[1] A. Travers, G. Muskhelishvili, DNA structure and function, FEBS J. 282 (2015) 2279–2295. https://doi.org/10.1111/febs.13307.
[2] O. Morrison, J. Thakur, Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin, Int. J. Mol. Sci. 22 (2021) 6922. https://doi.org/10.3390/ijms22136922.
[3] K. Maeshima, S. Iida, S. Tamura, Physical Nature of Chromatin in the Nucleus, Cold Spring Harb. Perspect. Biol. 13 (2021) a040675. https://doi.org/10.1101/cshperspect.a040675.
[4] S. Minchin, J. Lodge, Understanding biochemistry: structure and function of nucleic acids, Essays Biochem. 63 (2019) 433–456. https://doi.org/10.1042/ebc20180038.
[5] L. Loewe, W.G. Hill, The population genetics of mutations: good, bad and indifferent, Philos. Trans. R. Soc. B: Biol. Sci. 365 (2010) 1153–1167. https://doi.org/10.1098/rstb.2009.0317.
[6] B.L. Lee, A. Singh, J.N.M. Glover, M.J. Hendzel, L. Spyracopoulos, Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics, J. Mol. Biol. 429 (2017) 3409–3429. https://doi.org/10.1016/j.jmb.2017.05.029.
[7] R. Huang, P.-K. Zhou, DNA damage repair: historical perspectives, mechanistic pathways and clinical translation for targeted cancer therapy, Signal Transduct. Target. Ther. 6 (2021) 254. https://doi.org/10.1038/s41392-021-00648-7.
[8] A. Ui, N. Chiba, A. Yasui, Relationship among DNA double‐strand break (DSB), DSB repair, and transcription prevents genome instability and cancer, Cancer Sci. 111 (2020) 1443–1451. https://doi.org/10.1111/cas.14404.
[9] E.R. Stead, I. Bjedov, Balancing DNA repair to prevent ageing and cancer, Exp. Cell Res. 405 (2021) 112679. https://doi.org/10.1016/j.yexcr.2021.112679.
[10] N. Nair, M. Shoaib, C.S. Sørensen, Chromatin Dynamics in Genome Stability: Roles in Suppressing Endogenous DNA Damage and Facilitating DNA Repair, Int. J. Mol. Sci. 18 (2017) 1486. https://doi.org/10.3390/ijms18071486.
[11] J. Ferrand, A. Plessier, S.E. Polo, Control of the chromatin response to DNA damage: Histone proteins pull the strings, Semin. Cell Dev. Biol. 113 (2021) 75–87. https://doi.org/10.1016/j.semcdb.2020.07.002.
[12] U. Chakraborty, Z.-J. Shen, J. Tyler, Chaperoning histones at the DNA repair dance, DNA Repair 108 (2021) 103240. https://doi.org/10.1016/j.dnarep.2021.103240.
[13] J. Stadler, H. Richly, Regulation of DNA Repair Mechanisms: How the Chromatin Environment Regulates the DNA Damage Response, Int. J. Mol. Sci. 18 (2017) 1715. https://doi.org/10.3390/ijms18081715.
[14] X. Wu, M. Xu, M. Geng, S. Chen, P.J. Little, S. Xu, J. Weng, Targeting protein modifications in metabolic diseases: molecular mechanisms and targeted therapies, Signal Transduct. Target. Ther. 8 (2023) 220. https://doi.org/10.1038/s41392-023-01439-y.
[15] H. Xu, Y. Wang, S. Lin, W. Deng, D. Peng, Q. Cui, Y. Xue, PTMD: A Database of Human Disease-associated Post-translational Modifications, Genom., Proteom. Bioinform. 16 (2018) 244–251. https://doi.org/10.1016/j.gpb.2018.06.004.
[16] K. Hyun, J. Jeon, K. Park, J. Kim, Writing, erasing and reading histone lysine methylations, Exp. Mol. Med. 49 (2017) e324–e324. https://doi.org/10.1038/emm.2017.11.
[17] D. Nicetto, K.S. Zaret, Role of H3K9me3 heterochromatin in cell identity establishment and maintenance, Curr. Opin. Genet. Dev. 55 (2019) 1–10. https://doi.org/10.1016/j.gde.2019.04.013.
[18] H.-Y. Jeon, A. Hussain, J. Qi, Role of H3K9 demethylases in DNA doublestrand break repair, J. Cancer Biol. 1 (2020) 10–15. https://doi.org/10.46439/cancerbiology.1.003.
[19] F. Gong, K.M. Miller, Histone methylation and the DNA damage response, Mutat. Res.Rev. Mutat. Res. 780 (2019) 37–47. https://doi.org/10.1016/j.mrrev.2017.09.003.
[20] M. Zhou, J. Yan, Q. Chen, Y. Yang, Y. Li, Y. Ren, Z. Weng, X. Zhang, J. Guan, L. Tang, Z. Ren, Association of H3K9me3 with breast cancer prognosis by estrogen receptor status, Clin. Epigenetics 14 (2022) 135. https://doi.org/10.1186/s13148-022-01363-y.
[21] Y.-C. Wang, S.E. Peterson, J.F. Loring, Protein post-translational modifications and regulation of pluripotency in human stem cells, Cell Res. 24 (2014) 143–160. https://doi.org/10.1038/cr.2013.151.
[22] M. Moutin, C. Bosc, L. Peris, A. Andrieux, Tubulin post‐translational modifications control neuronal development and functions, Dev. Neurobiol. 81 (2021) 253–272. https://doi.org/10.1002/dneu.22774.
[23] L. Chen, S. Liu, Y. Tao, Regulating tumor suppressor genes: post-translational modifications, Signal Transduct. Target. Ther. 5 (2020) 90. https://doi.org/10.1038/s41392-020-0196-9.
[24] Y. Yang, M. Zhang, Y. Wang, The roles of histone modifications in tumorigenesis and associated inhibitors in cancer therapy, J. Natl. Cancer Cent. 2 (2022) 277–290. https://doi.org/10.1016/j.jncc.2022.09.002.
[25] M.V. de la Peña, P.A.M. Summanen, M. Liukkonen, I. Kronholm, Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa, Genome Res. 33 (2023) 599–611. https://doi.org/10.1101/gr.276992.122.
[26] M. Habig, C. Lorrain, A. Feurtey, J. Komluski, E.H. Stukenbrock, Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus, Nat. Commun. 12 (2021) 5869. https://doi.org/10.1038/s41467-021-26108-y.
[27] P. Polak, R. Karlić, A. Koren, R. Thurman, R. Sandstrom, M.S. Lawrence, A. Reynolds, E. Rynes, K. Vlahoviček, J.A. Stamatoyannopoulos, S.R. Sunyaev, Cell-of-origin chromatin organization shapes the mutational landscape of cancer, Nature 518 (2015) 360–364. https://doi.org/10.1038/nature14221.
[28] J.G. Prendergast, H. Campbell, N. Gilbert, M.G. Dunlop, W.A. Bickmore, C.A. Semple, Chromatin structure and evolution in the human genome, BMC Evol. Biol. 7 (2007) 72. https://doi.org/10.1186/1471-2148-7-72.
[29] J. Xia, L. Han, Z. Zhao, Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome, BMC Genom. 13 (2012) S7. https://doi.org/10.1186/1471-2164-13-s8-s7.
[30] K.D. Makova, R.C. Hardison, The effects of chromatin organization on variation in mutation rates in the genome, Nat. Rev. Genet. 16 (2015) 213–223. https://doi.org/10.1038/nrg3890.
[31] A. Gonzalez-Perez, R. Sabarinathan, N. Lopez-Bigas, Local Determinants of the Mutational Landscape of the Human Genome, Cell 177 (2019) 101–114. https://doi.org/10.1016/j.cell.2019.02.051.
[32] S. Heerboth, K. Lapinska, N. Snyder, M. Leary, S. Rollinson, S. Sarkar, Use of Epigenetic Drugs in Disease: An Overview, Genet. Epigenetics 6 (2014) GEG.S12270. https://doi.org/10.4137/geg.s12270.
[33] Z. Liu, Y. Ren, S. Weng, H. Xu, L. Li, X. Han, A New Trend in Cancer Treatment: The Combination of Epigenetics and Immunotherapy, Front. Immunol. 13 (2022) 809761. https://doi.org/10.3389/fimmu.2022.809761.
[34] N. Ahuja, A.R. Sharma, S.B. Baylin, Epigenetic Therapeutics: A New Weapon in the War Against Cancer, Annu. Rev. Med. 67 (2016) 73–89. https://doi.org/10.1146/annurev-med-111314-035900.
[35] M.I. Lind, F. Spagopoulou, Evolutionary consequences of epigenetic inheritance, Heredity 121 (2018) 205–209. https://doi.org/10.1038/s41437-018-0113-y.
[36] A. Fortuny, S.E. Polo, The response to DNA damage in heterochromatin domains, Chromosoma 127 (2018) 291–300. https://doi.org/10.1007/s00412-018-0669-6.
[37] J. Du, W. Liao, H. Wang, G. Hou, M. Liao, L. Xu, J. Huang, K. Yuan, X. Chen, Y. Zeng, MDIG-mediated H3K9me3 demethylation upregulates Myc by activating OTX2 and facilitates liver regeneration, Signal Transduct. Target. Ther. 8 (2023) 351. https://doi.org/10.1038/s41392-023-01575-5.
[38] L. Monaghan, M.E. Massett, R.P. Bunschoten, A. Hoose, P.-A. Pirvan, R.M.J. Liskamp, H.G. Jørgensen, X. Huang, The Emerging Role of H3K9me3 as a Potential Therapeutic Target in Acute Myeloid Leukemia, Front. Oncol. 9 (2019) 705. https://doi.org/10.3389/fonc.2019.00705.
[39] R. Ferreira, A. Limeta, J. Nielsen, Tackling Cancer with Yeast-Based Technologies, Trends Biotechnol. 37 (2019) 592–603. https://doi.org/10.1016/j.tibtech.2018.11.013.
[40] N. Guaragnella, V. Palermo, A. Galli, L. Moro, C. Mazzoni, S. Giannattasio, The expanding role of yeast in cancer research and diagnosis: insights into the function of the oncosuppressors p53 and BRCA1/2, FEMS Yeast Res. 14 (2014) 2–16. https://doi.org/10.1111/1567-1364.12094.
[41] M.-A. Bjornsti, Cancer therapeutics in yeast, Cancer Cell 2 (2002) 267–273. https://doi.org/10.1016/s1535-6108(02)00160-5.
[42] G. Cazzanelli, F. Pereira, S. Alves, R. Francisco, L. Azevedo, P.D. Carvalho, A. Almeida, M. Côrte-Real, M. Oliveira, C. Lucas, M. Sousa, A. Preto, The Yeast Saccharomyces cerevisiae as a Model for Understanding RAS Proteins and their Role in Human Tumorigenesis, Cells 7 (2018) 14. https://doi.org/10.3390/cells7020014.
[43] C.S. Hoffman, V. Wood, P.A. Fantes, An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System, Genetics 201 (2015) 403–423. https://doi.org/10.1534/genetics.115.181503.
[44] PomBase - Gene - ura4 (SPCC330.05c) - orotidine 5’-phosphate decarboxylase Ura4, (n.d.). https://www.pombase.org/gene/SPCC330.05c (accessed June 3, 2024).
[45] H.P. Cam, S. Whitehall, Reporter Gene Silencing Assays in Fission Yeast, Cold Spring Harb. Protoc. 2016 (2016) pdb.prot091512. https://doi.org/10.1101/pdb.prot091512.
[46] K. Ragunathan, G. Jih, D. Moazed, Epigenetic inheritance uncoupled from sequence-specific recruitment, Science 348 (2015) 1258699. https://doi.org/10.1126/science.1258699.
[47] J. Petersen, P. Russell, Growth and the Environment of Schizosaccharomyces pombe, Cold Spring Harb. Protoc. 2016 (2016) pdb.top079764. https://doi.org/10.1101/pdb.top079764.
[48] G.I. Lang, Genome Instability, Methods and Protocols, Methods Mol. Biol. 1672 (2017) 21–31. https://doi.org/10.1007/978-1-4939-7306-4_3.
[49] S.E. Luria, M. Delbrück, MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE, Genetics 28 (1943) 491–511. https://doi.org/10.1093/genetics/28.6.491.
[50] P.L. Foster, Methods for Determining Spontaneous Mutation Rates, Methods Enzym. 409 (2006) 195–213. https://doi.org/10.1016/s0076-6879(05)09012-9.
[51] W.A. Rosche, P.L. Foster, Determining Mutation Rates in Bacterial Populations, Methods 20 (2000) 4–17. https://doi.org/10.1006/meth.1999.0901.
[52] O. Abdalla, C. Walker, K. Ishimori, R-code for calculating fluctuation assay results and 95% confidence intervals based on Ma-Sandri-Sarkar maximum likelihood, Softw. Impacts (2024) 100661. https://doi.org/10.1016/j.simpa.2024.100661.
[53] G.I. Lang, A.W. Murray, Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae, Genetics 178 (2008) 67–82. https://doi.org/10.1534/genetics.107.071506.
[54] O. Abdalla, C. Walker, R-codes for Calculating Fluctuation Assay Results and 95% Confidence Intervals Based on Ma-Sandri-Sarkar Maximum Likelihood, (2023). https://doi.org/10.21203/rs.3.rs-3646152/v1.
[55] O. Abdalla, C. Walker, Estimation of mutation rate for fluctuation assay via MSS Maximum Likelihood | Code Ocean, (n.d.). https://codeocean.com/capsule/8197897/tree/v1 (accessed April 28, 2024).
[56] O. Abdalla, C. Walker, GitHub - OlaAbdalla/Fluctuation-Assay: R-code for Calculating Fluctuation Assay Results and 95% Confidence Intervals Based on Ma-Sandri-Sarkar Maximum Likelihood, (n.d.). https://github.com/OlaAbdalla/Fluctuation-Assay (accessed April 28, 2024).
[57] C.L. Zheng, N.J. Wang, J. Chung, H. Moslehi, J.Z. Sanborn, J.S. Hur, E.A. Collisson, S.S. Vemula, A. Naujokas, K.E. Chiotti, J.B. Cheng, H. Fassihi, A.J. Blumberg, C.V. Bailey, G.M. Fudem, F.G. Mihm, B.B. Cunningham, I.M. Neuhaus, W. Liao, D.H. Oh, J.E. Cleaver, P.E. LeBoit, J.F. Costello, A.R. Lehmann, J.W. Gray, P.T. Spellman, S.T. Arron, N. Huh, E. Purdom, R.J. Cho, Transcription Restores DNA Repair to Heterochromatin, Determining Regional Mutation Rates in Cancer Genomes, Cell Rep. 9 (2014) 1228–1234. https://doi.org/10.1016/j.celrep.2014.10.031.
[58] B. Schuster-Böckler, B. Lehner, Chromatin organization is a major influence on regional mutation rates in human cancer cells, Nature 488 (2012) 504–507. https://doi.org/10.1038/nature11273.
[59] A. Barski, S. Cuddapah, K. Cui, T.-Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev, K. Zhao, High-Resolution Profiling of Histone Methylations in the Human Genome, Cell 129 (2007) 823–837. https://doi.org/10.1016/j.cell.2007.05.009.
[60] T.S. Mikkelsen, M. Ku, D.B. Jaffe, B. Issac, E. Lieberman, G. Giannoukos, P. Alvarez, W. Brockman, T.-K. Kim, R.P. Koche, W. Lee, E. Mendenhall, A. O’Donovan, A. Presser, C. Russ, X. Xie, A. Meissner, M. Wernig, R. Jaenisch, C. Nusbaum, E.S. Lander, B.E. Bernstein, Genome-wide maps of chromatin state in pluripotent and lineage-committed cells, Nature 448 (2007) 553–560. https://doi.org/10.1038/nature06008.
[61] E.D. Pleasance, R.K. Cheetham, P.J. Stephens, D.J. McBride, S.J. Humphray, C.D. Greenman, I. Varela, M.-L. Lin, G.R. Ordóñez, G.R. Bignell, K. Ye, J. Alipaz, M.J. Bauer, D. Beare, A. Butler, R.J. Carter, L. Chen, A.J. Cox, S. Edkins, P.I. Kokko-Gonzales, N.A. Gormley, R.J. Grocock, C.D. Haudenschild, M.M. Hims, T. James, M. Jia, Z. Kingsbury, C. Leroy, J. Marshall, A. Menzies, L.J. Mudie, Z. Ning, T. Royce, O.B. Schulz-Trieglaff, A. Spiridou, L.A. Stebbings, L. Szajkowski, J. Teague, D. Williamson, L. Chin, M.T. Ross, P.J. Campbell, D.R. Bentley, P.A. Futreal, M.R. Stratton, A comprehensive catalogue of somatic mutations from a human cancer genome, Nature 463 (2010) 191–196. https://doi.org/10.1038/nature08658.
[62] S.P. Rowbotham, F. Li, A.F.M. Dost, S.M. Louie, B.P. Marsh, P. Pessina, C.R. Anbarasu, C.F. Brainson, S.J. Tuminello, A. Lieberman, S. Ryeom, T.M. Schlaeger, B.J. Aronow, H. Watanabe, K.K. Wong, C.F. Kim, H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression, Nat. Commun. 9 (2018) 4559. https://doi.org/10.1038/s41467-018-07077-1.