Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140

Lindahl, 1999, Quality control by DNA repair, Science, 286, 1897, 10.1126/science.286.5446.1897 Olivieri, 2020, A genetic map of the response to DNA damage in human cells, Cell, 182, 481, 10.1016/j.cell.2020.05.040 Garcia-Nieto, 2019, The somatic mutation landscape of the human body, Genome Biol., 20, 298, 10.1186/s13059-019-1919-5 Watson, 2020, The evolutionary dynamics and fitness landscape of clonal hematopoiesis, Science, 367, 1449, 10.1126/science.aay9333 Schuster-Bockler, 2012, Chromatin organization is a major influence on regional mutation rates in human cancer cells, Nature, 488, 504, 10.1038/nature11273 Sabarinathan, 2016, Nucleotide excision repair is impaired by binding of transcription factors to DNA, Nature, 532, 264, 10.1038/nature17661 Perera, 2016, Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes, Nature, 532, 259, 10.1038/nature17437 Akdemir, 2020, Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure, Nat. Genet., 52, 1178, 10.1038/s41588-020-0708-0 Michael, 2021, Reading the chromatinized genome, Cell, 184, 3599, 10.1016/j.cell.2021.05.029 Szpiech, 2017, Prominent features of the amino acid mutation landscape in cancer, PLoS One, 12, 10.1371/journal.pone.0183273 Bestor, 2000, The DNA methyltransferases of mammals, Hum. Mol. Genet., 9, 2395, 10.1093/hmg/9.16.2395 Krokan, 2002, Uracil in DNA--occurrence, consequences and repair, Oncogene, 21, 8935, 10.1038/sj.onc.1205996 Prorok, 2013, Uracil in duplex DNA is a substrate for the nucleotide incision repair pathway in human cells, Proc. Natl. Acad. Sci. USA, 110, E3695, 10.1073/pnas.1305624110 Duncan, 1980, Mutagenic deamination of cytosine residues in DNA, Nature, 287, 560, 10.1038/287560a0 Li, 1992, Targeted mutation of the DNA methyltransferase gene results in embryonic lethality, Cell, 69, 915, 10.1016/0092-8674(92)90611-F Okano, 1999, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development, Cell, 99, 247, 10.1016/S0092-8674(00)81656-6 Ko, 2013, Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX, Nature, 497, 122, 10.1038/nature12052 Ley, 2010, DNMT3A mutations in acute myeloid leukemia, New Engl. J. Med., 363, 2424, 10.1056/NEJMoa1005143 Figueroa, 2010, Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation, Cancer Cell, 18, 553, 10.1016/j.ccr.2010.11.015 Ko, 2010, Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2, Nature, 468, 839, 10.1038/nature09586 Asada, 2021, Clonal hematopoiesis and associated diseases: a review of recent findings, Cancer Sci., 112, 3962, 10.1111/cas.15094 Poon, 2021, Synonymous mutations reveal genome-wide levels of positive selection in healthy tissues, Nat. Genet., 53, 1597, 10.1038/s41588-021-00957-1 Bick, 2020, Inherited causes of clonal haematopoiesis in 97,691 whole genomes, Nature, 586, 763, 10.1038/s41586-020-2819-2 Bhagwat, 2016, Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli, Proc. Natl. Acad. Sci. USA, 113, 2176, 10.1073/pnas.1522325113 Hollenhorst, 2011, Genomic and biochemical insights into the specificity of ETS transcription factors, Annu. Rev. Biochem., 80, 437, 10.1146/annurev.biochem.79.081507.103945 Mao, 2018, ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma, Nat. Commun., 9, 2626, 10.1038/s41467-018-05064-0 Elliott, 2018, Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers, PLoS Genet., 14, 10.1371/journal.pgen.1007849 Barak, 1995, Deamination of cytosine-containing pyrimidine photodimers in UV-irradiated DNA. Significance for UV light mutagenesis, J. Biol. Chem., 270, 24174, 10.1074/jbc.270.41.24174 Jin, 2021, The major mechanism of melanoma mutations is based on deamination of cytosine in pyrimidine dimers as determined by circle damage sequencing, Sci. Adv., 7 Yang, 2021, Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations, Nucleic Acids Res., 49, 5084, 10.1093/nar/gkab276 Wu, 2003, Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4, J. Biol. Chem., 278, 5285, 10.1074/jbc.M210884200 Hashimoto, 2012, Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation, Nucleic Acids Res., 40, 8276, 10.1093/nar/gks628 Hashimoto, 2012, Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation, Nucleic Acids Res., 40, 10203, 10.1093/nar/gks845 Hashimoto, 2013, Selective excision of 5-carboxylcytosine by a thymine DNA glycosylase mutant, J. Mol. Biol., 425, 971, 10.1016/j.jmb.2013.01.013 Hashimoto, 2013, Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH, DNA Repair, 12, 535, 10.1016/j.dnarep.2013.04.003 Emsley, 2010, Features and development of coot, Acta Crystallogr. D. Biol. Crystallogr., 66, 486, 10.1107/S0907444910007493 Garvie, 2001, Structural studies of Ets-1/Pax5 complex formation on DNA, Mol. Cell, 8, 1267, 10.1016/S1097-2765(01)00410-5 Cherry, 2018, Methylation-induced hypermutation in natural populations of bacteria, J. Bacteriol., 200, e00371, 10.1128/JB.00371-18 Zhou, 2020, The impact of DNA methylation dynamics on the mutation rate during human germline Development, G3, 10, 3337, 10.1534/g3.120.401511 Ershova, 2021, Enhanced C/EBP binding to G.T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells, Cell Rep., 36, 10.1016/j.celrep.2021.109365 Afek, 2020, DNA mismatches reveal conformational penalties in protein-DNA recognition, Nature, 587, 291, 10.1038/s41586-020-2843-2 Stephens, 2016, Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains, Nucleic Acids Res., 44, 8671, 10.1093/nar/gkw528 Hong, 2017, Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta, Nucleic Acids Res., 45, 2503, 10.1093/nar/gkx057 Liu, 2013, A common mode of recognition for methylated CpG, Trends Biochem. Sci., 38, 177, 10.1016/j.tibs.2012.12.005 Lindberg, 2019, Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light, Proc. Natl. Acad. Sci. USA, 116, 20411, 10.1073/pnas.1909021116 Zhang, 2011, International cancer genome consortium data portal--a one-stop shop for cancer genomics data, Database, 2011 Hendrich, 1999, The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites, Nature, 401, 301, 10.1038/45843 Neddermann, 1996, Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase, J. Biol. Chem., 271, 12767, 10.1074/jbc.271.22.12767 Cortazar, 2011, Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability, Nature, 470, 419, 10.1038/nature09672 Sanders, 2018, MBD4 guards against methylation damage and germ line deficiency predisposes to clonal hematopoiesis and early-onset AML, Blood, 132, 1526, 10.1182/blood-2018-05-852566 Onodera, 2021, Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells, Genome Biol., 22, 186, 10.1186/s13059-021-02384-1 Xu, 2018, Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1, Nat. Commun., 9, 3183, 10.1038/s41467-018-05644-0 Zhao, 2013, Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta, Proc. Natl. Acad. Sci. USA, 110, 8146, 10.1073/pnas.1303126110 Gross, 2010, Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations, J. Exp. Med., 207, 339, 10.1084/jem.20092506 Chou, 2011, The prognostic impact and stability of Isocitrate dehydrogenase 2 mutation in adult patients with acute myeloid leukemia, Leukemia, 25, 246, 10.1038/leu.2010.267 Rakheja, 2012, IDH mutations in acute myeloid leukemia, Hum. Pathol., 43, 1541, 10.1016/j.humpath.2012.05.003 Montalban-Bravo, 2018, The role of IDH mutations in acute myeloid leukemia, Future Oncol., 14, 979, 10.2217/fon-2017-0523