Acknowledgement
This work was supported by the 2022 Research Fund of the University of Seoul. Figures were generated using BioRender. The author gratefully acknowledges Dayeong Kim, and Yeonggeun Yu for their valuable support and insightful comments on this manuscript.
References
- Agger, K., Cloos, P. A., Christensen, J., Pasini, D., Rose, S., Rappsilber, J., Issaeva, I., Canaani, E., Salcini, A. E. and Helin, K. (2007) UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731-734. https://doi.org/10.1038/nature06145
- Baker, D. J. and Sedivy, J. M. (2013) Probing the depths of cellular senescence. J. Cell Biol. 202, 11-13. https://doi.org/10.1083/jcb.201305155
- Belaghzal, H., Borrman, T., Stephens, A. D., Lafontaine, D. L., Venev, S. V., Weng, Z., Marko, J. F. and Dekker, J. (2021) Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nat. Genet. 53, 367-378. https://doi.org/10.1038/s41588-021-00784-4
- Bell, E. L., Klimova, T. A., Eisenbart, J., Schumacker, P. T. and Chandel, N. S. (2007) Mitochondrial reactive oxygen species trigger hypoxia-inducible factor-dependent extension of the replicative life span during hypoxia. Mol. Cell. Biol. 27, 5737-5745. https://doi.org/10.1128/MCB.02265-06
- Bellot, G., Garcia-Medina, R., Gounon, P., Chiche, J., Roux, D., Pouyssegur, J. and Mazure, N. M. (2009) Hypoxia-induced autophagy is mediated through hypoxia-inducible factor induction of BNIP3 and BNIP3L via their BH3 domains. Mol. Cell. Biol. 29, 2570-2581. https://doi.org/10.1128/MCB.00166-09
- Black, J. C., Van Rechem, C. and Whetstine, J. R. (2012) Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol. Cell 48, 491-507. https://doi.org/10.1016/j.molcel.2012.11.006
- Bonawitz, N. D., Chatenay-Lapointe, M., Pan, Y. and Shadel, G. S. (2007) Reduced TOR signaling extends chronological life span via increased respiration and upregulation of mitochondrial gene expression. Cell Metab. 5, 265-277. https://doi.org/10.1016/j.cmet.2007.02.009
- Burtscher, J., Mallet, R. T., Sah, A., Gassmann, M., Burtscher, M. and Iturriaga, R. (2025) Physiological differences underlying divergent hypoxia responses and altitude adaptations in humans, rats and mice. Compr. Physiol. 15, e70077. https://doi.org/10.1002/cph4.v15.6
- Butturini, E., Carcereri de Prati, A., Boriero, D. and Mariotto, S. (2019) Tumor dormancy and interplay with hypoxic tumor microenvironment. Int. J. Mol. Sci. 20, 4305.
- Cagan, A., Baez-Ortega, A., Brzozowska, N., Abascal, F., Coorens, T. H. H., Sanders, M. A., Lawson, A. R. J., Harvey, L. M. R., Bhosle, S., Jones, D., Alcantara, R. E., Butler, T. M., Hooks, Y., Roberts, K., Anderson, E., Lunn, S., Flach, E., Spiro, S., Januszczak, I., Wrigglesworth, E., Jenkins, H., Dallas, T., Masters, N., Perkins, M. W., Deaville, R., Druce, M., Bogeska, R., Milsom, M. D., Neumann, B., Gorman, F., Constantino-Casas, F., Peachey, L., Bochynska, D., Smith, E. S. J., Gerstung, M., Campbell, P. J., Murchison, E. P., Stratton, M. R. and Martincorena, I. (2022) Somatic mutation rates scale with lifespan across mammals. Nature 604, 517-524. https://doi.org/10.1038/s41586-022-04618-z
- Chang, S., Moon, R., Nam, D., Lee, S. W., Yoon, I., Lee, D. S., Choi, S., Paek, E., Hwang, D., Hur, J. K., Nam, Y., Chang, R. and Park, H. (2025) Hypoxia increases methylated histones to prevent histone clipping and heterochromatin redistribution during Raf-induced senescence. Nucleic Acids Res. 53, gkae1210. https://doi.org/10.1093/nar/gkae1210
- Chang, S., Yim, S. and Park, H. (2019) The cancer driver genes IDH1/2, JARID1C/ KDM5C, and UTX/ KDM6A: crosstalk between histone demethylation and hypoxic reprogramming in cancer metabolism. Exp. Mol. Med. 51, 1-17.
- Chen, F., Bian, K., Tang, Q., Fedeles, B. I., Singh, V., Humulock, Z. T., Essigmann, J. M. and Li, D. (2017) Oncometabolites d- and l-2-hydroxyglutarate inhibit the AlkB family DNA repair enzymes under physiological conditions. Chem. Res. Toxicol. 30, 1102-1110. https://doi.org/10.1021/acs.chemrestox.7b00009
- Cheung, P., Schaffert, S., Chang, S. E., Dvorak, M., Donato, M., Macaubas, C., Foecke, M. H., Li, T. M., Zhang, L., Coan, J. P., Schulert, G. S., Grom, A. A., Henderson, L. A., Nigrovic, P. A., Elias, J. E., Gozani, O., Mellins, E. D., Khatri, P., Utz, P. J. and Kuo, A. J. (2021) Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation. Nat. Immunol. 22, 711-722.
- Chiang, M., Michieletto, D., Brackley, C. A., Rattanavirotkul, N., Mohammed, H., Marenduzzo, D. and Chandra, T. (2019) Polymer modeling predicts chromosome reorganization in senescence. Cell Rep. 28, 3212-3223.e6. https://doi.org/10.1016/j.celrep.2019.08.045
- Chowdhury, R., Yeoh, K. K., Tian, Y. M., Hillringhaus, L., Bagg, E. A., Rose, N. R., Leung, I. K., Li, X. S., Woon, E. C., Yang, M., McDonough, M. A., King, O. N., Clifton, I. J., Klose, R. J., Claridge, T. D., Ratcliffe, P. J., Schofield, C. J. and Kawamura, A. (2011) The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 12, 463-469. https://doi.org/10.1038/embor.2011.43
- Corpet, A., Olbrich, T., Gwerder, M., Fink, D. and Stucki, M. (2014) Dynamics of histone H3.3 deposition in proliferating and senescent cells reveals a DAXX-dependent targeting to PML-NBs important for pericentromeric heterochromatin organization. Cell Cycle 13, 249-267. https://doi.org/10.4161/cc.26988
- Dang, L., White, D. W., Gross, S., Bennett, B. D., Bittinger, M. A., Driggers, E. M., Fantin, V. R., Jang, H. G., Jin, S., Keenan, M. C., Marks, K. M., Prins, R. M., Ward, P. S., Yen, K. E., Liau, L. M., Rabinowitz, J. D., Cantley, L. C., Thompson, C. B., Vander Heiden, M. G. and Su, S. M. (2009) Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature 462, 739-744. https://doi.org/10.1038/nature08617
- Di Micco, R., Fumagalli, M., Cicalese, A., Piccinin, S., Gasparini, P., Luise, C., Schurra, C., Garre, M., Nuciforo, P. G., Bensimon, A., Maestro, R., Pelicci, P. G. and d'Adda di Fagagna, F. (2006) Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 444, 638-642. https://doi.org/10.1038/nature05327
- Diehl, K. L. and Muir, T. W. (2020) Chromatin as a key consumer in the metabolite economy. Nat. Chem. Biol. 16, 620-629. https://doi.org/10.1038/s41589-020-0517-x
- Duarte, L. F., Young, A. R., Wang, Z., Wu, H. A., Panda, T., Kou, Y., Kapoor, A., Hasson, D., Mills, N. R., Ma'ayan, A., Narita, M. and Bernstein, E. (2014) Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nat. Commun. 5, 5210.
- Duncan, E. M. (2025) The common yet enigmatic activity of histone tail clipping. J. Biol. Chem. 301, 110239.
- Duncan, E. M., Muratore-Schroeder, T. L., Cook, R. G., Garcia, B. A., Shabanowitz, J., Hunt, D. F. and Allis, C. D. (2008) Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell 135, 284-294. https://doi.org/10.1016/j.cell.2008.09.055
- Enge, M., Arda, H. E., Mignardi, M., Beausang, J., Bottino, R., Kim, S. K. and Quake, S. R. (2017) Single-cell analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. Cell 171, 321-330.e14. https://doi.org/10.1016/j.cell.2017.09.004
- Ezzati, M., Murray Horwitz, M. E., Thomas, D. S., Friedman, A. B., Roach, R., Clark, T., Murray, C. J. and Honigman, B. (2012) Altitude, life expectancy and mortality from ischaemic heart disease, stroke, COPD and cancers: national population-based analysis of US counties. J. Epidemiol. Community Health 66, e17. https://doi.org/10.1136/jech.2010.112938
- Falk, M., Feodorova, Y., Naumova, N., Imakaev, M., Lajoie, B. R., Leonhardt, H., Joffe, B., Dekker, J., Fudenberg, G., Solovei, I. and Mirny, L. A. (2019) Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature 570, 395-399. https://doi.org/10.1038/s41586-019-1275-3
- Ferrari, K. J., Amato, S., Noberini, R., Toscani, C., Fernandez-Perez, D., Rossi, A., Conforti, P., Zanotti, M., Bonaldi, T., Tamburri, S. and Pasini, D. (2021) Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases. Nucleic Acids Res. 49, 791-804. https://doi.org/10.1093/nar/gkaa1228
- Gong, F. and Miller, K. M. (2019) Histone methylation and the DNA damage response. Mutat. Res. Rev. Mutat. Res. 780, 37-47. https://doi.org/10.1016/j.mrrev.2017.09.003
- Goodell, M. A. and Rando, T. A. (2015) Stem cells and healthy aging. Science 350, 1199-1204. https://doi.org/10.1126/science.aab3388
- Gorgoulis, V., Adams, P. D., Alimonti, A., Bennett, D. C., Bischof, O., Bishop, C., Campisi, J., Collado, M., Evangelou, K., Ferbeyre, G., Gil, J., Hara, E., Krizhanovsky, V., Jurk, D., Maier, A. B., Narita, M., Niedernhofer, L., Passos, J. F., Robbins, P. D., Schmitt, C. A., Sedivy, J., Vougas, K., von Zglinicki, T., Zhou, D., Serrano, M. and Demaria, M. (2019) Cellular senescence: defining a path forward. Cell 179, 813-827. https://doi.org/10.1016/j.cell.2019.10.005
- Hamanaka, R. B., Weinberg, S. E., Reczek, C. R. and Chandel, N. S. (2016) The mitochondrial respiratory chain is required for organismal adaptation to hypoxia. Cell Rep. 15, 451-459. https://doi.org/10.1016/j.celrep.2016.03.044
- Hernandez-Segura, A., Nehme, J. and Demaria, M. (2018) Hallmarks of cellular senescence. Trends Cell Biol. 28, 436-453. https://doi.org/10.1016/j.tcb.2018.02.001
- Hong, Y., Kim, H. J., Park, S., Yi, S., Lim, M. A., Lee, S. E., Chang, J. W., Won, H. R., Kim, J. R., Ko, H., Kim, S. Y., Kim, S. K., Park, J. L., Chu, I. S., Kim, J. M., Kim, K. H., Lee, J. H., Ju, Y. S., Shong, M., Koo, B. S., Park, W. Y. and Kang, Y. E. (2023) Single cell analysis of human thyroid reveals the transcriptional signatures of aging. Endocrinology 164, bqad029. https://doi.org/10.1210/endocr/bqad029
- Horvath, S. (2013) DNA methylation age of human tissues and cell types. Genome Biol. 14, R115. https://doi.org/10.1186/gb-2013-14-10-r115
- Hutchaleelaha, A., Patel, M., Washington, C., Siu, V., Allen, E., Oksenberg, D., Gretler, D. D., Mant, T. and Lehrer-Graiwer, J. (2019) Pharmacokinetics and pharmacodynamics of voxelotor (GBT440) in healthy adults and patients with sickle cell disease. Br. J. Clin. Pharmacol. 85, 1290-1302. https://doi.org/10.1111/bcp.v85.6
- Hyun, K., Jeon, J., Park, K. and Kim, J. (2017) Writing, erasing and reading histone lysine methylations. Exp. Mol. Med. 49, e324. https://doi.org/10.1038/emm.2017.11
- Intlekofer, A. M., Dematteo, R. G., Venneti, S., Finley, L. W., Lu, C., Judkins, A. R., Rustenburg, A. S., Grinaway, P. B., Chodera, J. D., Cross, J. R. and Thompson, C. B. (2015) Hypoxia induces production of L-2-hydroxyglutarate. Cell Metab. 22, 304-311. https://doi.org/10.1016/j.cmet.2015.06.023
- Ivan, M., Kondo, K., Yang, H., Kim, W., Valiando, J., Ohh, M., Salic, A., Asara, J. M., Lane, W. S. and Kaelin, W. G., Jr. (2001) HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing. Science 292, 464-468. https://doi.org/10.1126/science.1059817
- Jaakkola, P., Mole, D. R., Tian, Y. M., Wilson, M. I., Gielbert, J., Gaskell, S. J., von Kriegsheim, A., Hebestreit, H. F., Mukherji, M., Schofield, C. J., Maxwell, P. H., Pugh, C. W. and Ratcliffe, P. J. (2001) Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292, 468-472. https://doi.org/10.1126/science.1059796
- Jain, I. H., Zazzeron, L., Goli, R., Alexa, K., Schatzman-Bone, S., Dhillon, H., Goldberger, O., Peng, J., Shalem, O., Sanjana, N. E., Zhang, F., Goessling, W., Zapol, W. M. and Mootha, V. K. (2016) Hypoxia as a therapy for mitochondrial disease. Science 352, 54-61. https://doi.org/10.1126/science.aad9642
- Jenuwein, T. and Allis, C. D. (2001) Translating the histone code. Science 293, 1074-1080. https://doi.org/10.1126/science.1063127
- Jia, M., Agudelo Garcia, P. A., Ovando-Ricardez, J. A., Tabib, T., Bittar, H. T., Lafyatis, R. A., Mora, A. L., Benos, P. V. and Rojas, M. (2023) Transcriptional changes of the aging lung. Aging Cell 22, e13969. https://doi.org/10.1111/acel.v22.10
- Kim, J. W., Tchernyshyov, I., Semenza, G. L. and Dang, C. V. (2006) HIF-1-mediated expression of pyruvate dehydrogenase kinase: a metabolic switch required for cellular adaptation to hypoxia. Cell Metab. 3, 177-185. https://doi.org/10.1016/j.cmet.2006.02.002
- Kim, K., Punj, V., Kim, J. M., Lee, S., Ulmer, T. S., Lu, W., Rice, J. C. and An, W. (2016) MMP-9 facilitates selective proteolysis of the histone H3 tail at genes necessary for proficient osteoclastogenesis. Genes Dev. 30, 208-219. https://doi.org/10.1101/gad.268714.115
- Klemm, S. L., Shipony, Z. and Greenleaf, W. J. (2019) Chromatin accessibility and the regulatory epigenome. Nat. Rev. Genet. 20, 207-220. https://doi.org/10.1038/s41576-018-0089-8
- Kooistra, S. M. and Helin, K. (2012) Molecular mechanisms and potential functions of histone demethylases. Nat. Rev. Mol. Cell Biol. 13, 297-311. https://doi.org/10.1038/nrm3327
- Krieg, A. J., Rankin, E. B., Chan, D., Razorenova, O., Fernandez, S. and Giaccia, A. J. (2010) Regulation of the histone demethylase JMJD1A by hypoxia-inducible factor 1 alpha enhances hypoxic gene expression and tumor growth. Mol. Cell. Biol. 30, 344-353. https://doi.org/10.1128/MCB.00444-09
- Krivoruchko, A. and Storey, K. B. (2010) Forever young: mechanisms of natural anoxia tolerance and potential links to longevity. Oxid. Med. Cell. Longev. 3, 186-198. https://doi.org/10.4161/oxim.3.3.12356
- Laukka, T., Myllykoski, M., Looper, R. E. and Koivunen, P. (2018) Cancer-associated 2-oxoglutarate analogues modify histone methylation by inhibiting histone lysine demethylases. J. Mol. Biol. 430, 3081-3092. https://doi.org/10.1016/j.jmb.2018.06.048
- Lee, H. Y., Yang, E. G. and Park, H. (2013) Hypoxia enhances the expression of prostate-specific antigen by modifying the quantity and catalytic activity of Jumonji C domain-containing histone demethylases. Carcinogenesis 34, 2706-2715. https://doi.org/10.1093/carcin/bgt256
- Lee, P., Chandel, N. S. and Simon, M. C. (2020) Cellular adaptation to hypoxia through hypoxia inducible factors and beyond. Nat. Rev. Mol. Cell Biol. 21, 268-283. https://doi.org/10.1038/s41580-020-0227-y
- Lee, S., Lee, J., Chae, S., Moon, Y., Lee, H. Y., Park, B., Yang, E. G., Hwang, D. and Park, H. (2017) Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. Nucleic Acids Res. 45, 11643-11657. https://doi.org/10.1093/nar/gkx747
- Leiser, S. F., Fletcher, M., Begun, A. and Kaeberlein, M. (2013) Lifespan extension from hypoxia in Caenorhabditis elegans requires both HIF-1 and DAF-16 and is antagonized by SKN-1. J. Gerontol. A Biol. Sci. Med. Sci. 68, 1135-1144. https://doi.org/10.1093/gerona/glt016
- Leontieva, O. V., Natarajan, V., Demidenko, Z. N., Burdelya, L. G., Gudkov, A. V. and Blagosklonny, M. V. (2012) Hypoxia suppresses conversion from proliferative arrest to cellular senescence. Proc. Natl. Acad. Sci. U. S. A. 109, 13314-13318. https://doi.org/10.1073/pnas.1205690109
- Levy, O., Amit, G., Vaknin, D., Snir, T., Efroni, S., Castaldi, P., Liu, Y. Y., Cohen, H. Y. and Bashan, A. (2020) Age-related loss of gene-to-gene transcriptional coordination among single cells. Nat. Metab. 2, 1305-1315. https://doi.org/10.1038/s42255-020-00304-4
- Li, Y., Wang, M. S., Otecko, N. O., Wang, W., Shi, P., Wu, D. D. and Zhang, Y. P. (2017) Hypoxia potentially promotes Tibetan longevity. Cell Res. 27, 302-305. https://doi.org/10.1038/cr.2016.105
- Lim, S. A., Moon, Y., Shin, M. H., Kim, T. J., Chae, S., Yee, C., Hwang, D., Park, H. and Lee, K. M. (2021) Hypoxia-driven HIF-1alpha activation reprograms pre-activated NK cells towards highly potent effector phenotypes via ERK/STAT3 pathways. Cancers (Basel) 13, 1904. https://doi.org/10.3390/cancers13081904
- Lopez-Otin, C., Blasco, M. A., Partridge, L., Serrano, M. and Kroemer, G. (2013) The hallmarks of aging. Cell 153, 1194-1217. https://doi.org/10.1016/j.cell.2013.05.039
- Lutz, P. L., Prentice, H. M. and Milton, S. L. (2003) Is turtle longevity linked to enhanced mechanisms for surviving brain anoxia and reoxygenation? Exp. Gerontol. 38, 797-800. https://doi.org/10.1016/S0531-5565(03)00111-6
- Mahon, P. C., Hirota, K. and Semenza, G. L. (2001) FIH-1: a novel protein that interacts with HIF-1alpha and VHL to mediate repression of HIF-1 transcriptional activity. Genes Dev. 15, 2675-2686. https://doi.org/10.1101/gad.924501
- Maierhofer, A., Flunkert, J., Oshima, J., Martin, G. M., Haaf, T. and Horvath, S. (2017) Accelerated epigenetic aging in Werner syndrome. Aging (Albany N.Y.) 9, 1143-1152.
- Millan-Zambrano, G., Burton, A., Bannister, A. J. and Schneider, R. (2022) Histone post-translational modifications - cause and consequence of genome function. Nat. Rev. Genet. 23, 563-580. https://doi.org/10.1038/s41576-022-00468-7
- Miwa, S., Kashyap, S., Chini, E. and von Zglinicki, T. (2022) Mitochondrial dysfunction in cell senescence and aging. J. Clin. Invest. 132, e158447. https://doi.org/10.1172/JCI158447
- Mohyeldin, A., Garzon-Muvdi, T. and Quinones-Hinojosa, A. (2010) Oxygen in stem cell biology: a critical component of the stem cell niche. Cell Stem Cell 7, 150-161. https://doi.org/10.1016/j.stem.2010.07.007
- Moiseeva, O., Bourdeau, V., Roux, A., Deschenes-Simard, X. and Ferbeyre, G. (2009) Mitochondrial dysfunction contributes to oncogene-induced senescence. Mol. Cell. Biol. 29, 4495-4507. https://doi.org/10.1128/MCB.01868-08
- Nakada, Y., Canseco, D. C., Thet, S., Abdisalaam, S., Asaithamby, A., Santos, C. X., Shah, A. M., Zhang, H., Faber, J. E., Kinter, M. T., Szweda, L. I., Xing, C., Hu, Z., Deberardinis, R. J., Schiattarella, G., Hill, J. A., Oz, O., Lu, Z., Zhang, C. C., Kimura, W. and Sadek, H. A. (2017) Hypoxia induces heart regeneration in adult mice. Nature 541, 222-227. https://doi.org/10.1038/nature20173
- O'Sullivan, R. J., Kubicek, S., Schreiber, S. L. and Karlseder, J. (2010) Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat. Struct. Mol. Biol. 17, 1218-1225. https://doi.org/10.1038/nsmb.1897
- Olan, I., Handa, T. and Narita, M. (2023) Beyond SAHF: an integrative view of chromatin compartmentalization during senescence. Curr. Opin. Cell Biol. 83, 102206. https://doi.org/10.1016/j.ceb.2023.102206
- Oldham, W. M., Clish, C. B., Yang, Y. and Loscalzo, J. (2015) Hypoxia-mediated increases in L-2-hydroxyglutarate coordinate the metabolic response to reductive stress. Cell Metab. 22, 291-303. https://doi.org/10.1016/j.cmet.2015.06.021
- Otero-Albiol, D. and Carnero, A. (2021) Cellular senescence or stemness: hypoxia flips the coin. J. Exp. Clin. Cancer Res. 40, 243.
- Pamenter, M. E. (2022) Adaptations to a hypoxic lifestyle in naked mole-rats. J. Exp. Biol. 225, jeb196725. https://doi.org/10.1242/jeb.196725
- Parrinello, S., Samper, E., Krtolica, A., Goldstein, J., Melov, S. and Campisi, J. (2003) Oxygen sensitivity severely limits the replicative lifespan of murine fibroblasts. Nature Cell Biol. 5, 741-747. https://doi.org/10.1038/ncb1024
- Petkovich, D. A., Podolskiy, D. I., Lobanov, A. V., Lee, S. G., Miller, R. A. and Gladyshev, V. N. (2017) Using DNA methylation profiling to evaluate biological age and longevity interventions. Cell Metab. 25, 954-960.e6. https://doi.org/10.1016/j.cmet.2017.03.016
- Pollex, T., Rabinowitz, A., Gambetta, M. C., Marco-Ferreres, R., Viales, R. R., Jankowski, A., Schaub, C. and Furlong, E. E. M. (2024) Enhancer-promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation. Nat. Genet. 56, 686-696. https://doi.org/10.1038/s41588-024-01678-x
- Rieckher, M., Garinis, G. A. and Schumacher, B. (2021) Molecular pathology of rare progeroid diseases. Trends Mol. Med. 27, 907-922. https://doi.org/10.1016/j.molmed.2021.06.011
- Rogers, R. S. and Mootha, V. K. (2025) Hypoxia as a medicine. Sci. Transl. Med. 17, eadr4049. https://doi.org/10.1126/scitranslmed.adr4049
- Rogers, R. S., Wang, H., Durham, T. J., Stefely, J. A., Owiti, N. A., Markhard, A. L., Sandler, L., To, T. L. and Mootha, V. K. (2023) Hypoxia extends lifespan and neurological function in a mouse model of aging. PLoS Biol. 21, e3002117. https://doi.org/10.1371/journal.pbio.3002117
- Sadaie, M., Salama, R., Carroll, T., Tomimatsu, K., Chandra, T., Young, A. R., Narita, M., Perez-Mancera, P. A., Bennett, D. C., Chong, H., Kimura, H. and Narita, M. (2013) Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev. 27, 1800-1808. https://doi.org/10.1101/gad.217281.113
- 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. and Cavalli, G. (2020) 4D genome rewiring during oncogene-induced and replicative senescence. Mol. Cell 78, 522-538.e9. https://doi.org/10.1016/j.molcel.2020.03.007
- Schvartzman, J. M., Thompson, C. B. and Finley, L. W. S. (2018) Metabolic regulation of chromatin modifications and gene expression. J. Cell Biol. 217, 2247-2259. https://doi.org/10.1083/jcb.201803061
- Semenza, G. L. (2001) HIF-1, O(2), and the 3 PHDs: how animal cells signal hypoxia to the nucleus. Cell 107, 1-3. https://doi.org/10.1016/S0092-8674(01)00518-9
- Semenza, G. L. (2012) Hypoxia-inducible factors in physiology and medicine. Cell 148, 399-408. https://doi.org/10.1016/j.cell.2012.01.021
- Sen, P., Shah, P. P., Nativio, R. and Berger, S. L. (2016) Epigenetic mechanisms of longevity and aging. Cell 166, 822-839. https://doi.org/10.1016/j.cell.2016.07.050
- Seward, D. J., Cubberley, G., Kim, S., Schonewald, M., Zhang, L., Tripet, B. and Bentley, D. L. (2007) Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 14, 240-242. https://doi.org/10.1038/nsmb1200
- Shaban, H. A. and Gasser, S. M. (2025) Dynamic 3D genome reorganization during senescence: defining cell states through chromatin. Cell Death Differ. 32, 9-15. https://doi.org/10.1038/s41418-023-01197-y
- Shen, L., Song, C. X., He, C. and Zhang, Y. (2014) Mechanism and function of oxidative reversal of DNA and RNA methylation. Annu. Rev. Biochem. 83, 585-614. https://doi.org/10.1146/biochem.2014.83.issue-1
- Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J. R., Cole, P. A., Casero, R. A. and Shi, Y. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941-953. https://doi.org/10.1016/j.cell.2004.12.012
- Shi, Y. and Whetstine, J. R. (2007) Dynamic regulation of histone lysine methylation by demethylases. Mol. Cell 25, 1-14.
- Solovei, I., Wang, A. S., Thanisch, K., Schmidt, C. S., Krebs, S., Zwerger, M., Cohen, T. V., Devys, D., Foisner, R., Peichl, L., Herrmann, H., Blum, H., Engelkamp, D., Stewart, C. L., Leonhardt, H. and Joffe, B. (2013) LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation. Cell 152, 584-598. https://doi.org/10.1016/j.cell.2013.01.009
- Soto-Palma, C., Niedernhofer, L. J., Faulk, C. D. and Dong, X. (2022) Epigenetics, DNA damage, and aging. J. Clin. Invest. 132, e158446. https://doi.org/10.1172/JCI158446
- Stephens, R. K. and Miroshnikova, Y. A. (2024) Nuclear periphery and its mechanical regulation in cell fate transitions. Curr. Opin. Struct. Biol. 87, 102867.
- Su, Z. and Denu, J. M. (2016) Reading the combinatorial histone language. ACS Chem. Biol. 11, 564-574. https://doi.org/10.1021/acschembio.5b00864
- Sullivan, R., Pare, G. C., Frederiksen, L. J., Semenza, G. L. and Graham, C. H. (2008) Hypoxia-induced resistance to anticancer drugs is associated with decreased senescence and requires hypoxia-inducible factor-1 activity. Mol. Cancer Ther. 7, 1961-1973. https://doi.org/10.1158/1535-7163.MCT-08-0198
- Sun, N., Youle, R. J. and Finkel, T. (2016) The mitochondrial basis of aging. Mol. Cell 61, 654-666. https://doi.org/10.1016/j.molcel.2016.01.028
- Swisa, A., Kaestner, K. H. and Dor, Y. (2017) Transcriptional noise and somatic mutations in the aging pancreas. Cell Metab. 26, 809-811. https://doi.org/10.1016/j.cmet.2017.11.009
- Tagami, H., Ray-Gallet, D., Almouzni, G. and Nakatani, Y. (2004) Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116, 51-61. https://doi.org/10.1016/S0092-8674(03)01064-X
- Takasugi, M., Yoshida, Y., Hara, E. and Ohtani, N. (2023) The role of cellular senescence and SASP in tumour microenvironment. FEBS J. 290, 1348-1361. https://doi.org/10.1111/febs.v290.5
- Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. and Patel, D. J. (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers Nat. Struct. Mol. Biol. 14, 1025-1040. https://doi.org/10.1038/nsmb1338
- Teefy, B. B. and Benayoun, B. A. (2023) Putting aging on ICE. Cell Metab. 35, 383-385. https://doi.org/10.1016/j.cmet.2023.02.012
- Tessarz, P., Santos-Rosa, H., Robson, S. C., Sylvestersen, K. B., Nelson, C. J., Nielsen, M. L. and Kouzarides, T. (2014) Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature 505, 564-568. https://doi.org/10.1038/nature12819
- Triana-Martinez, F., Loza, M. I. and Dominguez, E. (2020) Beyond tumor suppression: senescence in cancer stemness and tumor dormancy. Cells 9, 346. https://doi.org/10.3390/cells9020346
- Tsai, C. C., Chen, Y. J., Yew, T. L., Chen, L. L., Wang, J. Y., Chiu, C. H. and Hung, S. C. (2011) Hypoxia inhibits senescence and maintains mesenchymal stem cell properties through down-regulation of E2A-p21 by HIF-TWIST. Blood 117, 459-469. https://doi.org/10.1182/blood-2010-05-287508
- Ungricht, R. and Kutay, U. (2017) Mechanisms and functions of nuclear envelope remodelling. Nat. Rev. Mol. Cell Biol. 18, 229-245. https://doi.org/10.1038/nrm.2016.153
- Unnikrishnan, A., Freeman, W. M., Jackson, J., Wren, J. D., Porter, H. and Richardson, A. (2019) The role of DNA methylation in epigenetics of aging. Pharmacol. Ther. 195, 172-185. https://doi.org/10.1016/j.pharmthera.2018.11.001
- Uyehara, C. M. and Apostolou, E. (2023) 3D enhancer-promoter interactions and multi-connected hubs: organizational principles and functional roles. Cell Rep. 42, 112068. https://doi.org/10.1016/j.celrep.2023.112068
- Wang, H., Miranda, M., Marutani, E., Lichtenegger, P., Wojtkiewicz, G. R., Ichinose, F. and Mootha, V. K. (2024) Therapeutic hypoxia for mitochondrial disease via enhancement of hemoglobin affinity and inhibition of HIF-2alpha. J. Clin. Invest. 134, e185569.
- Wang, T., Tsui, B., Kreisberg, J. F., Robertson, N. A., Gross, A. M., Yu, M. K., Carter, H., Brown-Borg, H. M., Adams, P. D. and Ideker, T. (2017) Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 18, 57. https://doi.org/10.1186/s13059-017-1186-2
- Wang, W., Meadows, L. R., den Haan, J. M., Sherman, N. E., Chen, Y., Blokland, E., Shabanowitz, J., Agulnik, A. I., Hendrickson, R. C., Bishop, C. E. , Hunt, D. F., Goulmy, E. and Engelhard, V. H. (1995) Human H-Y: a male-specific histocompatibility antigen derived from the SMCY protein. Science 269, 1588-1590. https://doi.org/10.1126/science.7667640
- Weeda, G., Donker, I., de Wit, J., Morreau, H., Janssens, R., Vissers, C. J., Nigg, A., van Steeg, H., Bootsma, D. and Hoeijmakers, J. H. (1997) Disruption of mouse ERCC1 results in a novel repair syndrome with growth failure, nuclear abnormalities and senescence. Curr. Biol. 7, 427-439. https://doi.org/10.1016/S0960-9822(06)00190-4
- Whetstine, J. R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M. and Shi, Y. (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467-481. https://doi.org/10.1016/j.cell.2006.03.028
- Wicks, E. E. and Semenza, G. L. (2022) Hypoxia-inducible factors: cancer progression and clinical translation. J. Clin. Invest. 132, e159839. https://doi.org/10.1172/JCI159839
- Wilber, R. L. (2007) Application of altitude/hypoxic training by elite athletes. Med. Sci. Sports Exerc. 39, 1610-1624. https://doi.org/10.1249/mss.0b013e3180de49e6
- Wu, R., Wang, Z., Zhang, H., Gan, H. and Zhang, Z. (2017) H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication. Nucleic Acids Res. 45, 169-180. https://doi.org/10.1093/nar/gkw848
- Wuren, T., Simonson, T. S., Qin, G., Xing, J., Huff, C. D., Witherspoon, D. J., Jorde, L. B. and Ge, R. L. (2014) Shared and unique signals of high-altitude adaptation in geographically distinct Tibetan populations. PLoS One 9, e88252. https://doi.org/10.1371/journal.pone.0088252
- Xin, Y., Okamoto, H., Kim, J., Ni, M., Adler, C., Cavino, K., Na, E., Murphy, A. J., Yancopoulos, G. D., Lin, C. and Gromada, J. (2016) Single-cell RNAseq reveals that pancreatic beta-cells from very old male mice have a young gene signature. Endocrinology 157, 3431-3438. https://doi.org/10.1210/en.2016-1235
- Xu, W., Yang, H., Liu, Y., Yang, Y., Wang, P., Kim, S. H., Ito, S., Yang, C., Wang, P., Xiao, M. T., Liu, L. X., Jiang, W. Q., Liu, J., Zhang, J. Y., Wang, B., Frye, S., Zhang, Y., Xu, Y. H., Lei, Q. Y., Guan, K. L., Zhao, S. M. and Xiong, Y. (2011) Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer Cell 19, 17-30. https://doi.org/10.1016/j.ccr.2010.12.014
- Yang, H., Sui, P., Guo, Y., Chen, S., Maloof, M. E., Ge, G., Nihozeko, F., Delma, C. R., Zhu, G., Zhang, P., Ye, Z., Medina, E. A., Ayad, N. G., Mesa, R., Nimer, S. D., Chiang, C. M., Xu, M., Chen, Y. and Yang, F. C. (2023a) Loss of BRD4 induces cell senescence in HSC/HPCs by deregulating histone H3 clipping. EMBO Rep. 24, e57032. https://doi.org/10.15252/embr.202357032
- Yang, J. H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., Chew, Y. C., Guo, W., Yang, X., Maybury-Lewis, S., Tian, X., Ross, J. M., Coppotelli, G., Meer, M. V., Rogers-Hammond, R., Vera, D. L., Lu, Y. R., Pippin, J. W., Creswell, M. L., Dou, Z., Xu, C., Mitchell, S. J., Das, A., O'Connell, B. L., Thakur, S., Kane, A. E., Su, Q., Mohri, Y., Nishimura, E. K., Schaevitz, L., Garg, N., Balta, A. M., Rego, M. A., Gregory-Ksander, M., Jakobs, T. C., Zhong, L., Wakimoto, H., El Andari, J., Grimm, D., Mostoslavsky, R., Wagers, A. J., Tsubota, K., Bonasera, S. J., Palmeira, C. M., Seidman, J. G., Seidman, C. E., Wolf, N. S., Kreiling, J. A., Sedivy, J. M., Murphy, G. F., Green, R. E., Garcia, B. A., Berger, S. L., Oberdoerffer, P., Shankland, S. J., Gladyshev, V. N., Ksander, B. R., Pfenning, A. R., Rajman, L. A. and Sinclair, D. A. (2023b) Loss of epigenetic information as a cause of mammalian aging. Cell 186, 305-326.e27. https://doi.org/10.1016/j.cell.2022.12.027
- Zirkel, A., Nikolic, M., Sofiadis, K., Mallm, J. P., Brackley, C. A., Gothe, H., Drechsel, O., Becker, C., Altmuller, J., Josipovic, N., Georgomanolis, T., Brant, L., Franzen, J., Koker, M., Gusmao, E. G., Costa, I. G., Ullrich, R. T., Wagner, W., Roukos, V., Nurnberg, P., Marenduzzo, D., Rippe, K. and Papantonis, A. (2018) HMGB2 loss upon senescence entry disrupts genomic organization and induces CTCF clustering across cell types. Mol. Cell 70, 730-744.e6. https://doi.org/10.1016/j.molcel.2018.03.030
- Zubieta-Calleja, G. R., Paulev, P. E., Zubieta-Calleja, L. and Zubieta-Castillo, G. (2007) Altitude adaptation through hematocrit changes. J. Physiol. Pharmacol. 58 Suppl 5, 811-818.