Cited by 30 · see citing works
Self-citationPredicting genome organisation and function with mechanistic modelling.
Chiang, M., Brackley, C., Marenduzzo, D., & Gilbert, N. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.11.001 · Cited by 23 · see citing works
Ling, X., Liu, X., Jiang, S., Fan, L., & Ding, J. (2022) · Cell Regeneration · doi:10.1186/s13619-022-00145-4 · Cited by 29 · see citing works
Wang, J., Zhou, X., Yu, P., Yao, J., Guo, P., Xu, Q., Zhao, Y., Wang, G., Li, Q., Zhu, X., et al. (2025) · Nature Aging · doi:10.1038/s43587-025-00886-2 · Cited by 28 · see citing works
Olan, I., Ando‐Kuri, M., Parry, A., Handa, T., Schoenfelder, S., Fraser, P., Ohkawa, Y., Kimurâ, H., Narita, M., & Narita, M. (2024) · Nature Communications · doi:10.1038/s41467-024-51153-8 · Cited by 27 · see citing works
Grosse, L., & Bulavin, D. V. (2020) · Aging · doi:10.18632/aging.103492 · Cited by 27 · see citing works
Ramponi, V., Richart, L., Kovatcheva, M., Attolini, C. S., Capellades, J., Lord, A. E., Yanes, Ó., Ficz, G., & Serrano, M. (2024) · Cancer Research · doi:10.1158/0008-5472.can-24-0529 · Cited by 26 · see citing works
El‐Sappah, A. H., Metwally, M., Rady, M. M., Ali, H. M., Wang, L., Maitra, P., Ihtisham, M., Yan, K., Zhao, X., Li, J., et al. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1144319 · Cited by 26 · see citing works
Locus-specific induction of gene expression from heterochromatin loci during cellular senescence
Tomimatsu, K., Bihary, D., Olan, I., Parry, A. J., Schoenfelder, S., Chan, A. S. L., Slater, G. S. C., Ito, Y., Rugg-Gunn, P. J., Kirschner, K., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00147-y · Cited by 25 · see citing works
LncRNAs: the missing link to senescence nuclear architecture
Han, J. J. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.03.007 · Cited by 25 · see citing works
Giorgio, E. D., Dalla, E., Tolotto, V., D’Este, F., Paluvai, H., Ranzino, L., & Brancolini, C. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae501 · Cited by 24 · see citing works
Desoky, E. M., Selem, E., El‐Maati, M. F. A., Hassn, A. A. S. A., Belal, H. E. E., Rady, M. M., Al-Harbi, M. S., & Ali, E. F. (2021) · Horticulturae · doi:10.3390/horticulturae7110435 · Cited by 24 · see citing works
Deciphering aging at three-dimensional genomic resolution
Liu, Z., Belmonte, J. C. I., Zhang, W., Qu, J. T., & Liu, G. (2022) · Cell Insight · doi:10.1016/j.cellin.2022.100034 · Cited by 23 · see citing works
Senescence: An Identity Crisis Originating from Deep Within the Nucleus
Olan, I., & Narita, M. (2022) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-013537 · Cited by 23 · see citing works
Restructuring of Lamina-Associated Domains in Senescence and Cancer
Bellanger, A., Madsen‐Østerbye, J., Galigniana, N. M., & Collas, P. (2022) · Cells · doi:10.3390/cells11111846 · Cited by 23 · see citing works
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 · see citing works
Transcription-Replication Collisions—A Series of Unfortunate Events
Germain, C. S., Zhao, H., & Barlow, J. H. (2021) · Biomolecules · doi:10.3390/biom11081249 · Cited by 22 · see citing works
HiCRes: a computational method to estimate and predict the genomic resolution of Hi-C libraries
Marchal, C., Singh, N., Corso‐Díaz, X., & Swaroop, A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1235 · Cited by 22 · see citing works
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 21 · see citing works
Self-citationCell 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 20 · see citing works
Tolokh, I. S., Kinney, N. A., Sharakhov, I. V., & Onufriev, A. V. (2023) · Epigenetics & Chromatin · doi:10.1186/s13072-023-00492-9 · Cited by 20 · see citing works
Fang, Y.-P., Yang, X., Zhang, Y., Zhu, X., Wang, X., Liu, Y., Shi, W., Huang, J., Zhao, Y., & Zhang, X.-L. (2024) · Renal Failure · doi:10.1080/0886022x.2024.2367708 · Cited by 21 · see citing works
Integrative studies of 3D genome organization and chromatin structure
Stefano, M. D., & Cavalli, G. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102493 · Cited by 18 · see citing works
Self-citationTargeting cellular senescence to combat cancer and ageing
Wang, C., Hao, X., & Zhang, R. (2022) · Molecular Oncology · doi:10.1002/1878-0261.13266 · Cited by 19 · see citing works
Palikyras, S., Sofiadis, K., Stavropoulou, A., Danieli‐Mackay, A., Varamogianni‐Mamatsi, V., Hörl, D., Nasiscionyte, S., Zhu, Y., Papadionysiou, I., Papadakis, A., et al. (2024) · Aging Cell · doi:10.1111/acel.14083 · Cited by 15 · see citing works
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 18 · see citing works
Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics
Pancaldi, V. (2021) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2021.742216 · Cited by 17 · see citing works
Senescence in cancer: Hallmarks, paradoxes, and therapeutic promise
Hinterleitner, C., Goldberg, H. V., McHugh, D., Barthet, V. J. A., Filliol, A. A., & Lowe, S. W. (2026) · Cell · doi:10.1016/j.cell.2026.03.005 · Cited by 18 · see citing works
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 16 · see citing works
Bisht, S., Mao, Y., & Easwaran, H. (2024) · Current Opinion in Oncology · doi:10.1097/cco.0000000000001020 · Cited by 17 · see citing works
Magnitov, M. D., Garaev, A. K., Tyakht, A., Ulianov, S. V., & Razin, S. V. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04654-6 · Cited by 15 · see citing works
Abdulla, A. Z., Salari, H., Tortora, M. M. C., Vaillant, C., & Jost, D. (2023) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2023.102033 · Cited by 12 · see citing works
Self-citationThe Quest for Eternal Youth: Hallmarks of Aging and Rejuvenating Therapeutic Strategies
Nunkoo, V. S., Cristian, A., Jurcău, A., Diaconu, R. G., & Jurcău, M. C. (2024) · Biomedicines · doi:10.3390/biomedicines12112540 · Cited by 15 · see citing works
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 · see citing works
Liu, X., Tao, Y., Zhang, L., Liu, Y., Shi, D., Wang, J., Xue, P., Xu, B., Fang, W., & Ran, Y. (2025) · Redox Biology · doi:10.1016/j.redox.2025.103708 · Cited by 13 · see citing works
Fraile‐Μartinez, O., León-Oliva, D. D., Boaru, D. L., Castro-Martinez, P. D., Montero, C. G., Barrena-Blázquez, S., García-García, J., García‐Honduvilla, N., Álvarez‐Mon, M., López-González, L., et al. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1345459 · Cited by 14 · see citing works
Desoky, E. M., Mahmood, M., Feng, D., Ahmed, A. F., Masoudi, L. M. A., Alahmari, A. S., Eid, R. S. M., Rady, M. M., Ayyoub, A., & Taha, N. A. (2025) · BMC Plant Biology · doi:10.1186/s12870-025-06234-1 · Cited by 13 · see citing works
Brunet, A., Destainville, N., & Collas, P. (2021) · Nucleus · doi:10.1080/19491034.2020.1868105 · Cited by 13 · see citing works
Active RB causes visible changes in nuclear organization
Krishnan, B., Yasuhara, T., Rumde, P. H., Stanzione, M., Lu, C., Lee, H., Lawrence, M. S., Zou, L., Nieman, L. T., Sanidas, I., et al. (2022) · The Journal of Cell Biology · doi:10.1083/jcb.202102144 · Cited by 13 · see citing works
Unravelling the genetics and epigenetics of the ageing tumour microenvironment in cancer
Easwaran, H., & Weeraratna, A. T. (2025) · Nature reviews. Cancer · doi:10.1038/s41568-025-00868-x · Cited by 14 · see citing works
The role of high mobility group proteins in cellular senescence mechanisms
Chen, J., Li, H., Huang, Y., & Tang, Q. (2024) · Frontiers in Aging · doi:10.3389/fragi.2024.1486281 · Cited by 12 · see citing works
Increased chromatin accessibility underpins senescence
Lopes‐Paciencia, S., & Ferbeyre, G. (2025) · FEBS Journal · doi:10.1111/febs.70136 · Cited by 14 · see citing works
Global early replication disrupts gene expression and chromatin conformation in a single cell cycle
Santos, M., Johnson, M. C., Fiedler, L., & Zegerman, P. (2022) · Genome biology · doi:10.1186/s13059-022-02788-7 · Cited by 12 · see citing works
Balaji, A., Saha, S., Deshpande, S., Poola, D., & Sengupta, K. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1068347 · Cited by 11 · see citing works
Keenan, C. R., Coughlan, H. D., Iannarella, N., del Fierro, A. T., Keniry, A., Johanson, T. M., Chan, W. F., Garnham, A. L., Whitehead, L. W., Blewitt, M. E., et al. (2024) · Genome Research · doi:10.1101/gr.279119.124 · Cited by 12 · see citing works
Nuclear expansion and chromatin structure remodeling in mouse aging neurons
Kriukov, D. V., Eremenko, E., Smirnov, D., Stein, D., Tsitrina, A. A., Golova, A., Einav, M., Khrameeva, E. E., & Toiber, D. (2024) · NAR Molecular Medicine · doi:10.1093/narmme/ugae011 · Cited by 11 · see citing works
HMGs as rheostats of chromosomal structure and cell proliferation
Papantonis, A. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.07.004 · Cited by 11 · see citing works
Nath, S., Dutta, S., Sarkar, S. D., Sengupta, D., Mitra, M. K., & Sengupta, K. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf615 · Cited by 10 · see citing works
Madsen-Østerbye, J., Bellanger, A., Galigniana, N., & Collas, P. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.913458 · Cited by 9 · see citing works
Wen, X., Ding, T., Li, F., Fan, J., Fan, X., Jia, R., & Zhang, H. (2022) · Communications Biology · doi:10.1038/s42003-022-04007-2 · Cited by 10 · see citing works
Jin, W. Z., Jiang, S., Liu, X., He, Y., Li, T., Ma, J., Chen, Z., Lu, X., Liu, X., Shou, W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54338-3 · Cited by 8 · see citing works
Chang, S., Moon, R., Nam, D., Lee, S., Yoon, I., Lee, D.-S., Choi, S., Paek, E., Hwang, D., Hur, J. K., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1210 · Cited by 9 · see citing works
- Authors
- Sati, S., Bonev, B., Szabo, Q., Jost, D., Bensadoun, P., Serra, F., Loubiere, V., Papadopoulos, G. L., Rivera-Mulia, J.-C., Fritsch, L., Bouret, P., Castillo, D., Gelpi, J. L., Orozco, M., Vaillant, C., Pellestor, F., Bantignies, F., Marti-Renom, M. A., Gilbert, D. M., Lemaitre, J.-M., & Cavalli, G.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Institut polytechnique de Grenoble (FR)
- Inserm (FR)
- Centre Hospitalier Universitaire de Montpellier (FR)
- Barcelona Institute of Science and Technology (ES)
- Institute for Research in Biomedicine (ES)
- Florida State University (US)
- Corresponding author
- Cavalli, Giacomo
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2020-05
- Volume
- 78
- Issue
- 3
- Pages
- 522-538.e9
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC7208559
- OpenAlex
- W3013543222
- Cited by
- 170
- References
- 78
- Citations by year
- 2026: 16 · 2025: 21 · 2024: 30 · 2023: 26 · 2022: 32 · 2021: 28 · 2020: 17
- FWCI
- 15.49
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Dipòsit Digital de la Universitat de Barcelona (Universitat de Barcelona) (submittedVersion, cc-by-nc-nd)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by-nc-nd)
- Funders
- LabEx EPIGENMED postdoctoral fellowship
- MuG project
- CNRS
- University of Montpellier
- European Research Council (ERC-2008-AdG No 232947)
- European Union’s Horizon 2020 research and innovation programme (676556)
- European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie (813327)
- Agence Nationale de la Recherche (N. ANR-15-CE12-006-01, ANR-15-CE12-006-03)
- Fondation pour la Recherche Médicale (N. DEI20151234396, DEI20151234396)
- French National Cancer Institute (N. PLBIO16-222, PLBIO18-362, PLBIO12-103)
- Laboratory of Excellence EpiGenMed (N. ANR-10-LABX-12)
- MSD Grant “GENE-IGH.”
- INSERM
- CHRU Montpellier/SAFE-iPSC facility
- Ligue National Centre le Contre le cancer “Equipe Labellisée (2015, –, 2019)
- French Ministry of Higher Education and Research and La Ligue Nationale Contre le Cancer
- CNRS Mission Interdisciplinarité
- CIMENT infrastructure (CPER07 13 CIRA)
- 7th Framework Program (FP7/2007-2013, 609989)
- Ministry of Economy and Competitiveness (BFU2017-85926-P)
- Agència de Gestió d'Ajuts Universitaris i de Recerca (SGR468)
- Spanish Ministry of Economy and Competitiveness (SEV-2012-0208)
- European Cooperation in Science and Technology
- Topics
- Health Sciences › Medicine › Physiology › Telomeres, Telomerase, and Senescence
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
- Keywords
- 3D genome organization, oncogene-induced senescence, replicative senescence, senescence-associated heterochromatin foci, chromatin interactions, DNMT1, HMGA2, DNA methylation, heterochromatin, gene expression regulation, epigenome
- MeSH terms
- DNA (Cytosine-5-)-Methyltransferase 1, Cells, Cultured, Fibroblasts, Heterochromatin, Humans, Oncogenes, Genome, Human, Cellular Senescence, In Situ Hybridization, Fluorescence, DNA Methylation, Chromatin Assembly and Disassembly
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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