Abstract
The term epigenetics dates back to the 1940s, when Conrad Waddington introduced it to refer to gene expression changes that occur during development and do not involve alterations in the DNA sequence. Subsequently the definition expanded beyond development, and the field became one of the most rapidly developing ones in life sciences. Advances in epigenetics transformed our understanding of cellular and molecular events that occur during development, homeostasis, and disease and helped explain processes that have long fascinated and puzzled scientists, such as the link between inflammation and disease, the intricacies of memory formation and maintenance, and the connection between the social environment/social adversity and chronic disease risk. Epigenetically mediated gene expression changes were described in a broad group of medical conditions, including cancer and neurodegenerative, metabolic, autoimmune, psychiatric, and cardiovascular diseases and, of these, the most advanced understanding of their contribution, so far, has occurred for cancer. Changes in DNA methylation, histone posttranslational modifications, and microRNA alterations, described in a broad group of human cancers, were implicated in all stages of carcinogenesis, including initiation, progression, invasion, and metastasis. The discovery of epigenetic biomarkers facilitated novel strategies for the early detection of disease, helped better monitor progression, therapeutic response, and prognosis, and revolutionized personalized medicine. Moreover, the reversible nature of epigenetic marks opened the possibility to therapeutically reverse aberrant gene expression patterns and catalyzed the emergence of epigenetic drugs. Besides their promise as monotherapies, epigenetic drugs show considerable interest thanks to the possibility to combine them with other cancer therapeutic modalities, such as chemotherapy, hormone therapy, and radiation therapy.
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References
Ackloo S, Brown PJ, Müller S (2017) Chemical probes targeting epigenetic proteins: applications beyond oncology. Epigenetics 12:378–400
Adams D, Gonzalez-Duarte A, O’Riordan WD, Yang CC, Ueda M, Kristen AV, Tournev I, Schmidt HH, Coelho T, Berk JL, Lin KP, Vita G, Attarian S, Planté-Bordeneuve V, Mezei MM, Campistol JM, Buades J, Brannagan TH 3rd, Kim BJ, Oh J, Parman Y, Sekijima Y, Hawkins PN, Solomon SD, Polydefkis M, Dyck PJ, Gandhi PJ, Goyal S, Chen J, Strahs AL, Nochur SV, Sweetser MT, Garg PP, Vaishnaw AK, Gollob JA, Suhr OB (2018) Patisiran, an RNAi therapeutic, for hereditary transthyretin amyloidosis. N Engl J Med 379:11–21
Adeegbe DO, Freeman GJ, Wong K-K (2016) BET bromodomain inhibition synergizes with immune checkpoint blockade to facilitate anti-tumor response in a murine model of non-small cell lung cancer harboring activating KRAS mutation. J Immunol 196:74.10
Agarwal S, Simon AR, Goel V, Habtemariam BA, Clausen VA, Kim JB, Robbie GJ (2020) Pharmacokinetics and pharmacodynamics of the small interfering ribonucleic acid, Givosiran, in patients with acute hepatic porphyria. Clin Pharmacol Ther 108:63–72
Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM (2021) Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biol 22:136
Ahmad K, Henikoff S (2002) The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9:1191–1200
Ahmad W, Shabbiri K, Nazar N, Nazar S, Qaiser S, Shabbir Mughal MA (2011) Human linker histones: interplay between phosphorylation and O-β-GlcNAc to mediate chromatin structural modifications. Cell Div 6:15
Ahuja N, Sharma AR, Baylin SB (2016) Epigenetic therapeutics: a new weapon in the war against cancer. Annu Rev Med 67:73–89
Al Shaer D, Al Musaimi O, Albericio F, de la Torre BG (2022) 2021 FDA TIDES (peptides and oligonucleotides) harvest. Pharmaceuticals (Basel) 15:222
Alam H, Gu B, Lee MG (2015) Histone methylation modifiers in cellular signaling pathways. Cell Mol Life Sci 72:4577–4592
Alberts BJA, Lewis J et al (2002) Molecular biology of the cell, 4th edn. Garland Science, New York. An Overview of Gene Control. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26885/
Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A 51:786–794
Allis CD, Richman R, Gorovsky MA, Ziegler YS, Touchstone B, Bradley WA, Cook RG (1986) hv1 is an evolutionarily conserved H2A variant that is preferentially associated with active genes. J Biol Chem 261:1941–1948
Anderson C, Stern CD (2016) Organizers in Development. Curr Top Dev Biol 117:435–454
Angeloni A, Bogdanovic O (2021) Sequence determinants, function, and evolution of CpG islands. Biochem Soc Trans 49:1109–1119
Anghel SA, Ioniță-Mîndrican CB, Luca I, Pop AL (2021) Promising epigenetic biomarkers for the early detection of colorectal cancer: a systematic review. Cancers (Basel) 13:4965
Aran D, Toperoff G, Rosenberg M, Hellman A (2011) Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 20:670–680
Ardekani AM, Naeini MM (2010) The role of MicroRNAs in human diseases. Avicenna J Med Biotechnol 2:161–179
Asangani IA, Wilder-Romans K, Dommeti VL, Krishnamurthy PM, Apel IJ, Escara-Wilke J, Plymate SR, Navone NM, Wang S, Feng FY, Chinnaiyan AM (2016) BET Bromodomain inhibitors enhance efficacy and disrupt resistance to AR antagonists in the treatment of prostate cancer. Mol Cancer Res 14:324–331
Bagherani N, Smoller BR (2016) An overview of cutaneous T cell lymphomas. F1000Res 5. https://doi.org/10.12688/f1000research.8829.1
Bai Y, Zhou BR (2021) Structures of native-like nucleosomes: one step closer toward understanding the structure and function of chromatin. J Mol Biol 433:166648
Baldan F, Mio C, Allegri L, Conzatti K, Toffoletto B, Puppin C, Radovic S, Vascotto C, Russo D, Di Loreto C, Damante G (2016) Identification of tumorigenesis-related mRNAs associated with RNA-binding protein HuR in thyroid cancer cells. Oncotarget 7:63388–63407
Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, Park IH, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361–368
Ballman KV (2015) Biomarker: predictive or prognostic? J Clin Oncol 33:3968–3971
Balzeau J, Menezes MR, Cao S, Hagan JP (2017) The LIN28/let-7 pathway in cancer. Front Genet 8:31
Banach M, Kaźmierczak J, Mitkowski P, Wita K, Broncel M, Gąsior M, Gierlotka M, Gil R, Jankowski P, Niewada M, Witkowski A (2022) Which patients at risk of cardiovascular disease might benefit the most from inclisiran? Polish experts’ opinion. The compromise between EBM and possibilities in healthcare. Arch Med Sci 18:569–576
Banaszynski LA, Wen D, Dewell S, Whitcomb SJ, Lin M, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng D, Allis CD (2013) Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155:107–120
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
Bao Y, Konesky K, Park YJ, Rosu S, Dyer PN, Rangasamy D, Tremethick DJ, Laybourn PJ, Luger K (2004) Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. EMBO J 23:3314–3324
Barbarotta L, Hurley K (2015) Romidepsin for the treatment of peripheral T-cell lymphoma. J Adv Pract Oncol 6:22–36
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Baud’huin M, Lamoureux F, Jacques C, Rodriguez Calleja L, Quillard T, Charrier C, Amiaud J, Berreur M, Brounais-LeRoyer B, Owen R, Reilly GC, Bradner JE, Heymann D, Ory B (2017) Inhibition of BET proteins and epigenetic signaling as a potential treatment for osteoporosis. Bone 94:10–21
Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome – biological and translational implications. Nat Rev Cancer 11:726–734
Bellazzo A, Di Minin G, Collavin L (2017) Block one, unleash a hundred. Mechanisms of DAB2IP inactivation in cancer. Cell Death Differ 24:15–25
Beltrán-García J, Osca-Verdegal R, Mena-Mollá S, García-Giménez JL (2019) Epigenetic IVD tests for personalized precision medicine in cancer. Front Genet 10:621
Berdeja JG, Laubach JP, Richter J, Stricker S, Spencer A, Richardson PG, Chari A (2021) Panobinostat from bench to bedside: rethinking the treatment paradigm for multiple myeloma. Clin Lymphoma Myeloma Leuk 21:752–765
Berger NA (2018a) Young adult cancer: influence of the obesity pandemic. Obesity (Silver Spring) 26:641–650
Berger NA (2018b) Young adult cancer: influence of the obesity pandemic. Obesity 26:641–650
Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition of epigenetics. Genes Dev 23:781–783
Bian C, Yu X (2014) PGC7 suppresses TET3 for protecting DNA methylation. Nucleic Acids Res 42:2893–2905
Blum R (2015) Stepping inside the realm of epigenetic modifiers. Biomol Concepts 6:119–136
Bondarev AD, Attwood MM, Jonsson J, Chubarev VN, Tarasov VV, Schiöth HB (2021) Recent developments of HDAC inhibitors: emerging indications and novel molecules. Br J Clin Pharmacol 87:4577–4597
Bönisch C, Hake SB (2012) Histone H2A variants in nucleosomes and chromatin: more or less stable? Nucleic Acids Res 40:10719–10741
Bonner WM, Redon CE, Dickey JS, Nakamura AJ, Sedelnikova OA, Solier S, Pommier Y (2008) GammaH2AX and cancer. Nat Rev Cancer 8:957–967
Borchiellini M, Ummarino S, Di Ruscio A (2019) The bright and dark side of DNA methylation: a matter of balance. Cell 8:1243
Branco MR, Ficz G, Reik W (2011) Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 13:7–13
Browne TR (1980) Valproic Acid. N Engl J Med 302:661–666
Brownell JE, Allis CD (1995) An activity gel assay detects a single, catalytically active histone acetyltransferase subunit in Tetrahymena macronuclei. Proc Natl Acad Sci U S A 92:6364–6368
Brunner PM, Jonak C, Knobler R (2020) Recent advances in understanding and managing cutaneous T-cell lymphomas. F1000Res 9:F1000
Bubna AK (2015) Vorinostat-An Overview. Indian J Dermatol 60:419
Bukowski K, Kciuk M, Kontek R (2020) Mechanisms of multidrug resistance in cancer chemotherapy. Int J Mol Sci 21:3233
Burge C, Campbell AM, Karlin S (1992) Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci U S A 89:1358–1362
Butler LM, Agus DB, Scher HI, Higgins B, Rose A, Cordon-Cardo C, Thaler HT, Rifkind RA, Marks PA, Richon VM (2000) Suberoylanilide hydroxamic acid, an inhibitor of histone deacetylase, suppresses the growth of prostate cancer cells in vitro and in vivo. Cancer Res 60:5165–5170
Califf RM (2018) Biomarker definitions and their applications. Exp Biol Med (Maywood) 243:213–221
Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 99:15524–15529
Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, Croce CM (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A 101:2999–3004
Calle EE, Rodriguez C, Walker-Thurmond K, Thun MJ (2003) Overweight, obesity, and mortality from cancer in a prospectively studied cohort of U.S. adults. N Engl J Med 348:1625–1638
Campos EI, Reinberg D (2009) Histones: annotating chromatin. Annu Rev Genet 43:559–599
Capp JP (2021) Interplay between genetic, epigenetic, and gene expression variability: considering complexity in evolvability. Evol Appl 14:893–901
Carlomagno N, Incollingo P, Tammaro V, Peluso G, Rupealta N, Chiacchio G, Sandoval Sotelo ML, Minieri G, Pisani A, Riccio E, Sabbatini M, Bracale UM, Calogero A, Dodaro CA, Santangelo M (2017) Diagnostic, predictive, prognostic, and therapeutic molecular biomarkers in third millennium: a breakthrough in gastric cancer. Biomed Res Int 2017:7869802
Catalanotto C, Cogoni C, Zardo G (2016) MicroRNA in control of gene expression: An overview of nuclear functions. Int J Mol Sci 17:1712
Celeste A, Petersen S, Romanienko PJ, Fernandez-Capetillo O, Chen HT, Sedelnikova OA, Reina-San-Martin B, Coppola V, Meffre E, Difilippantonio MJ, Redon C, Pilch DR, Olaru A, Eckhaus M, Camerini-Otero RD, Tessarollo L, Livak F, Manova K, Bonner WM, Nussenzweig MC, Nussenzweig A (2002) Genomic instability in mice lacking histone H2AX. Science 296:922–927
Cervoni N, Szyf M (2001) Demethylase activity is directed by histone acetylation. J Biol Chem 276:40778–40787
Chadwick BP, Willard HF (2001) A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive X chromosome. J Cell Biol 152:375–384
Chadwick BP, Valley CM, Willard HF (2001) Histone variant macroH2A contains two distinct macrochromatin domains capable of directing macroH2A to the inactive X chromosome. Nucleic Acids Res 29:2699–2705
Chakravarthy S, Bao Y, Roberts VA, Tremethick D, Luger K (2004) Structural characterization of histone H2A variants. Cold Spring Harb Symp Quant Biol 69:227–234
Chan TS, Tse E, Kwong YL (2017) Chidamide in the treatment of peripheral T-cell lymphoma. Onco Targets Ther 10:347–352
Changolkar LN, Singh G, Pehrson JR (2008) macroH2A1-dependent silencing of endogenous murine leukemia viruses. Mol Cell Biol 28:2059–2065
Chateauvieux S, Morceau F, Dicato M, Diederich M (2010) Molecular and therapeutic potential and toxicity of valproic acid. J Biomed Biotechnol 2010:479364
Chédin F (2011) The DNMT3 family of mammalian de novo DNA methyltransferases. Prog Mol Biol Transl Sci 101:255–285
Chen H, Toyooka S, Gazdar AF, Hsieh JT (2003) Epigenetic regulation of a novel tumor suppressor gene (hDAB2IP) in prostate cancer cell lines. J Biol Chem 278:3121–3130
Chen H, Tu SW, Hsieh JT (2005) Down-regulation of human DAB2IP gene expression mediated by polycomb Ezh2 complex and histone deacetylase in prostate cancer. J Biol Chem 280:22437–22444
Chen Y, Sprung R, Tang Y, Ball H, Sangras B, Kim SC, Falck JR, Peng J, Gu W, Zhao Y (2007) Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics 6:812–819
Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W, Li X, Feng H, Zhao H, Zhu P, Li M, Wang QF, Li G (2013) H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev 27:2109–2124
Chen K, Zhang J, Guo Z, Ma Q, Xu Z, Zhou Y, Xu Z, Li Z, Liu Y, Ye X, Li X, Yuan B, Ke Y, He C, Zhou L, Liu J, Ci W (2016) Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res 26:103–118
Chen R, Zhang Q, Duan X, York P, Chen GD, Yin P, Zhu H, Xu M, Chen P, Wu Q, Li D, Samarut J, Xu G, Zhang P, Cao X, Li J, Wong J (2017) The 5-Hydroxymethylcytosine (5hmC) reader UHRF2 is required for Normal levels of 5hmC in mouse adult brain and spatial learning and memory. J Biol Chem 292:4533–4543
Cheng Y, Li Z, Manupipatpong S, Lin L, Li X, Xu T, Jiang YH, Shu Q, Wu H, Jin P (2018) 5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder. Hum Mol Genet 27:2955–2964
Chern YJ, Tai IT (2020) Adaptive response of resistant cancer cells to chemotherapy. Cancer Biol Med 17:842–863
Chew YC, Camporeale G, Kothapalli N, Sarath G, Zempleni J (2006) Lysine residues in N-terminal and C-terminal regions of human histone H2A are targets for biotinylation by biotinidase. J Nutr Biochem 17:225–233
Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J (2021) Short H2A histone variants are expressed in cancer. Nat Commun 12:490
Chi P, Allis CD, Wang GG (2010) Covalent histone modifications–miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10:457–469
Chinaranagari S, Sharma P, Bowen NJ, Chaudhary J (2015) Prostate cancer epigenome. Methods Mol Biol 1238:125–140
Chirshev E, Oberg KC, Ioffe YJ, Unternaehrer JJ (2019) Let-7 as biomarker, prognostic indicator, and therapy for precision medicine in cancer. Clin Transl Med 8:24
Choghaei E, Khamisipour G, Falahati M, Naeimi B, Mossahebi-Mohammadi M, Tahmasebi R, Hasanpour M, Shamsian S, Hashemi ZS (2016) Knockdown of microRNA-29a changes the expression of heat shock proteins in breast carcinoma MCF-7 cells. Oncol Res 23:69–78
Choi JD, Lee JS (2013) Interplay between epigenetics and genetics in cancer. Genomics Inform 11:164–173
Choi HS, Choi BY, Cho YY, Mizuno H, Kang BS, Bode AM, Dong Z (2005) Phosphorylation of histone H3 at serine 10 is indispensable for neoplastic cell transformation. Cancer Res 65:5818–5827
Choi C, Lee GH, Son A, Yoo GS, Yu JI, Park HC (2021) Downregulation of Mcl-1 by Panobinostat potentiates proton beam therapy in hepatocellular carcinoma cells. Cell 10:554
Chokkalla AK, Mehta SL, Vemuganti R (2022) Epitranscriptomic modifications modulate Normal and pathological functions in CNS. Transl Stroke Res 13:1–11
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325:834–840
Ciechomska M, O’Reilly S (2016) Epigenetic modulation as a therapeutic Prospect for treatment of autoimmune rheumatic diseases. Mediat Inflamm 2016:9607946
Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M, Wojcik SE, Aqeilan RI, Zupo S, Dono M, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM (2005) miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A 102:13944–13949
Cloonan N (2015) Re-thinking miRNA-mRNA interactions: intertwining issues confound target discovery. BioEssays 37:379–388
Cobos SN, Bennett SA, Torrente MP (2019) The impact of histone post-translational modifications in neurodegenerative diseases. Biochim Biophys Acta Mol basis Dis 1865:1982–1991
Cohen LA, Amin S, Marks PA, Rifkind RA, Desai D, Richon VM (1999) Chemoprevention of carcinogen-induced mammary tumorigenesis by the hybrid polar cytodifferentiation agent, suberanilohydroxamic acid (SAHA). Anticancer Res 19:4999–5005
Cohen I, Poręba E, Kamieniarz K, Schneider R (2011) Histone modifiers in cancer: friends or foes? Genes Cancer 2:631–647
Colino-Sanguino Y, Clark SJ, Valdes-Mora F (2016) H2A.Z acetylation and transcription: ready, steady, go! Epigenomics 8:583–586
Connolly DR, Zhou Z (2019) Genomic insights into MeCP2 function: a role for the maintenance of chromatin architecture. Curr Opin Neurobiol 59:174–179
Coomer MA, Ham L, Stumpf MPH (2022) Noise distorts the epigenetic landscape and shapes cell-fate decisions. Cell Syst 13:83–102.e106
Cooper DN, Mort M, Stenson PD, Ball EV, Chuzhanova NA (2010) Methylation-mediated deamination of 5-methylcytosine appears to give rise to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides. Hum Genomics 4:406–410
Corujo D, Buschbeck M (2018) Post-translational modifications of H2A histone variants and their role in cancer. Cancers (Basel) 10:59
Costanzi C, Pehrson JR (1998) Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 393:599–601
Costa-Pinheiro P, Montezuma D, Henrique R, Jerónimo C (2015) Diagnostic and prognostic epigenetic biomarkers in cancer. Epigenomics 7:1003–1015
Coussens LM, Werb Z (2002) Inflammation and cancer. Nature 420:860–867
Daher-Reyes GS, Merchan BM, Yee KWL (2019) Guadecitabine (SGI-110): an investigational drug for the treatment of myelodysplastic syndrome and acute myeloid leukemia. Expert Opin Investig Drugs 28:835–849
Dai L, Xie X, Zhou Z (2018) Crystal structure of the histone heterodimer containing histone variant H2A.Bbd. Biochem Biophys Res Commun 503:1786–1791
Dalvai M, Bellucci L, Fleury L, Lavigne AC, Moutahir F, Bystricky K (2013) H2A.Z-dependent crosstalk between enhancer and promoter regulates cyclin D1 expression. Oncogene 32:4243–4251
Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R (2015) Evolving insights on how cytosine methylation affects protein-DNA binding. Brief Funct Genomics 14:61–73
Das PM, Singal R (2004) DNA methylation and cancer. J Clin Oncol 22:4632–4642
Davis-Dusenbery BN, Hata A (2010) MicroRNA in cancer: the involvement of aberrant MicroRNA biogenesis regulatory pathways. Genes Cancer 1:1100–1114
de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R (2021) The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 5:369–378
De Pergola G, Silvestris F (2013) Obesity as a major risk factor for cancer. J Obes 2013:291546
de Vos D, van Overveld W (2005) Decitabine: a historical review of the development of an epigenetic drug. Ann Hematol 84:3
Deng T, Lyon CJ, Bergin S, Caligiuri MA, Hsueh WA (2016) Obesity, inflammation, and cancer. Annu Rev Pathol 11:421–449
Denissenko MF, Chen JX, Tang MS, Pfeifer GP (1997) Cytosine methylation determines hot spots of DNA damage in the human P53 gene. Proc Natl Acad Sci U S A 94:3893–3898
Desrosiers R, Friderici K, Rottman F (1974) Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc Natl Acad Sci U S A 71:3971–3975
Diamantopoulos MA, Tsiakanikas P, Scorilas A (2018) Non-coding RNAs: the riddle of the transcriptome and their perspectives in cancer. Ann Transl Med 6:241
Dickey JS, Redon CE, Nakamura AJ, Baird BJ, Sedelnikova OA, Bonner WM (2009) H2AX: functional roles and potential applications. Chromosoma 118:683–692
Diesch J, Zwick A, Garz A-K, Palau A, Buschbeck M, Götze KS (2016) A clinical-molecular update on azanucleoside-based therapy for the treatment of hematologic cancers. Clin Epigenetics 8:71
do Canto LM, Barros-Filho MC, Rainho CA, Marinho D, BEC K, Begnami M, Scapulatempo-Neto C, Havelund BM, Lindebjerg J, Marchi FA, Baumbach J, Aguiar S Jr, Rogatto SR (2020) Comprehensive analysis of DNA methylation and prediction of response to NeoadjuvantTherapy in locally advanced rectal cancer. Cancers (Basel) 12:3079
Dong E, Chen Y, Gavin DP, Grayson DR, Guidotti A (2010) Valproate induces DNA demethylation in nuclear extracts from adult mouse brain. Epigenetics 5:730–735
Dryhurst D, Ishibashi T, Rose KL, Eirín-López JM, McDonald D, Silva-Moreno B, Veldhoen N, Helbing CC, Hendzel MJ, Shabanowitz J, Hunt DF, Ausió J (2009) Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates. BMC Biol 7:86
Duan Q, Chen H, Costa M, Dai W (2008) Phosphorylation of H3S10 blocks the access of H3K9 by specific antibodies and histone methyltransferase. Implication in regulating chromatin dynamics and epigenetic inheritance during mitosis. J Biol Chem 283:33585–33590
Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma’ayan A, Narita M, Bernstein E (2014) Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nat Commun 5:5210
Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561
Duncan EM, Muratore-Schroeder TL, Cook RG, Garcia BA, Shabanowitz J, Hunt DF, Allis CD (2008) Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell 135:284–294
Dürig J, Bug S, Klein-Hitpass L, Boes T, Jöns T, Martin-Subero JI, Harder L, Baudis M, Dührsen U, Siebert R (2007) Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32). Leukemia 21:2153–2163
Duvic M, Talpur R, Ni X, Zhang C, Hazarika P, Kelly C, Chiao JH, Reilly JF, Ricker JL, Richon VM, Frankel SR (2007) Phase 2 trial of oral vorinostat (suberoylanilide hydroxamic acid, SAHA) for refractory cutaneous T-cell lymphoma (CTCL). Blood 109:31–39
Eleutherakis-Papaiakovou E, Kanellias N, Kastritis E, Gavriatopoulou M, Terpos E, Dimopoulos MA (2020) Efficacy of Panobinostat for the treatment of multiple myeloma. J Oncol 2020:7131802
Elsheikh SE, Green AR, Rakha EA, Powe DG, Ahmed RA, Collins HM, Soria D, Garibaldi JM, Paish CE, Ammar AA, Grainge MJ, Ball GR, Abdelghany MK, Martinez-Pomares L, Heery DM, Ellis IO (2009) Global histone modifications in breast cancer correlate with tumor phenotypes, prognostic factors, and patient outcome. Cancer Res 69:3802–3809
Esquela-Kerscher A, Slack FJ (2006) Oncomirs — microRNAs with a role in cancer. Nat Rev Cancer 6:259–269
Esteller M, Toyota M, Sanchez-Cespedes M, Capella G, Peinado MA, Watkins DN, Issa JP, Sidransky D, Baylin SB, Herman JG (2000) Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is associated with G to A mutations in K-ras in colorectal tumorigenesis. Cancer Res 60:2368–2371
Faast R, Thonglairoam V, Schulz TC, Beall J, Wells JR, Taylor H, Matthaei K, Rathjen PD, Tremethick DJ, Lyons I (2001) Histone variant H2A.Z is required for early mammalian development. Curr Biol 11:1183–1187
Feinberg AP (2014) Epigenetic stochasticity, nuclear structure and cancer: the implications for medicine. J Intern Med 276:5–11
Feinberg AP, Vogelstein B (1983a) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92
Feinberg AP, Vogelstein B (1983b) Hypomethylation of ras oncogenes in primary human cancers. Biochem Biophys Res Commun 111:47–54
Feng Y, Fan Y, Huiqing C, Zicai L, Quan D (2014) The emerging landscape of long non-coding RNAs. Yi Chuan 36:456–468
Ferrand J, Rondinelli B, Polo SE (2020) Histone variants: guardians of genome integrity. Cell 9:2424
Festuccia C, Gravina GL, D’Alessandro AM, Muzi P, Millimaggi D, Dolo V, Ricevuto E, Vicentini C, Bologna M (2009) Azacitidine improves antitumor effects of docetaxel and cisplatin in aggressive prostate cancer models. Endocr Relat Cancer 16:401–413
Ficz G, Gribben JG (2014) Loss of 5-hydroxymethylcytosine in cancer: cause or consequence? Genomics 104:352–357
Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, Hunt DF, Funabiki H, Allis CD (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438:1116–1122
Flatmark K, Nome RV, Folkvord S, Bratland A, Rasmussen H, Ellefsen MS, Fodstad Ø, Ree AH (2006) Radiosensitization of colorectal carcinoma cell lines by histone deacetylase inhibition. Radiat Oncol 1:25
Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet 37:391–400
Francescone R, Hou V, Grivennikov SI (2014) Microbiome, inflammation, and cancer. Cancer J 20:181–189
Frey A, Listovsky T, Guilbaud G, Sarkies P, Sale JE (2014) Histone H3.3 is required to maintain replication fork progression after UV damage. Curr Biol 24:2195–2201
Fryxell KJ, Moon W-J (2004) CpG mutation rates in the human genome are highly dependent on local GC content. Mol Biol Evol 22:650–658
Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T (2003) The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 278:4035–4040
Furman D, Campisi J, Verdin E, Carrera-Bastos P, Targ S, Franceschi C, Ferrucci L, Gilroy DW, Fasano A, Miller GW, Miller AH, Mantovani A, Weyand CM, Barzilai N, Goronzy JJ, Rando TA, Effros RB, Lucia A, Kleinstreuer N, Slavich GM (2019) Chronic inflammation in the etiology of disease across the life span. Nat Med 25:1822–1832
Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, Ehrlich M (1983) The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res 11:6883–6894
Gangopadhyay S, Gore KR (2022) Advances in siRNA therapeutics and synergistic effect on siRNA activity using emerging dual ribose modifications. RNA Biol 19:452–467
Garcia JS, Jain N, Godley LA (2010) An update on the safety and efficacy of decitabine in the treatment of myelodysplastic syndromes. Onco Targets Ther 3:1–13
García-Giménez JL, Seco-Cervera M, Tollefsbol TO, Romá-Mateo C, Peiró-Chova L, Lapunzina P, Pallardó FV (2017) Epigenetic biomarkers: current strategies and future challenges for their use in the clinical laboratory. Crit Rev Clin Lab Sci 54:529–550
Garcia-Manero G, Roboz G, Walsh K, Kantarjian H, Ritchie E, Kropf P, O’Connell C, Tibes R, Lunin S, Rosenblat T, Yee K, Stock W, Griffiths E, Mace J, Podoltsev N, Berdeja J, Jabbour E, Issa JJ, Hao Y, Keer HN, Azab M, Savona MR (2019) Guadecitabine (SGI-110) in patients with intermediate or high-risk myelodysplastic syndromes: phase 2 results from a multicentre, open-label, randomised, phase 1/2 trial. Lancet Haematol 6:e317–e327
Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282
Garnock-Jones KP (2015) Panobinostat: first global approval. Drugs 75:695–704
Gebeshuber CA, Zatloukal K, Martinez J (2009) miR-29a suppresses tristetraprolin, which is a regulator of epithelial polarity and metastasis. EMBO Rep 10:400–405
Georgoulis A, Vorgias CE, Chrousos GP, Rogakou EP (2017) Genome instability and γH2AX. Int J Mol Sci 18:1979
Gertz MA, Mauermann ML, Grogan M, Coelho T (2019) Advances in the treatment of hereditary transthyretin amyloidosis: a review. Brain Behav 9:e01371
Gévry N, Hardy S, Jacques PE, Laflamme L, Svotelis A, Robert F, Gaudreau L (2009) Histone H2A.Z is essential for estrogen receptor signaling. Genes Dev 23:1522–1533
Gielen GH, Gessi M, Hammes J, Kramm CM, Waha A, Pietsch T (2013) H3F3A K27M mutation in pediatric CNS tumors: a marker for diffuse high-grade astrocytomas. Am J Clin Pathol 139:345–349
Gilles ME, Slack FJ (2018) Let-7 microRNA as a potential therapeutic target with implications for immunotherapy. Expert Opin Ther Targets 22:929–939
Globisch D, Münzel M, Müller M, Michalakis S, Wagner M, Koch S, Brückl T, Biel M, Carell T (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5:e15367
Goel S, Bhatia V, Biswas T, Ateeq B (2021) Epigenetic reprogramming during prostate cancer progression: a perspective from development. Semin Cancer Biol 83:136
Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a landscape takes shape. Cell 128:635–638
González-Romero R, Méndez J, Ausió J, Eirín-López JM (2008) Quickly evolving histones, nucleosome stability and chromatin folding: all about histone H2A.Bbd. Gene 413:1–7
Goossens N, Nakagawa S, Sun X, Hoshida Y (2015) Cancer biomarker discovery and validation. Transl Cancer Res 4:256–269
Gore SD, Jones C, Kirkpatrick P (2006) Decitabine. Nat Rev Drug Discov 5:891–892
Gorodilov Iu N (2001) Spemann’s organizer—it’s origin and derivatives (cellular-tissue and molecular-genetic aspects). Tsitologiia 43:182–203
Göttlicher M, Minucci S, Zhu P, Krämer OH, Schimpf A, Giavara S, Sleeman JP, Lo Coco F, Nervi C, Pelicci PG, Heinzel T (2001) Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. EMBO J 20:6969–6978
Gowher H, Jeltsch A (2018) Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 46:1191–1202
Grippo P, Iaccarino M, Parisi E, Scarano E (1968) Methylation of DNA in developing sea urchin embryos. J Mol Biol 36:195–208
Grivennikov SI, Greten FR, Karin M (2010) Immunity, inflammation, and cancer. Cell 140:883–899
Gromova M, Vaggelas A, Dallmann G, Seimetz D (2020) Biomarkers: opportunities and challenges for drug development in the current regulatory landscape. Biomark Insights 15:1177271920974652
Group BDW (2001) Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clin Pharmacol Ther 69:89–95
Guo JU, Ma DK, Mo H, Ball MP, Jang MH, Bonaguidi MA, Balazer JA, Eaves HL, Xie B, Ford E, Zhang K, Ming GL, Gao Y, Song H (2011) Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat Neurosci 14:1345–1351
Guo R, Zheng L, Park JW, Lv R, Chen H, Jiao F, Xu W, Mu S, Wen H, Qiu J, Wang Z, Yang P, Wu F, Hui J, Fu X, Shi X, Shi YG, Xing Y, Lan F, Shi Y (2014a) BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Mol Cell 56:298–310
Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ (2014b) Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res 42:3009–3016
Gurdon JB, Uehlinger V (1966) “Fertile” intestine nuclei. Nature 210:1240–1241
Hake SB, Garcia BA, Kauer M, Baker SP, Shabanowitz J, Hunt DF, Allis CD (2005) Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes. Proc Natl Acad Sci U S A 102:6344–6349
Hall BK (2015) Waddington’s legacy in development and Evolution1. Am Zool 32:113–122
Hamamoto R, Furukawa Y, Morita M, Iimura Y, Silva FP, Li M, Yagyu R, Nakamura Y (2004) SMYD3 encodes a histone methyltransferase involved in the proliferation of cancer cells. Nat Cell Biol 6:731–740
Hamm CA, Costa FF (2015) Epigenomes as therapeutic targets. Pharmacol Ther 151:72–86
Han L, Chen C, Lu X, Song Y, Zhang Z, Zeng C, Chiu R, Li L, Xu M, He C, Zhang W, Duan S (2021) Alterations of 5-hydroxymethylcytosines in circulating cell-free DNA reflect retinopathy in type 2 diabetes. Genomics 113:79–87
Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9:e1003569
Hatch CL, Bonner WM (1990) The human histone H2A.Z gene. Sequence and regulation. J Biol Chem 265:15211–15218
Hayashi-Takanaka Y, Yamagata K, Nozaki N, Kimura H (2009) Visualizing histone modifications in living cells: spatiotemporal dynamics of H3 phosphorylation during interphase. J Cell Biol 187:781–790
He PC, He C (2021) M(6) a RNA methylation: from mechanisms to therapeutic potential. EMBO J 40:e105977
He RZ, Jiang J, Luo DX (2020a) The functions of N6-methyladenosine modification in lncRNAs. Genes Dis 7:598–605
He Y, Chen D, Yi Y, Zeng S, Liu S, Li P, Xie H, Yu P, Jiang G, Liu H (2020b) Histone deacetylase inhibitor sensitizes ERCC1-high non-small-cell lung cancer cells to cisplatin via regulating miR-149. Mol Ther Oncolytics 17:448–459
Héberlé É, Bardet AF (2019) Sensitivity of transcription factors to DNA methylation. Essays Biochem 63:727–741
Hermann A, Gowher H, Jeltsch A (2004) Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 61:2571–2587
Hirayama F, Takagi S, Yokoyama Y, Yamamoto K, Iwao E, Haga K (2002) Long-term effects of helicobacter pylori eradication in Mongolian gerbils. J Gastroenterol 37:779–784
Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226–232
Hollstein M, Sidransky D, Vogelstein B, Harris CC (1991) p53 mutations in human cancers. Science 253:49–53
Hollstein M, Shomer B, Greenblatt M, Soussi T, Hovig E, Montesano R, Harris CC (1996) Somatic point mutations in the p53 gene of human tumors and cell lines: updated compilation. Nucleic Acids Res 24:141–146
Holmila R, Sklias A, Muller DC, Degli Esposti D, Guilloreau P, McKay J, Sangrajrang S, Srivatanakul P, Hainaut P, Merle P, Herceg Z, Nogueira da Costa A (2017) Targeted deep sequencing of plasma circulating cell-free DNA reveals vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma. PLoS One 12:e0174265
Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84
Honda S, Fujioka T, Tokieda M, Satoh R, Nishizono A, Nasu M (1998) Development of helicobacter pylori-induced gastric carcinoma in Mongolian gerbils. Cancer Res 58:4255–4259
Hoque MO, Begum S, Topaloglu O, Jeronimo C, Mambo E, Westra WH, Califano JA, Sidransky D (2004) Quantitative detection of promoter hypermethylation of multiple genes in the tumor, urine, and serum DNA of patients with renal cancer. Cancer Res 64:5511–5517
Horwitz GA, Zhang K, McBrian MA, Grunstein M, Kurdistani SK, Berk AJ (2008) Adenovirus small e1a alters global patterns of histone modification. Science 321:1084–1085
Hosseinahli N, Aghapour M, Duijf PHG, Baradaran B (2018) Treating cancer with microRNA replacement therapy: a literature review. J Cell Physiol 233:5574–5588
Hotchkiss RD (1948) The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem 175:315–332
Hoy SM (2020) Tazemetostat: First Approval. Drugs 80:513–521
Hsu CC, Shi J, Yuan C, Zhao D, Jiang S, Lyu J, Wang X, Li H, Wen H, Li W, Shi X (2018) Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes Dev 32:58–69
Hsu CJ, Meers O, Buschbeck M, Heidel FH (2021) The role of MacroH2A histone variants in cancer. Cancers (Basel) 13:3003
Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia S, Liu S, Lyu H, Ming GL, Wade H, Song H, Qian J, Zhu H (2013) DNA methylation presents distinct binding sites for human transcription factors. elife 2:e00726
Hu C, Liu T, Xu Y, Han C, Yang S, Yang K (2022) METTL14 promotes the proliferation and migration of cervical cancer cells by up-regulating m(6)a Myc expression. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 38:131–137
Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP (2008) Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol 4:188
Hussain SP, Harris CC (2007) Inflammation and cancer: an ancient link with novel potentials. Int J Cancer 121:2373–2380
Hutt DM, Roth DM, Vignaud H, Cullin C, Bouchecareilh M (2014) The histone deacetylase inhibitor, Vorinostat, represses hypoxia inducible factor 1 alpha expression through translational inhibition. PLoS One 9:e106224
Iliopoulos D, Hirsch HA, Struhl K (2009) An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell 139:693–706
Iliopoulos D, Jaeger SA, Hirsch HA, Bulyk ML, Struhl K (2010) STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer. Mol Cell 39:493–506
Ilse P, Biesterfeld S, Pomjanski N, Wrobel C, Schramm M (2014) Analysis of SHOX2 methylation as an aid to cytology in lung cancer diagnosis. Cancer Genomics Proteomics 11:251–258
Inoue A, Fujimoto D (1969) Enzymatic deacetylation of histone. Biochem Biophys Res Commun 36:146–150
Irizarry RA, Wu H, Feinberg AP (2009) A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome 20:674–680
Ishibashi T, Li A, Eirín-López JM, Zhao M, Missiaen K, Abbott DW, Meistrich M, Hendzel MJ, Ausió J (2009) H2A.Bbd: an X-chromosome-encoded histone involved in mammalian spermiogenesis. Nucleic Acids Res 38:1780–1789
Issa JP, Kantarjian H (2005) Azacitidine. Nat Rev Drug Discov 4(Suppl S6–7):275
Issa JJ, Roboz G, Rizzieri D, Jabbour E, Stock W, O’Connell C, Yee K, Tibes R, Griffiths EA, Walsh K, Daver N, Chung W, Naim S, Taverna P, Oganesian A, Hao Y, Lowder JN, Azab M, Kantarjian H (2015) Safety and tolerability of guadecitabine (SGI-110) in patients with myelodysplastic syndrome and acute myeloid leukaemia: a multicentre, randomised, dose-escalation phase 1 study. Lancet Oncol 16:1099–1110
Jabbour E, Issa JP, Garcia-Manero G, Kantarjian H (2008) Evolution of decitabine development: accomplishments, ongoing investigations, and future strategies. Cancer 112:2341–2351
Jain K, Fraser CS, Marunde MR, Parker MM, Sagum C, Burg JM, Hall N, Popova IK, Rodriguez KL, Vaidya A, Krajewski K, Keogh MC, Bedford MT, Strahl BD (2020) Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions. Epigenetics Chromatin 13:3
James SJ, Shpyleva S, Melnyk S, Pavliv O, Pogribny IP (2014) Elevated 5-hydroxymethylcytosine in the Engrailed-2 (EN-2) promoter is associated with increased gene expression and decreased MeCP2 binding in autism cerebellum. Transl Psychiatry 4:e460
Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T (2015) Histone H3.3 maintains genome integrity during mammalian development. Genes Dev 29:1377–1392
Jang HS, Shin WJ, Lee JE, Do JT (2017) CpG and non-CpG methylation in epigenetic gene regulation and brain function. Genes (Basel) 8:148
Jankowski J, Holst MI, Liebig C, Oberdick J, Baader SL (2004) Engrailed-2 negatively regulates the onset of perinatal Purkinje cell differentiation. J Comp Neurol 472:87–99
Jeffery NN, Davidson C, Peslak SA, Kingsley PD, Nakamura Y, Palis J, Bulger M (2021) Histone H2A.X phosphorylation and caspase-initiated chromatin condensation in late-stage erythropoiesis. Epigenetics Chromatin 14:37
Jiang X, Wen J, Paver E, Wu Y-H, Sun G, Bullman A, Dahlstrom Jane E, Tremethick DJ, Soboleva TA (2021) H2A.B is a cancer/testis factor involved in the activation of ribosome biogenesis in Hodgkin lymphoma. EMBO Rep 22:e52462
Jin Z, Liu Y (2018) DNA methylation in human diseases. Genes Dis 5:1–8
Jin B, Li Y, Robertson KD (2011a) DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer 2:607–617
Jin S-G, Jiang Y, Qiu R, Rauch TA, Wang Y, Schackert G, Krex D, Lu Q, Pfeifer GP (2011b) 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels Do not correlate with IDH1 mutations. Cancer Res 71:7360–7365
Jirtle RL (2009) Epigenome: the program for human health and disease. Epigenomics 1:13–16
Johansen KM, Johansen J (2006) Regulation of chromatin structure by histone H3S10 phosphorylation. Chromosom Res 14:393–404
Johnson TB, Coghill RD (1925) Researches on pyrimidines. C111. The discovery of 5-methyl-cytosine in Tuberculinic acid, the nucleic acid of the tubercle Bacillus1. J Am Chem Soc 47:2838–2844
Jones PA, Taylor SM (1980) Cellular differentiation, cytidine analogs and DNA methylation. Cell 20:85–93
Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19:187–191
Jueliger S, Lyons J, Cannito S, Pata I, Pata P, Shkolnaya M, Lo Re O, Peyrou M, Villarroya F, Pazienza V, Rappa F, Cappello F, Azab M, Taverna P, Vinciguerra M (2016) Efficacy and epigenetic interactions of novel DNA hypomethylating agent guadecitabine (SGI-110) in preclinical models of hepatocellular carcinoma. Epigenetics 11:709–720
Julia E, Salles G (2021) EZH2 inhibition by tazemetostat: mechanisms of action, safety and efficacy in relapsed/refractory follicular lymphoma. Future Oncol 17:2127–2140
Jung S, Yi L, Kim J, Jeong D, Oh T, Kim CH, Kim CJ, Shin J, An S, Lee MS (2011) The role of vimentin as a methylation biomarker for early diagnosis of cervical cancer. Mol Cells 31:405–411
Jurkowska RZ, Jurkowski TP, Jeltsch A (2011) Structure and function of mammalian DNA methyltransferases. Chembiochem 12:206–222
Jutras S, Bachvarova M, Keita M, Bascands J-L, Mes-Masson A-M, Stewart JM, Bachvarov D (2010) Strong cytotoxic effect of the bradykinin antagonist BKM-570 in ovarian cancer cells – analysis of the molecular mechanisms of its antiproliferative action. FEBS J 277:5146–5160
Kaczmarek JV, Bogan CM, Pierce JM, Tao YK, Chen SC, Liu Q, Liu X, Boyd KL, Calcutt MW, Bridges TM, Lindsley CW, Friedman DL, Richmond A, Daniels AB (2021) Intravitreal HDAC inhibitor Belinostat effectively eradicates vitreous seeds without retinal toxicity in vivo in a rabbit retinoblastoma model. Invest Ophthalmol Vis Sci 62:8
Kalari S, Pfeifer GP (2010a) Chapter 10: identification of driver and passenger DNA methylation in cancer by Epigenomic analysis. In: Herceg Z, Ushijima T (eds) Advances in genetics, vol 70. Academic, pp 277–308
Kalari S, Pfeifer GP (2010b) Identification of driver and passenger DNA methylation in cancer by epigenomic analysis. Adv Genet 70:277–308
Kallappagoudar S, Yadav RK, Lowe BR, Partridge JF (2015) Histone H3 mutations--a special role for H3.3 in tumorigenesis? Chromosoma 124:177–189
Kamińska K, Nalejska E, Kubiak M, Wojtysiak J, Żołna Ł, Kowalewski J, Lewandowska MA (2019) Prognostic and predictive epigenetic biomarkers in oncology. Mol Diagn Ther 23:83–95
Kaminskas E, Farrell AT, Wang YC, Sridhara R, Pazdur R (2005) FDA drug approval summary: azacitidine (5-azacytidine, Vidaza) for injectable suspension. Oncologist 10:176–182
Kanai Y, Ushijima S, Nakanishi Y, Sakamoto M, Hirohashi S (2003) Mutation of the DNA methyltransferase (DNMT) 1 gene in human colorectal cancers. Cancer Lett 192:75–82
Kantarjian H, Issa JP, Rosenfeld CS, Bennett JM, Albitar M, DiPersio J, Klimek V, Slack J, de Castro C, Ravandi F, Helmer R 3rd, Shen L, Nimer SD, Leavitt R, Raza A, Saba H (2006) Decitabine improves patient outcomes in myelodysplastic syndromes: results of a phase III randomized study. Cancer 106:1794–1803
Kapoor A, Goldberg MS, Cumberland LK, Ratnakumar K, Segura MF, Emanuel PO, Menendez S, Vardabasso C, Leroy G, Vidal CI, Polsky D, Osman I, Garcia BA, Hernando E, Bernstein E (2010) The histone variant macroH2A suppresses melanoma progression through regulation of CDK8. Nature 468:1105–1109
Kato S, Alsafar A, Walavalkar V, Hainsworth J, Kurzrock R (2021) Cancer of unknown primary in the molecular era. Trends Cancer 7:465–477
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC (2014) Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A 111:6131–6138
Khan C, Pathe N, Fazal S, Lister J, Rossetti JM (2012) Azacitidine in the management of patients with myelodysplastic syndromes. Ther Adv Hematol 3:355–373
Khan SA, Reddy D, Gupta S (2015) Global histone post-translational modifications and cancer: biomarkers for diagnosis, prognosis and treatment? World J Biol Chem 6:333–345
Khan SA, Amnekar R, Khade B, Barreto SG, Ramadwar M, Shrikhande SV, Gupta S (2016) p38-MAPK/MSK1-mediated overexpression of histone H3 serine 10 phosphorylation defines distance-dependent prognostic value of negative resection margin in gastric cancer. Clin Epigenetics 8:88
Khuong-Quang DA, Buczkowicz P, Rakopoulos P, Liu XY, Fontebasso AM, Bouffet E, Bartels U, Albrecht S, Schwartzentruber J, Letourneau L, Bourgey M, Bourque G, Montpetit A, Bourret G, Lepage P, Fleming A, Lichter P, Kool M, von Deimling A, Sturm D, Korshunov A, Faury D, Jones DT, Majewski J, Pfister SM, Jabado N, Hawkins C (2012) K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol 124:439–447
Kim K, Punj V, Choi J, Heo K, Kim JM, Laird PW, An W (2013) Gene dysregulation by histone variant H2A.Z in bladder cancer. Epigenetics Chromatin 6:34
Kim K, Skora AD, Li Z, Liu Q, Tam AJ, Blosser RL, Diaz LA Jr, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S (2014) Eradication of metastatic mouse cancers resistant to immune checkpoint blockade by suppression of myeloid-derived cells. Proc Natl Acad Sci U S A 111:11774–11779
Kimura H, Shiota K (2003) Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmt1. J Biol Chem 278:4806–4812
Komar D, Juszczynski P (2020) Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy. Clin Epigenetics 12:147
Kota J, Chivukula RR, O’Donnell KA, Wentzel EA, Montgomery CL, Hwang HW, Chang TC, Vivekanandan P, Torbenson M, Clark KR, Mendell JR, Mendell JT (2009) Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model. Cell 137:1005–1017
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Kozlowski M, Corujo D, Hothorn M, Guberovic I, Mandemaker IK, Blessing C, Sporn J, Gutierrez-Triana A, Smith R, Portmann T, Treier M, Scheffzek K, Huet S, Timinszky G, Buschbeck M, Ladurner AG (2018) MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms. EMBO Rep 19:e44445
Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929–930
Kroeze LI, Aslanyan MG, van Rooij A, Koorenhof-Scheele TN, Massop M, Carell T, Boezeman JB, Marie JP, Halkes CJ, de Witte T, Huls G, Suciu S, Wevers RA, van der Reijden BA, Jansen JH (2014) Characterization of acute myeloid leukemia based on levels of global hydroxymethylation. Blood 124:1110–1118
Krug RM, Morgan MA, Shatkin AJ (1976) Influenza viral mRNA contains internal N6-methyladenosine and 5′-terminal 7-methylguanosine in cap structures. J Virol 20:45–53
Krützfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M (2005) Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438:685–689
Kumar S, Mohapatra T (2021) Deciphering Epitranscriptome: modification of mRNA bases provides a new perspective for post-transcriptional regulation of gene expression. Front Cell Dev Biol 9:628415
Laganà A, Russo F, Sismeiro C, Giugno R, Pulvirenti A, Ferro A (2010) Variability in the incidence of miRNAs and genes in fragile sites and the role of repeats and CpG islands in the distribution of genetic material. PLoS One 5:e11166
Lagger S, Connelly JC, Schweikert G, Webb S, Selfridge J, Ramsahoye BH, Yu M, He C, Sanguinetti G, Sowers LC, Walkinshaw MD, Bird A (2017) MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain. PLoS Genet 13:e1006793
Lakshminarasimhan R, Liang G (2016) The role of DNA methylation in cancer. Adv Exp Med Biol 945:151–172
Lamaa A, Humbert J, Aguirrebengoa M, Cheng X, Nicolas E, Côté J, Trouche D (2020) Integrated analysis of H2A.Z isoforms function reveals a complex interplay in gene regulation. elife 9:e53375
Lamb YN (2021) Inclisiran: first approval. Drugs 81:389–395
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Laubach JP, Schjesvold F, Mariz M, Dimopoulos MA, Lech-Maranda E, Spicka I, Hungria VTM, Shelekhova T, Abdo A, Jacobasch L, Polprasert C, Hájek R, Illés Á, Wróbel T, Sureda A, Beksac M, Gonçalves IZ, Bladé J, Rajkumar SV, Chari A, Lonial S, Spencer A, Maison-Blanche P, Moreau P, San-Miguel JF, Richardson PG (2021) Efficacy and safety of oral panobinostat plus subcutaneous bortezomib and oral dexamethasone in patients with relapsed or relapsed and refractory multiple myeloma (PANORAMA 3): an open-label, randomised, phase 2 study. Lancet Oncol 22:142–154
Ledford H (2018) Gene-silencing technology gets first drug approval after 20-year wait. Nature 560:291–292
Lee YS, Dutta A (2009) MicroRNAs in cancer. Annu Rev Pathol 4:199–227
Lee MS, Sanoff HK (2020) Cancer of unknown primary. BMJ 371:m4050
Lee J, Stephanie Huang R (2013) Cancer epigenetics: mechanisms and crosstalk of a HDAC inhibitor, Vorinostat. Chemotherapy (Los Angel) 2:14934
Lee AS, Seo YC, Chang A, Tohari S, Eu KW, Seow-Choen F, McGee JO (2000) Detailed deletion mapping at chromosome 11q23 in colorectal carcinoma. Br J Cancer 83:750–755
Lee HZ, Kwitkowski VE, Del Valle PL, Ricci MS, Saber H, Habtemariam BA, Bullock J, Bloomquist E, Li Shen Y, Chen XH, Brown J, Mehrotra N, Dorff S, Charlab R, Kane RC, Kaminskas E, Justice R, Farrell AT, Pazdur R (2015) FDA approval: Belinostat for the treatment of patients with relapsed or refractory peripheral T-cell lymphoma. Clin Cancer Res 21:2666–2670
Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ (2019) Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 143:573–593
Leone G, D’Alò F, Zardo G, Voso MT, Nervi C (2008) Epigenetic treatment of myelodysplastic syndromes and acute myeloid leukemias. Curr Med Chem 15:1274–1287
Li M, Chen SS (2011) The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evol Biol 11:3
Li W, Liu M (2011) Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucleic Acids 2011:870726
Li Y, Seto E (2016) HDACs and HDAC inhibitors in cancer development and therapy. Cold Spring Harb Perspect Med 6:a026831
Li E, Zhang Y (2014) DNA methylation in mammals. Cold Spring Harb Perspect Biol 6:a019133
Li B, Huang G, Zhang X, Li R, Wang J, Dong Z, He Z (2013a) Increased phosphorylation of histone H3 at serine 10 is involved in Epstein-Barr virus latent membrane protein-1-induced carcinogenesis of nasopharyngeal carcinoma. BMC Cancer 13:124
Li S, Liu L, Zhuang X, Yu Y, Liu X, Cui X, Ji L, Pan Z, Cao X, Mo B, Zhang F, Raikhel N, Jiang L, Chen X (2013b) MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153:562–574
Li J, Jin H, Wang X (2014) Epigenetic biomarkers: potential applications in gastrointestinal cancers. ISRN Gastroenterol 2014:464015
Lian CG, Xu Y, Ceol C, Wu F, Larson A, Dresser K, Xu W, Tan L, Hu Y, Zhan Q, Lee CW, Hu D, Lian BQ, Kleffel S, Yang Y, Neiswender J, Khorasani AJ, Fang R, Lezcano C, Duncan LM, Scolyer RA, Thompson JF, Kakavand H, Houvras Y, Zon LI, Mihm MC Jr, Kaiser UB, Schatton T, Woda BA, Murphy GF, Shi YG (2012) Loss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma. Cell 150:1135–1146
Liang G, Weisenberger DJ (2017) DNA methylation aberrancies as a guide for surveillance and treatment of human cancers. Epigenetics 12:416–432
Lin CJ, Koh FM, Wong P, Conti M, Ramalho-Santos M (2014) Hira-mediated H3.3 incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote. Dev Cell 30:268–279
Lin G, Wang H, Wu Y, Wang K, Li G (2021) Hub Long noncoding RNAs with m6A modification for signatures and prognostic values in kidney renal clear cell carcinoma. Front Mol Biosci 8:682471
Liu BL, Cheng JX, Zhang X, Wang R, Zhang W, Lin H, Xiao X, Cai S, Chen XY, Cheng H (2010) Global histone modification patterns as prognostic markers to classify glioma patients. Cancer Epidemiol Biomark Prev 19:2888–2896
Liu C, Liu L, Chen X, Shen J, Shan J, Xu Y, Yang Z, Wu L, Xia F, Bie P, Cui Y, Bian XW, Qian C (2013) Decrease of 5-hydroxymethylcytosine is associated with progression of hepatocellular carcinoma through downregulation of TET1. PLoS One 8:e62828
Liu L, Xu C, Hsieh JT, Gong J, Xie D (2016) DAB2IP in cancer. Oncotarget 7:3766–3776
Liu J, Eckert MA, Harada BT, Liu SM, Lu Z, Yu K, Tienda SM, Chryplewicz A, Zhu AC, Yang Y, Huang JT, Chen SM, Xu ZG, Leng XH, Yu XC, Cao J, Zhang Z, Liu J, Lengyel E, He C (2018a) M(6)a mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol 20:1074–1083
Liu X, Lv X, Yang Q, Jin H, Zhou W, Fan Q (2018b) MicroRNA-29a functions as a tumor suppressor and increases cisplatin sensitivity by targeting NRAS in lung cancer. Technol Cancer Res Treat 17:1533033818758905
Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KYC, Ross JP (2019) DNA methylation cancer biomarkers: translation to the clinic. Front Genet 10:1150
Long MD, Smiraglia DJ, Campbell MJ (2017) The genomic impact of DNA CpG methylation on gene expression; Relationships in prostate cancer. Biomolecules 7:15
Long M, Sun X, Shi W, Yanru A, Leung STC, Ding D, Cheema MS, MacPherson N, Nelson CJ, Ausio J, Yan Y, Ishibashi T (2019) A novel histone H4 variant H4G regulates rDNA transcription in breast cancer. Nucleic Acids Res 47:8399–8409
Loppin B, Bonnefoy E, Anselme C, Laurençon A, Karr TL, Couble P (2005) The histone H3.3 chaperone HIRA is essential for chromatin assembly in the male pronucleus. Nature 437:1386–1390
Lord RV, Brabender J, Gandara D, Alberola V, Camps C, Domine M, Cardenal F, Sánchez JM, Gumerlock PH, Tarón M, Sánchez JJ, Danenberg KD, Danenberg PV, Rosell R (2002) Low ERCC1 expression correlates with prolonged survival after cisplatin plus gemcitabine chemotherapy in non-small cell lung cancer. Clin Cancer Res 8:2286–2291
Lorincz AT (2011) The promise and the problems of epigenetics biomarkers in cancer. Expert Opin Med Diagn 5:375–379
Lu R, Wang GG (2013) Tudor: a versatile family of histone methylation ‘readers’. Trends Biochem Sci 38:546–555
Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838
Lu Y, Cao M, Gao K, Jiang J, Shi X (2015) The role of O(6)-methylguanine-DNA methyltransferase polymorphisms in colorectal cancer susceptibility: a meta analysis. Int J Clin Exp Med 8:791–799
Lu X, Ning Z, Li Z, Cao H, Wang X (2016) Development of chidamide for peripheral T-cell lymphoma, the first orphan drug approved in China. Intractable Rare Dis Res 5:185–191
Lu Y, Chan YT, Tan HY, Li S, Wang N, Feng Y (2020) Epigenetic regulation in human cancer: the potential role of epi-drug in cancer therapy. Mol Cancer 19:79
Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260
Luger K, Dechassa ML, Tremethick DJ (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13:436–447
Lunke S, Maxwell S, Khurana I, Harikrishnan KN, Okabe J, Al-Hasani K, El-Osta A (2021) Epigenetic evidence of an ac/dc axis by VPA and SAHA. Clin Epigenetics 13:58
Ma Y, Shen N, Wicha MS, Luo M (2021) The roles of the Let-7 family of MicroRNAs in the regulation of cancer Stemness. Cell 10:2415
MacArthur BD (2022) The geometry of cell fate. Cell Syst 13:1–3
Maeda K, Kawakami K, Ishida Y, Ishiguro K, Omura K, Watanabe G (2003) Hypermethylation of the CDKN2A gene in colorectal cancer is associated with shorter survival. Oncol Rep 10:935–938
Majchrzak-Celińska A, Baer-Dubowska W (2017) Pharmacoepigenetics: an element of personalized therapy? Expert Opin Drug Metab Toxicol 13:387–398
Majchrzak-Celińska A, Warych A, Szoszkiewicz M (2021) Novel approaches to epigenetic therapies: from drug combinations to epigenetic editing. Genes (Basel) 12:208
Malik P, Cashen AF (2014) Decitabine in the treatment of acute myeloid leukemia in elderly patients. Cancer Manag Res 6:53–61
Mann BS, Johnson JR, Cohen MH, Justice R, Pazdur R (2007) FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist 12:1247–1252
Manuyakorn A, Paulus R, Farrell J, Dawson NA, Tze S, Cheung-Lau G, Hines OJ, Reber H, Seligson DB, Horvath S, Kurdistani SK, Guha C, Dawson DW (2010) Cellular histone modification patterns predict prognosis and treatment response in resectable pancreatic adenocarcinoma: results from RTOG 9704. J Clin Oncol 28:1358–1365
Mariño-Ramírez L, Kann MG, Shoemaker BA, Landsman D (2005) Histone structure and nucleosome stability. Expert Rev Proteomics 2:719–729
Marks PA, Xu WS (2009) Histone deacetylase inhibitors: potential in cancer therapy. J Cell Biochem 107:600–608
Marriott L, Charbonneau A, Moss B, Shannon J, Thornburg K, Turker M (2016) Epigenetics: a new science for middle school – and why you should teach it. Sci Scope (Wash, DC) 39:6–11
Matei D, Fang F, Shen C, Schilder J, Arnold A, Zeng Y, Berry WA, Huang T, Nephew KP (2012) Epigenetic resensitization to platinum in ovarian cancer. Cancer Res 72:2197–2205
Matilainen O, Quirós PM, Auwerx J (2017) Mitochondria and epigenetics – crosstalk in homeostasis and stress. Trends Cell Biol 27:453–463
Mayeux R (2004) Biomarkers: potential uses and limitations. NeuroRx 1:182–188
McGraw AL (2013) Romidepsin for the treatment of T-cell lymphomas. Am J Health Syst Pharm 70:1115–1122
Medina PP, Nolde M, Slack FJ (2010) OncomiR addiction in an in vivo model of microRNA-21-induced pre-B-cell lymphoma. Nature 467:86–90
Méndez-Acuña L, Di Tomaso MV, Palitti F, Martínez-López W (2010) Histone post-translational modifications in DNA damage response. Cytogenet Genome Res 128:28–36
Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR (2015) 5′ UTR m(6)a promotes cap-independent translation. Cell 163:999–1010
Milutinovic S, D’Alessio AC, Detich N, Szyf M (2007) Valproate induces widespread epigenetic reprogramming which involves demethylation of specific genes. Carcinogenesis 28:560–571
Mitalipov S, Wolf D (2009) Totipotency, pluripotency and nuclear reprogramming. Adv Biochem Eng Biotechnol 114:185–199
Moen EL, Stark AL, Zhang W, Dolan ME, Godley LA (2014) The role of gene body cytosine modifications in MGMT expression and sensitivity to temozolomide. Mol Cancer Ther 13:1334–1344
Mogilyansky E, Rigoutsos I (2013) The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Diff 20:1603–1614
Molaro A, Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS (2020) Biparental contributions of the H2A.B histone variant control embryonic development in mice. PLoS Biol 18:e3001001
Mongan NP, Emes RD, Archer N (2019) Detection and analysis of RNA methylation. F1000Res 8:F1000
Moore D (2016) Panobinostat (Farydak): a novel option for the treatment of relapsed or relapsed and refractory multiple myeloma. P T 41:296–300
Moore LD, Le T, Fan G (2013) DNA methylation and its basic function. Neuropsychopharmacology 38:23–38
Moosavi A, Motevalizadeh Ardekani A (2016) Role of epigenetics in biology and human diseases. Iran Biomed J 20:246–258
Moran S, Martínez-Cardús A, Sayols S, Musulén E, Balañá C, Estival-Gonzalez A, Moutinho C, Heyn H, Diaz-Lagares A, de Moura MC, Stella GM, Comoglio PM, Ruiz-Miró M, Matias-Guiu X, Pazo-Cid R, Antón A, Lopez-Lopez R, Soler G, Longo F, Guerra I, Fernandez S, Assenov Y, Plass C, Morales R, Carles J, Bowtell D, Mileshkin L, Sia D, Tothill R, Tabernero J, Llovet JM, Esteller M (2016) Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis. Lancet Oncol 17:1386–1395
Morena F, Argentati C, Bazzucchi M, Emiliani C, Martino S (2018) Above the Epitranscriptome: RNA modifications and stem cell identity. Genes (Basel) 9:329
Mouhieddine TH, El Houjeiri L, Sabra M, Hayes RL, Mondello S (2015) Frontiers in Neuroengineering CNS trauma biomarkers and surrogate endpoints pipeline from bench to bedside: a translational perspective. In: Kobeissy FH (ed) Brain Neurotrauma: molecular, neuropsychological, and rehabilitation aspects. CRC Press/Taylor & Francis © 2015 by Taylor & Francis Group, LLC, Boca Raton
Mulero-Navarro S, Esteller M (2008) Epigenetic biomarkers for human cancer: the time is now. Crit Rev Oncol Hematol 68:1–11
Mullard A (2009) Epigenomic colon cancer kit. Nat Biotechnol 27:1066–1066
Multhoff G, Molls M, Radons J (2011) Chronic inflammation in cancer development. Front Immunol 2:98
Munari E, Chaux A, Vaghasia AM, Taheri D, Karram S, Bezerra SM, Gonzalez Roibon N, Nelson WG, Yegnasubramanian S, Netto GJ, Haffner MC (2016) Global 5-Hydroxymethylcytosine levels are profoundly reduced in multiple genitourinary malignancies. PLoS One 11:e0146302
Munn LL (2017) Cancer and inflammation. Wiley Interdiscip Rev Syst Biol Med 9:e1370
Munshi A, Tanaka T, Hobbs ML, Tucker SL, Richon VM, Meyn RE (2006) Vorinostat, a histone deacetylase inhibitor, enhances the response of human tumor cells to ionizing radiation through prolongation of gamma-H2AX foci. Mol Cancer Ther 5:1967–1974
Munster PN, Thurn KT, Thomas S, Raha P, Lacevic M, Miller A, Melisko M, Ismail-Khan R, Rugo H, Moasser M, Minton SE (2011) A phase II study of the histone deacetylase inhibitor vorinostat combined with tamoxifen for the treatment of patients with hormone therapy-resistant breast cancer. Br J Cancer 104:1828–1835
Murata M (2018) Inflammation and cancer. Environ Health Prev Med 23:50
Musselman CA, Lalonde ME, Côté J, Kutateladze TG (2012) Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol 19:1218–1227
Muthurajan UM, McBryant SJ, Lu X, Hansen JC, Luger K (2011) The linker region of macroH2A promotes self-association of nucleosomal arrays. J Biol Chem 286:23852–23864
Nabel CS, Manning SA, Kohli RM (2012) The curious chemical biology of cytosine: deamination, methylation, and oxidation as modulators of genomic potential. ACS Chem Biol 7:20–30
Nacev BA, Feng L, Bagert JD, Lemiesz AE, Gao J, Soshnev AA, Kundra R, Schultz N, Muir TW, Allis CD (2019) The expanding landscape of ‘oncohistone’ mutations in human cancers. Nature 567:473–478
Nagelkerke A, van Kuijk SJ, Sweep FC, Nagtegaal ID, Hoogerbrugge N, Martens JW, Timmermans MA, van Laarhoven HW, Bussink J, Span PN (2011) Constitutive expression of γ-H2AX has prognostic relevance in triple negative breast cancer. Radiother Oncol 101:39–45
Nakayama T, Watanabe M, Yamanaka M, Hirokawa Y, Suzuki H, Ito H, Yatani R, Shiraishi T (2001) The role of epigenetic modifications in retinoic acid receptor beta2 gene expression in human prostate cancers. Lab Investig 81:1049–1057
Nan P, Niu Y, Wang X, Li Q (2019) MiR-29a function as tumor suppressor in cervical cancer by targeting SIRT1 and predict patient prognosis. Onco Targets Ther 12:6917–6925
Napoli C, Grimaldi V, De Pascale MR, Sommese L, Infante T, Soricelli A (2016) Novel epigenetic-based therapies useful in cardiovascular medicine. World J Cardiol 8:211–219
Napoli C, Bontempo P, Palmieri V, Coscioni E, Maiello C, Donatelli F, Benincasa G (2021) Epigenetic therapies for heart failure: current insights and future potential. Vasc Health Risk Manag 17:247–254
Needham J, Waddington CH, Needham DMM, Hopkins FG (1934) Physico-chemical experiments on the amphibian organizer. Proc R Soc London Ser B Containing Papers Biol Character 114:393–422
Nepali K, Liou J-P (2021) Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends. J Biomed Sci 28:27
Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, Katz E, Dixon JM, Harrison DJ, Meehan RR (2012) Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res 22:467–477
Ng CS, Zhang J, Wan S, Lee TW, Arifi AA, Mok T, Lo DY, Yim AP (2002) Tumor p16M is a possible marker of advanced stage in non-small cell lung cancer. J Surg Oncol 79:101–106
Ni W-J, Leng X-M (2015) Dynamic miRNA–mRNA paradigms: new faces of miRNAs. Biochem Biophy Rep 4:337–341
Nichols JL (1979) N6-methyladenosine in maize poly(a)-containing RNA. Plant Sci Lett 15:357–361
Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H, White J, Kirilovsky J, Rice CM, Lora JM, Prinjha RK, Lee K, Tarakhovsky A (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468:1119–1123
Nicoglou A (2018) Waddington’s epigenetics or the pictorial meetings of development and genetics. Hist Philos Life Sci 40:61
Ning B, Li W, Zhao W, Wang R (2016) Targeting epigenetic regulations in cancer. Acta Biochim Biophys Sin Shanghai 48:97–109
Nishibuchi I, Suzuki H, Kinomura A, Sun J, Liu NA, Horikoshi Y, Shima H, Kusakabe M, Harata M, Fukagawa T, Ikura T, Ishida T, Nagata Y, Tashiro S (2014) Reorganization of damaged chromatin by the exchange of histone variant H2A.Z-2. Int J Radiat Oncol Biol Phys 89:736–744
Nishioka C, Ikezoe T, Yang J, Takeuchi S, Koeffler HP, Yokoyama A (2008) MS-275, a novel histone deacetylase inhibitor with selectivity against HDAC1, induces degradation of FLT3 via inhibition of chaperone function of heat shock protein 90 in AML cells. Leuk Res 32:1382–1392
Niwa T, Tsukamoto T, Toyoda T, Mori A, Tanaka H, Maekita T, Ichinose M, Tatematsu M, Ushijima T (2010a) Inflammatory processes triggered by helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res 70:1430–1440
Niwa T, Tsukamoto T, Toyoda T, Mori A, Tanaka H, Maekita T, Ichinose M, Tatematsu M, Ushijima T (2010b) Inflammatory processes triggered by helicobacter pylori infection cause aberrant DNA methylation in gastric epithelial cells. Cancer Res 70:1430–1440
Niwa T, Toyoda T, Tsukamoto T, Mori A, Tatematsu M, Ushijima T (2013) Prevention of helicobacter pylori-induced gastric cancers in gerbils by a DNA demethylating agent. Cancer Prev Res (Phila) 6:263–270
O’Brien J, Hayder H, Zayed Y, Peng C (2018) Overview of MicroRNA biogenesis, mechanisms of actions, and circulation. Front Endocrinol 9:402
O’Connor OA, Horwitz S, Masszi T, Van Hoof A, Brown P, Doorduijn J, Hess G, Jurczak W, Knoblauch P, Chawla S, Bhat G, Choi MR, Walewski J, Savage K, Foss F, Allen LF, Shustov A (2015) Belinostat in patients with relapsed or refractory peripheral T-cell lymphoma: results of the pivotal phase II BELIEF (CLN-19) study. J Clin Oncol 33:2492–2499
Olsen EA, Kim YH, Kuzel TM, Pacheco TR, Foss FM, Parker S, Frankel SR, Chen C, Ricker JL, Arduino JM, Duvic M (2007) Phase IIb multicenter trial of vorinostat in patients with persistent, progressive, or treatment refractory cutaneous T-cell lymphoma. J Clin Oncol 25:3109–3115
Oronsky B, Oronsky N, Scicinski J, Fanger G, Lybeck M, Reid T (2014) Rewriting the epigenetic code for tumor resensitization: a review. Transl Oncol 7:626–631
Pacaud R, Cheray M, Nadaradjane A, Vallette FM, Cartron PF (2015) Histone H3 phosphorylation in GBM: a new rational to guide the use of kinase inhibitors in anti-GBM therapy. Theranostics 5:12–22
Palazzo AF, Gregory TR (2014) The case for junk DNA. PLoS Genet 10:e1004351
Pan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D, Fink AM, Fischer K, Zhang C, Betel D, Gnirke A, Imielinski M, Moreaux J, Hallek M, Meissner A, Stilgenbauer S, Wu CJ, Elemento O, Landau DA (2021) Discovery of candidate DNA methylation cancer driver genes. Cancer Discov 11:2266–2281
Panchin AY, Makeev VJ, Medvedeva YA (2016) Preservation of methylated CpG dinucleotides in human CpG islands. Biol Direct 11:11
Pang AP, Sugai C, Maunakea AK (2016) High-throughput sequencing offers new insights into 5-hydroxymethylcytosine. Biomol Concepts 7:169–178
Pang MYH, Sun X, Ausió J, Ishibashi T (2020) Histone H4 variant, H4G, drives ribosomal RNA transcription and breast cancer cell proliferation by loosening nucleolar chromatin structure. J Cell Physiol 235:9601–9608
Papale LA, Madrid A, Zhang Q, Chen K, Sak L, Keleş S, Alisch RS (2022) Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders. Genome Res 32:266–279
Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer 2:1002–1017
Parbin S, Kar S, Shilpi A, Sengupta D, Deb M, Rath SK, Patra SK (2014) Histone deacetylases: a saga of perturbed acetylation homeostasis in cancer. J Histochem Cytochem 62:11–33
Park S-Y, Kim J-S (2020) A short guide to histone deacetylases including recent progress on class II enzymes. Exp Mol Med 52:204–212
Park YS, Jin MY, Kim YJ, Yook JH, Kim BS, Jang SJ (2008) The global histone modification pattern correlates with cancer recurrence and overall survival in gastric adenocarcinoma. Ann Surg Oncol 15:1968–1976
Park JL, Kim HJ, Seo EH, Kwon OH, Lim B, Kim M, Kim SY, Song KS, Kang GH, Kim HJ, Choi BY, Kim YS (2015) Decrease of 5hmC in gastric cancers is associated with TET1 silencing due to with DNA methylation and bivalent histone marks at TET1 CpG island 3′-shore. Oncotarget 6:37647–37662
Patil V, Ward RL, Hesson LB (2014) The evidence for functional non-CpG methylation in mammalian cells. Epigenetics 9:823–828
Pavlidis N, Fizazi K (2005) Cancer of unknown primary (CUP). Crit Rev Oncol Hematol 54:243–250
Peng J, Yuan C, Hua X, Zhang Z (2020) Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures. Epigenetics Chromatin 13:28
Peng Q, Weng K, Li S, Xu R, Wang Y, Wu Y (2021) A perspective of epigenetic regulation in radiotherapy. Front Cell Dev Biol 9:624312
Penn NW, Suwalski R, O’Riley C, Bojanowski K, Yura R (1972) The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J 126:781–790
Pertea M (2012) The human transcriptome: an unfinished story. Genes (Basel) 3:344–360
Pértille F, Da Silva VH, Johansson AM, Lindström T, Wright D, Coutinho LL, Jensen P, Guerrero-Bosagna C (2019) Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification. Epigenetics 14:685–707
Peserico A, Germani A, Sanese P, Barbosa AJ, Di Virgilio V, Fittipaldi R, Fabini E, Bertucci C, Varchi G, Moyer MP, Caretti G, Del Rio A, Simone C (2015) A SMYD3 small-molecule inhibitor impairing cancer cell growth. J Cell Physiol 230:2447–2460
Pfeifer GP (2018) Defining driver DNA methylation changes in human cancer. Int J Mol Sci 19:1166
Pfeifer GP, Xiong W, Hahn MA, Jin SG (2014) The role of 5-hydroxymethylcytosine in human cancer. Cell Tissue Res 356:631–641
Phiel CJ, Zhang F, Huang EY, Guenther MG, Lazar MA, Klein PS (2001) Histone deacetylase is a direct target of valproic acid, a potent anticonvulsant, mood stabilizer, and teratogen. J Biol Chem 276:36734–36741
Phillips DM (1963) The presence of acetyl groups of histones. Biochem J 87:258–263
Piljić Burazer M, Mladinov S, Matana A, Kuret S, Bezić J, Glavina Durdov M (2019) Low ERCC1 expression is a good predictive marker in lung adenocarcinoma patients receiving chemotherapy based on platinum in all TNM stages – a single-center study. Diagn Pathol 14:105
Pískala AŠF (1964) Nucleic acids components and their analogues. LI. Synthesis of 1-glycosyl derivatives of 5-azauracil and 5-azacytosine. Coll Czech Chem Commun 29:2060–2076
Pliml JŠF (1964) Synthesis of 2′-deoxy-D-ribofuranosyl-5-azacytosine. Coll Czech Chem Commun 29:2576–2577
Plotnik JP, Hollenhorst PC (2017) Interaction with ZMYND11 mediates opposing roles of Ras-responsive transcription factors ETS1 and ETS2. Nucleic Acids Res 45:4452–4462
Podhorecka M, Skladanowski A, Bozko P (2010) H2AX phosphorylation: its role in DNA damage response and cancer therapy. J Nucleic Acids 2010:920161
Ponnusamy L, Mahalingaiah PKS, Chang YW, Singh KP (2018) Reversal of epigenetic aberrations associated with the acquisition of doxorubicin resistance restores drug sensitivity in breast cancer cells. Eur J Pharm Sci 123:56–69
Powis G, Kirkpatrick L (2004) Hypoxia inducible factor-1alpha as a cancer drug target. Mol Cancer Ther 3:647–654
Pulido HA, Fakruddin MJ, Chatterjee A, Esplin ED, Beleño N, Martinez G, Posso H, Evans GA, Murty VV (2000) Identification of a 6-cM minimal deletion at 11q23.1-23.2 and exclusion of PPP2R1B gene as a deletion target in cervical cancer. Cancer Res 60:6677–6682
Pulitzer M (2017) Cutaneous T-cell lymphoma. Clin Lab Med 37:527–546
Qaseem A, Usman N, Jayaraj JS, Janapala RN, Kashif T (2019) Cancer of unknown primary: a review on clinical guidelines in the development and targeted Management of Patients with the unknown primary site. Cureus 11:e5552
Quagliano A, Gopalakrishnapillai A, Barwe SP (2020a) Understanding the mechanisms by which epigenetic modifiers avert therapy resistance in cancer. Front Oncol 10:992
Quagliano A, Gopalakrishnapillai A, Barwe SP (2020b) Understanding the mechanisms by which epigenetic modifiers avert therapy resistance in cancer. Front Oncol 10:992
Quénet D (2018) Histone variants and disease. Int Rev Cell Mol Biol 335:1–39
Ramazi S, Allahverdi A, Zahiri J (2020) Evaluation of post-translational modifications in histone proteins: a review on histone modification defects in developmental and neurological disorders. J Biosci 45:135
Rando OJ (2012) Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev 22:148–155
Raynal NJ, Da Costa EM, Lee JT, Gharibyan V, Ahmed S, Zhang H, Sato T, Malouf GG, Issa JJ (2017) Repositioning FDA-approved drugs in combination with epigenetic drugs to reprogram colon cancer epigenome. Mol Cancer Ther 16:397–407
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906
Ren M, Leng Y, Jeong M, Leeds PR, Chuang DM (2004) Valproic acid reduces brain damage induced by transient focal cerebral ischemia in rats: potential roles of histone deacetylase inhibition and heat shock protein induction. J Neurochem 89:1358–1367
Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X (2018) Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 53:88–99
Richon VM (2010) Targeting histone deacetylases: development of vorinostat for the treatment of cancer. Epigenomics 2:457–465
Richon VM, Sandhoff TW, Rifkind RA, Marks PA (2000) Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation. Proc Natl Acad Sci U S A 97:10014–10019
Riggs AD (1975) X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 14:9–25
Roberti A, Valdes AF, Torrecillas R, Fraga MF, Fernandez AF (2019) Epigenetics in cancer therapy and nanomedicine. Clin Epigenetics 11:81
Robinson EL, Anene-Nzelu CG, Rosa-Garrido M, Foo RSY (2021) Cardiac epigenetics: driving signals to the cardiac epigenome in development and disease. J Mol Cell Cardiol 151:88
Rogakou EP, Pilch DR, Orr AH, Ivanova VS, Bonner WM (1998) DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem 273:5858–5868
Rogakou EP, Boon C, Redon C, Bonner WM (1999) Megabase chromatin domains involved in DNA double-strand breaks in vivo. J Cell Biol 146:905–916
Roundtree IA, Evans ME, Pan T, He C (2017a) Dynamic RNA modifications in gene expression regulation. Cell 169:1187–1200
Roundtree IA, Luo GZ, Zhang Z, Wang X, Zhou T, Cui Y, Sha J, Huang X, Guerrero L, Xie P, He E, Shen B, He C (2017b) YTHDC1 mediates nuclear export of N(6)-methyladenosine methylated mRNAs. elife 6:e31311
Ruefli AA, Ausserlechner MJ, Bernhard D, Sutton VR, Tainton KM, Kofler R, Smyth MJ, Johnstone RW (2001) The histone deacetylase inhibitor and chemotherapeutic agent suberoylanilide hydroxamic acid (SAHA) induces a cell-death pathway characterized by cleavage of Bid and production of reactive oxygen species. Proc Natl Acad Sci U S A 98:10833–10838
Rutnam ZJ, Yang BB (2012) The involvement of microRNAs in malignant transformation. Histol Histopathol 27:1263–1270
Saba HI (2007) Decitabine in the treatment of myelodysplastic syndromes. Ther Clin Risk Manag 3:807–817
Sakabe K, Wang Z, Hart GW (2010) Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc Natl Acad Sci U S A 107:19915–19920
Sakai A, Schwartz BE, Goldstein S, Ahmad K (2009) Transcriptional and developmental functions of the H3.3 histone variant in drosophila. Curr Biol 19:1816–1820
Saleh K, Michot JM, Ribrag V (2021) Updates in the treatment of peripheral T-cell lymphomas. J Exp Pharmacol 13:577–591
Sales-Gil R, Kommer DC, de Castro IJ, Amin HA, Vinciotti V, Sisu C, Vagnarelli P (2021) Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression. EMBO Rep 22:e52061
San-Miguel JF, Hungria VT, Yoon SS, Beksac M, Dimopoulos MA, Elghandour A, Jedrzejczak WW, Günther A, Nakorn TN, Siritanaratkul N, Schlossman RL, Hou J, Moreau P, Lonial S, Lee JH, Einsele H, Sopala M, Bengoudifa BR, Binlich F, Richardson PG (2016) Overall survival of patients with relapsed multiple myeloma treated with panobinostat or placebo plus bortezomib and dexamethasone (the PANORAMA 1 trial): a randomised, placebo-controlled, phase 3 trial. Lancet Haematol 3:e506–e515
Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A (2014) The histone variant H2A.Bbd is enriched at sites of DNA synthesis. Nucleic Acids Res 42:6405–6420
Saravi S, Katsuta E, Jeyaneethi J, Amin HA, Kaspar M, Takabe K, Pados G, Drenos F, Hall M, Karteris E (2020) H2A histone family member X (H2AX) is upregulated in ovarian cancer and demonstrates utility as a prognostic biomarker in terms of overall survival. J Clin Med 9:2844
Sarg B, Lopez R, Lindner H, Ponte I, Suau P, Roque A (2015) Identification of novel post-translational modifications in linker histones from chicken erythrocytes. J Proteome 113:162–177
Sarver AE, Li L, Kartha RV, Subramanian S (2015) microRNAs in the malignant transformation process. Adv Exp Med Biol 889:1–21
Sassa A, Kanemaru Y, Kamoshita N, Honma M, Yasui M (2016) Mutagenic consequences of cytosine alterations site-specifically embedded in the human genome. Genes Environ 38:17
Sawas A, Radeski D, O’Connor OA (2015) Belinostat in patients with refractory or relapsed peripheral T-cell lymphoma: a perspective review. Ther Adv Hematol 6:202–208
Saxonov S, Berg P, Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103:1412–1417
Schiffer CA (2018) “Epigenetic” modification as therapy for acute myeloid leukemia. Cancer 124:242–244
Schneider BG, Piazuelo MB, Sicinschi LA, Mera R, Peng DF, Roa JC, Romero-Gallo J, Delgado AG, de Sablet T, Bravo LE, Wilson KT, El-Rifai W, Peek RM Jr, Correa P (2013) Virulence of infecting helicobacter pylori strains and intensity of mononuclear cell infiltration are associated with levels of DNA hypermethylation in gastric mucosae. Epigenetics 8:1153–1161
Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N (2012) Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 482:226–231
Scott LJ (2020) Givosiran: First Approval. Drugs 80:335–339
Scott LJ, Keam SJ (2021) Lumasiran: first approval. Drugs 81:277–282
Seligson DB, Horvath S, Shi T, Yu H, Tze S, Grunstein M, Kurdistani SK (2005) Global histone modification patterns predict risk of prostate cancer recurrence. Nature 435:1262–1266
Seligson DB, Horvath S, McBrian MA, Mah V, Yu H, Tze S, Wang Q, Chia D, Goodglick L, Kurdistani SK (2009) Global levels of histone modifications predict prognosis in different cancers. Am J Pathol 174:1619–1628
Sharma S, Kelly TK, Jones PA (2010) Epigenetics in cancer. Carcinogenesis 31:27–36
Shen JC, Rideout WM 3rd, Jones PA (1994) The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res 22:972–976
Shen L, Kondo Y, Rosner GL, Xiao L, Hernandez NS, Vilaythong J, Houlihan PS, Krouse RS, Prasad AR, Einspahr JG, Buckmeier J, Alberts DS, Hamilton SR, Issa JP (2005) MGMT promoter methylation and field defect in sporadic colorectal cancer. J Natl Cancer Inst 97:1330–1338
Shi Y, Dong M, Hong X, Zhang W, Feng J, Zhu J, Yu L, Ke X, Huang H, Shen Z, Fan Y, Li W, Zhao X, Qi J, Huang H, Zhou D, Ning Z, Lu X (2015) Results from a multicenter, open-label, pivotal phase II study of chidamide in relapsed or refractory peripheral T-cell lymphoma. Ann Oncol 26:1766–1771
Shi W, Palmer JD, Werner-Wasik M, Andrews DW, Evans JJ, Glass J, Kim L, Bar-Ad V, Judy K, Farrell C, Simone N, Liu H, Dicker AP, Lawrence YR (2016) Phase I trial of panobinostat and fractionated stereotactic re-irradiation therapy for recurrent high grade gliomas. J Neuro-Oncol 127:535–539
Shi D-Q, Ali I, Tang J, Yang W-C (2017a) New insights into 5hmC DNA modification: generation, distribution and function. Front Genet 8:100
Shi L, Wen H, Shi X (2017b) The histone variant H3.3 in transcriptional regulation and human disease. J Mol Biol 429:1934–1945
Shimony S, Horowitz N, Ribakovsky E, Rozovski U, Avigdor A, Zloto K, Berger T, Avivi I, Perry C, Abadi U, Raanani P, Gafter-Gvili A, Gurion R (2019) Romidepsin treatment for relapsed or refractory peripheral and cutaneous T-cell lymphoma: real-life data from a national multicenter observational study. Hematol Oncol 37:569–577
Shin YJ, Kim JH (2012) The role of EZH2 in the regulation of the activity of matrix metalloproteinases in prostate cancer cells. PLoS One 7:e30393
Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H (2013) Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 9:e1003439
Shirley M (2020) Epi proColon(®) for colorectal cancer screening: a profile of its use in the USA. Mol Diagn Ther 24:497–503
Shojaei F, Goodenow B, Lee G, Kabbinavar F, Gillings M (2021) HBI-8000, HUYABIO Lead clinical program, is a selective histone deacetylase inhibitor with therapeutic benefits in leukemia and in solid tumors. Front Oncol 11:768685
Shoji M, Ninomiya I, Makino I, Kinoshita J, Nakamura K, Oyama K, Nakagawara H, Fujita H, Tajima H, Takamura H, Kitagawa H, Fushida S, Harada S, Fujimura T, Ohta T (2012) Valproic acid, a histone deacetylase inhibitor, enhances radiosensitivity in esophageal squamous cell carcinoma. Int J Oncol 40:2140–2146
Siew-Gek Lee A, Rudduck-Sivaswaren C, Khun-Hong Lie D, Li-Ming Chua C, Tien SL, Morsberger L, Griffin CA (2004) Overlapping deletion regions at 11q23 in myelodysplastic syndrome and chronic lymphocytic leukemia, characterized by a novel BAC probe set. Cancer Genet Cytogenet 153:151–157
Silva G, Cardoso BA, Belo H, Almeida AM (2013) Vorinostat induces apoptosis and differentiation in myeloid malignancies: genetic and molecular mechanisms. PLoS One 8:e53766
Silverman L (1994) Azacitidine (Aza C) in myelodysplastic syndromes (MDS), CALGB studies 8421 and 8921. Ann Hematol 68:A12
Silverman L, Holland J, Ellison R (1990) Low dose continuous infusion azacytidine is an effective therapy for patients with myelodysplastic syndromes, a study of cancer and leukemia Group B. J Cancer Res Clin Oncol 116:816
Silverman LR, Demakos EP, Peterson BL, Kornblith AB, Holland JC, Odchimar-Reissig R, Stone RM, Nelson D, Powell BL, DeCastro CM, Ellerton J, Larson RA, Schiffer CA, Holland JF (2002) Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J Clin Oncol 20:2429–2440
Singh N, Baby D, Rajguru JP, Patil PB, Thakkannavar SS, Pujari VB (2019) Inflammation and cancer. Ann Afr Med 18:121–126
Skaland I, Janssen EA, Gudlaugsson E, Klos J, Kjellevold KH, Søiland H, Baak JP (2007) Phosphohistone H3 expression has much stronger prognostic value than classical prognosticators in invasive lymph node-negative breast cancer patients less than 55 years of age. Mod Pathol 20:1307–1315
Slupianek A, Yerrum S, Safadi FF, Monroy MA (2010) The chromatin remodeling factor SRCAP modulates expression of prostate specific antigen and cellular proliferation in prostate cancer cells. J Cell Physiol 224:369–375
Smith E, Jones ME, Drew PA (2009) Quantitation of DNA methylation by melt curve analysis. BMC Cancer 9:123
Smolewski P, Robak T (2017) The discovery and development of romidepsin for the treatment of T-cell lymphoma. Expert Opin Drug Discov 12:859–873
Soboleva TA, Parker BJ, Nekrasov M, Hart-Smith G, Tay YJ, Tng W-Q, Wilkins M, Ryan D, Tremethick DJ (2017) A new link between transcriptional initiation and pre-mRNA splicing: the RNA binding histone variant H2A.B. PLoS Genet 13:e1006633
Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, Wang J, Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29:68–72
Sotero-Caio CG, de Souza MJ, Cabral-de-Mello DC, Brasileiro-Vidal AC, Guerra M (2011) Phosphorylation of histone H3S10 in animal chromosomes: is there a uniform pattern? Cytogenet Genome Res 135:111–117
Spemann H, Mangold H (1924) über Induktion von Embryonalanlagen durch Implantation artfremder Organisatoren. Archiv für mikroskopische Anatomie und Entwicklungsmechanik 100:599–638
Spiers H, Hannon E, Schalkwyk LC, Bray NJ, Mill J (2017) 5-hydroxymethylcytosine is highly dynamic across human fetal brain development. BMC Genomics 18:738
Spineti PPM (2019) Biomarkers in heart failure. Arq Bras Cardiol 113:205–206
Sporn JC, Kustatscher G, Hothorn T, Collado M, Serrano M, Muley T, Schnabel P, Ladurner AG (2009) Histone macroH2A isoforms predict the risk of lung cancer recurrence. Oncogene 28:3423–3428
Stasik S, Middeke JM, Kramer M, Röllig C, Krämer A, Scholl S, Hochhaus A, Crysandt M, Brümmendorf TH, Naumann R, Steffen B, Kunzmann V, Einsele H, Schaich M, Burchert A, Neubauer A, Schäfer-Eckart K, Schliemann C, Krause S, Herbst R, Hänel M, Frickhofen N, Noppeney R, Kaiser U, Baldus CD, Kaufmann M, Rácil Z, Platzbecker U, Berdel WE, Mayer J, Serve H, Müller-Tidow C, Ehninger G, Bornhäuser M, Schetelig J, Thiede C (2020) EZH2 mutations and impact on clinical outcome: an analysis in 1,604 patients with newly diagnosed acute myeloid leukemia. Haematologica 105:e228–e231
Steensma DP (2009) Decitabine treatment of patients with higher-risk myelodysplastic syndromes. Leuk Res 33(Suppl 2):S12–S17
Steffan JS, Bodai L, Pallos J, Poelman M, McCampbell A, Apostol BL, Kazantsev A, Schmidt E, Zhu YZ, Greenwald M, Kurokawa R, Housman DE, Jackson GR, Marsh JL, Thompson LM (2001) Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila. Nature 413:739–743
Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45
Straining R, Eighmy W (2022) Tazemetostat: EZH2 Inhibitor. J Adv Pract Oncol 13:158–163
Strauss J, Figg WD (2016) Using epigenetic therapy to overcome chemotherapy resistance. Anticancer Res 36:1–4
Stresemann C, Lyko F (2008) Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine. Int J Cancer 123:8–13
Strimbu K, Tavel JA (2010) What are biomarkers? Curr Opin HIV AIDS 5:463–466
Sun W, Sun Y, Zhu M, Wang Z, Zhang H, Xin Y, Jiang G, Guo X, Zhang Z, Liu Y (2014a) The role of plasma cell-free DNA detection in predicting preoperative chemoradiotherapy response in rectal cancer patients. Oncol Rep 31:1466–1472
Sun W, Zang L, Shu Q, Li X (2014b) From development to diseases: the role of 5hmC in brain. Genomics 104:347–351
Sun XJ, Liu BY, Yan S, Jiang TH, Cheng HQ, Jiang HS, Cao Y, Mao AW (2015) MicroRNA-29a promotes pancreatic cancer growth by inhibiting Tristetraprolin. Cell Physiol Biochem 37:707–718
Sun L, Yao Y, Lu T, Shang Z, Zhan S, Shi W, Pan G, Zhu X, He S (2018a) DAB2IP downregulation enhances the proliferation and metastasis of human gastric cancer cells by Derepressing the ERK1/2 pathway. Gastroenterol Res Pract 2018:2968252
Sun X, Xu C, Xiao G, Meng J, Wang J, Tang SC, Qin S, Du N, Li G, Ren H, Liu D (2018b) Breast cancer stem-like cells are sensitized to tamoxifen induction of self-renewal inhibition with enforced let-7c dependent on Wnt blocking. Int J Mol Med 41:1967–1975
Sung H, Siegel RL, Rosenberg PS, Jemal A (2019) Emerging cancer trends among young adults in the USA: analysis of a population-based cancer registry. Lancet Public Health 4:e137–e147
Sved J, Bird A (1990) The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci U S A 87:4692–4696
Szenker E, Ray-Gallet D, Almouzni G (2011) The double face of the histone variant H3.3. Cell Res 21:421–434
Szulwach KE, Li X, Li Y, Song CX, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, Yoon YS, Ren B, He C, Jin P (2011) Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet 7:e1002154
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935
Takahashi H, Ogata H, Nishigaki R, Broide DH, Karin M (2010) Tobacco smoke promotes lung tumorigenesis by triggering IKKbeta- and JNK1-dependent inflammation. Cancer Cell 17:89–97
Talbert PB, Henikoff S (2010) Histone variants–ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11:264–275
Talbert PB, Henikoff S (2021) Histone variants at a glance. J Cell Sci 134:jcs244749
Tamaru H, Selker EU (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277–283
Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028
Tang S, Huang X, Wang X, Zhou X, Huang H, Qin L, Tao H, Wang Q, Tao Y (2020) Vital and distinct roles of H2A.Z isoforms in hepatocellular carcinoma. Onco Targets Ther 13:4319–4337
Taryma-Leśniak O, Sokolowska KE, Wojdacz TK (2020) Current status of development of methylation biomarkers for in vitro diagnostic IVD applications. Clin Epigenetics 12:100
Taunton J, Hassig CA, Schreiber SL (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272:408–411
Tepus M, Yau TO (2020) Non-invasive colorectal cancer screening: An overview. Gastrointest Tumors 7:62–73
Tiffon C, Adams J, van der Fits L, Wen S, Townsend P, Ganesan A, Hodges E, Vermeer M, Packham G (2011) The histone deacetylase inhibitors vorinostat and romidepsin downmodulate IL-10 expression in cutaneous T-cell lymphoma cells. Br J Pharmacol 162:1590–1602
Titze-de-Almeida SS, Brandão PRP, Faber I, Titze-de-Almeida R (2020) Leading RNA interference therapeutics part 1: silencing hereditary transthyretin amyloidosis, with a focus on Patisiran. Mol Diagn Ther 24:49–59
Tolstorukov MY, Goldman Joseph A, Gilbert C, Ogryzko V, Kingston Robert E, Park Peter J (2012) Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells. Mol Cell 47:596–607
Torrezan GT, Ferreira EN, Nakahata AM, Barros BD, Castro MT, Correa BR, Krepischi AC, Olivieri EH, Cunha IW, Tabori U, Grundy PE, Costa CM, de Camargo B, Galante PA, Carraro DM (2014) Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour. Nat Commun 5:4039
Trang P, Medina PP, Wiggins JF, Ruffino L, Kelnar K, Omotola M, Homer R, Brown D, Bader AG, Weidhaas JB, Slack FJ (2010) Regression of murine lung tumors by the let-7 microRNA. Oncogene 29:1580–1587
Trosko JE, Upham BL (2005) The emperor wears no clothes in the field of carcinogen risk assessment: ignored concepts in cancer risk assessment. Mutagenesis 20:81–92
Trovato M, Patil V, Gehre M, Noh KM (2020) Histone variant H3.3 mutations in defining the chromatin function in mammals. Cell 9:2716
Tsai C-H, Chen Y-J, Yu C-J, Tzeng S-R, Wu I-C, Kuo W-H, Lin M-C, Chan N-L, Wu K-J, Teng S-C (2016) SMYD3-mediated H2A.Z.1 methylation promotes cell cycle and cancer proliferation. Cancer Res 76:6043–6053
Turinetto V, Giachino C (2015) Multiple facets of histone variant H2AX: a DNA double-strand-break marker with several biological functions. Nucleic Acids Res 43:2489–2498
Tzao C, Tung HJ, Jin JS, Sun GH, Hsu HS, Chen BH, Yu CP, Lee SC (2009) Prognostic significance of global histone modifications in resected squamous cell carcinoma of the esophagus. Mod Pathol 22:252–260
Ueda H, Nakajima H, Hori Y, Fujita T, Nishimura M, Goto T, Okuhara M (1994) FR901228, a novel antitumor bicyclic depsipeptide produced by Chromobacterium violaceum no. 968. I. Taxonomy, fermentation, isolation, physico-chemical and biological properties, and antitumor activity. J Antibiot (Tokyo) 47:301–310
Uehara N, Yoshizawa K, Tsubura A (2012) Vorinostat enhances protein stability of p27 and p21 through negative regulation of Skp2 and Cks1 in human breast cancer cells. Oncol Rep 28:105–110
Uemura N, Okamoto S, Yamamoto S, Matsumura N, Yamaguchi S, Yamakido M, Taniyama K, Sasaki N, Schlemper RJ (2001) Helicobacter pylori infection and the development of gastric cancer. N Engl J Med 345:784–789
Ulirsch J, Fan C, Knafl G, Wu MJ, Coleman B, Perou CM, Swift-Scanlan T (2013) Vimentin DNA methylation predicts survival in breast cancer. Breast Cancer Res Treat 137:383–396
Vaisvila R, Ponnaluri VKC, Sun Z, Langhorst BW, Saleh L, Guan S, Dai N, Campbell MA, Sexton BS, Marks K, Samaranayake M, Samuelson JC, Church HE, Tamanaha E, Corrêa IR, Pradhan S, Dimalanta ET, Evans TC, Williams L, Davis TB (2021) Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res 31:1280–1289
Valdés-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C, Clark SJ (2012) Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Res 22:307–321
van Daal A, White EM, Gorovsky MA, Elgin SC (1988) Drosophila has a single copy of the gene encoding a highly conserved histone H2A variant of the H2A.F/Z type. Nucleic Acids Res 16:7487–7497
VanderMolen KM, McCulloch W, Pearce CJ, Oberlies NH (2011) Romidepsin (Istodax, NSC 630176, FR901228, FK228, depsipeptide): a natural product recently approved for cutaneous T-cell lymphoma. J Antibiot (Tokyo) 64:525–531
Vardabasso C, Hasson D, Ratnakumar K, Chung CY, Duarte LF, Bernstein E (2014) Histone variants: emerging players in cancer biology. Cell Mol Life Sci 71:379–404
Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Chung CY, Yao JL, Singh R, Segura MF, Fontanals-Cirera B, Verma A, Mann M, Hernando E, Hake SB, Bernstein E (2015) Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma. Mol Cell 59:75–88
Varvara PV, Karaolanis G, Valavanis C, Stanc G, Tzaida O, Trihia H, Patapis P, Dimitroulis D, Perrea D (2019) Gamma-H2AX: a potential biomarker in breast cancer. Tumour Biol 41:1010428319878536
Vavouri T, Lehner B (2012) Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol 13:R110
Verma M (2012) Epigenetic biomarkers in cancer epidemiology. Methods Mol Biol 863:467–480
Veronezi GM, Felisbino MB, Gatti MS, Mello ML, Vidal BC (2017) DNA methylation changes in Valproic acid-treated HeLa cells as assessed by image analysis, immunofluorescence and vibrational microspectroscopy. PLoS One 12:e0170740
Virchow R (1863) Cellular pathology as based upon physiological and pathological histology
Vogler C, Huber C, Waldmann T, Ettig R, Braun L, Izzo A, Daujat S, Chassignet I, Lopez-Contreras AJ, Fernandez-Capetillo O, Dundr M, Rippe K, Längst G, Schneider R (2010) Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding. PLoS Genet 6:e1001234
Voigt P, Tee WW, Reinberg D (2013) A double take on bivalent promoters. Genes Dev 27:1318–1338
Waddington CH (1940) Organisers and Genes. The Cambridge University Press, Cambridge
Waddington CH (1942) The epigenotype. Endeavour 1:18–20
Waddington CH (2012) The epigenotype. Int J Epidemiol 41:10–13
Waddington CH, Needham J, Needham DM (1933) Physico-chemical experiments on the amphibian Organiser. Nature 132:239–239
Waddington CH, Needham J, Nowinski WW, Needham DM, Lemberg R (1934) Active principle of the amphibian organisation Centre. Nature 134:103–103
Wagner RN, Piñón Hofbauer J, Wally V, Kofler B, Schmuth M, De Rosa L, De Luca M, Bauer JW (2021) Epigenetic and metabolic regulation of epidermal homeostasis. Exp Dermatol 30:1009–1022
Walser JC, Furano AV (2010) The mutational spectrum of non-CpG DNA varies with CpG content. Genome Res 20:875–882
Wang J, Tang J, Lai M, Zhang H (2014a) 5-Hydroxymethylcytosine and disease. Mutat Res Rev Mutat Res 762:167–175
Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C (2014b) N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505:117–120
Wang J, Zhu X, Hu J, He G, Li X, Wu P, Ren X, Wang F, Liao W, Liang L, Ding Y (2015a) The positive feedback between snail and DAB2IP regulates EMT, invasion and metastasis in colorectal cancer. Oncotarget 6:27427–27439
Wang T, Wang G, Hao D, Liu X, Wang D, Ning N, Li X (2015b) Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer. Mol Cancer 14:125
Wang T, Kong S, Tao M, Ju S (2020a) The potential role of RNA N6-methyladenosine in cancer progression. Mol Cancer 19:88
Wang Z, Du M, Yuan Q, Guo Y, Hutchinson JN, Su L, Zheng Y, Wang J, Mucci LA, Lin X, Hou L, Christiani DC (2020b) Epigenomic analysis of 5-hydroxymethylcytosine (5hmC) reveals novel DNA methylation markers for lung cancers. Neoplasia 22:154–161
Watanabe T, Tada M, Nagai H, Sasaki S, Nakao M (1998) Helicobacter pylori infection induces gastric cancer in mongolian gerbils. Gastroenterology 115:642–648
Wei CM, Gershowitz A, Moss B (1975) Methylated nucleotides block 5′-terminus of HeLa cell messenger RNA. Cell 4:379–386
Wei CM, Gershowitz A, Moss B (1976) 5′-terminal and internal methylated nucleotide sequences in HeLa cell mRNA. Biochemistry 15:397–401
Wei Y, Mizzen CA, Cook RG, Gorovsky MA, Allis CD (1998) Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena. Proc Natl Acad Sci 95:7480–7484
Wei JW, Huang K, Yang C, Kang CS (2017) Non-coding RNAs as regulators in epigenetics (review). Oncol Rep 37:3–9
Weinberg DN, Papillon-Cavanagh S, Chen H, Yue Y, Chen X, Rajagopalan KN, Horth C, McGuire JT, Xu X, Nikbakht H, Lemiesz AE, Marchione DM, Marunde MR, Meiners MJ, Cheek MA, Keogh MC, Bareke E, Djedid A, Harutyunyan AS, Jabado N, Garcia BA, Li H, Allis CD, Majewski J, Lu C (2019) The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape. Nature 573:281–286
Weinhold B (2006) Epigenetics: the science of change. Environ Health Perspect 114:A160–A167
Weisenberger DJ, Liang G, Lenz HJ (2018) DNA methylation aberrancies delineate clinically distinct subsets of colorectal cancer and provide novel targets for epigenetic therapies. Oncogene 37:566–577
Wen D, Banaszynski LA, Liu Y, Geng F, Noh KM, Xiang J, Elemento O, Rosenwaks Z, Allis CD, Rafii S (2014a) Histone variant H3.3 is an essential maternal factor for oocyte reprogramming. Proc Natl Acad Sci U S A 111:7325–7330
Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X (2014b) ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 508:263–268
West MH, Bonner WM (1980) Histone 2A, a heteromorphous family of eight protein species. Biochemistry 19:3238–3245
Wigle TJ (2011) Promoting illiteracy in epigenetics: an emerging therapeutic strategy. Curr Chem Genomics 5:48–50
Wijermans P, Lübbert M, Verhoef G, Bosly A, Ravoet C, Andre M, Ferrant A (2000) Low-dose 5-aza-2′-deoxycytidine, a DNA hypomethylating agent, for the treatment of high-risk myelodysplastic syndrome: a multicenter phase II study in elderly patients. J Clin Oncol 18:956–962
Wilkins OM, Johnson KC, Houseman EA, King JE, Marsit CJ, Christensen BC (2020) Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 15:398–418
Wolin KY, Carson K, Colditz GA (2010) Obesity and cancer. Oncologist 15:556–565
Wratting D, Thistlethwaite A, Harris M, Zeef LA, Millar CB (2012) A conserved function for the H2A.Z C terminus. J Biol Chem 287:19148–19157
Wu G, Broniscer A, McEachron TA, Lu C, Paugh BS, Becksfort J, Qu C, Ding L, Huether R, Parker M, Zhang J, Gajjar A, Dyer MA, Mullighan CG, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Ellison DW, Zhang J, Baker SJ (2012) Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet 44:251–253
Wu C, Du X, Tang L, Wu J, Zhao W, Guo X, Liu D, Hu W, Helmby H, Chen G, Wang Z (2020) Schistosoma japonicum SjE16.7 protein promotes tumor development via the receptor for advanced glycation end products (RAGE). Front Immunol 11:1767
Wyatt GR, Cohen SS (1952) A new Pyrimidine Base from bacteriophage nucleic acids. Nature 170:1072–1073
Wynder EL, Hoffmann D (1976) Tobacco and tobacco smoke. Semin Oncol 3:5–15
Xia J, Han L, Zhao Z (2012) Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics 13(Suppl 8):S7
Xiao C, Srinivasan L, Calado DP, Patterson HC, Zhang B, Wang J, Henderson JM, Kutok JL, Rajewsky K (2008) Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes. Nat Immunol 9:405–414
Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL, Yang YG (2016) Nuclear m(6)a reader YTHDC1 regulates mRNA splicing. Mol Cell 61:507–519
Xu T, Gao H (2020) Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment? Hum Genomics 14:15
Yan KS, Lin CY, Liao TW, Peng CM, Lee SC, Liu YJ, Chan WP, Chou RH (2017) EZH2 in cancer progression and potential application in cancer therapy: a friend or foe? Int J Mol Sci 18:1172
Yang HD, Kim PJ, Eun JW, Shen Q, Kim HS, Shin WC, Ahn YM, Park WS, Lee JY, Nam SW (2016) Oncogenic potential of histone-variant H2A.Z.1 and its regulatory role in cell cycle and epithelial-mesenchymal transition in liver cancer. Oncotarget 7:11412–11423
Yang SX, Polley EC, Nguyen D (2017) Association of γH2AX at diagnosis with chemotherapy outcome in patients with breast cancer. Theranostics 7:945–951
Yang Y, Zeng C, Lu X, Song Y, Nie J, Ran R, Zhang Z, He C, Zhang W, Liu SM (2019) 5-Hydroxymethylcytosines in circulating cell-free DNA reveal vascular complications of type 2 diabetes. Clin Chem 65:1414–1425
Yang YL, Chang YH, Li CJ, Huang YH, Tsai MC, Chu PY, Lin HY (2021) New insights into the role of miR-29a in hepatocellular carcinoma: implications in mechanisms and Theragnostics. J Pers Med 11:219
Ye C, Li L (2014) 5-hydroxymethylcytosine: a new insight into epigenetics in cancer. Cancer Biol Ther 15:10–15
Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG (2011) Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147:1498–1510
You JS, Jones PA (2012) Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22:9–20
Yu W, Zhang L, Wei Q, Shao A (2019) O(6)-Methylguanine-DNA methyltransferase (MGMT): challenges and new opportunities in glioma chemotherapy. Front Oncol 9:1547
Yuan EF, Yang Y, Cheng L, Deng X, Chen SM, Zhou X, Liu SM (2019) Hyperglycemia affects global 5-methylcytosine and 5-hydroxymethylcytosine in blood genomic DNA through upregulation of SIRT6 and TETs. Clin Epigenetics 11:63
Zaina S, Pérez-Luque EL, Lund G (2010) Genetics talks to epigenetics? The interplay between sequence variants and chromatin structure. Curr Genomics 11:359–367
Zampieri M, Bacalini MG, Barchetta I, Scalea S, Cimini FA, Bertoccini L, Tagliatesta S, De Matteis G, Zardo G, Cavallo MG, Reale A (2021) Increased PARylation impacts the DNA methylation process in type 2 diabetes mellitus. Clin Epigenetics 13:114
Zhang Y, Jeltsch A (2010) The application of next generation sequencing in DNA methylation analysis. Genes (Basel) 1:85–101
Zhang C, Richon V, Ni X, Talpur R, Duvic M (2005) Selective induction of apoptosis by histone deacetylase inhibitor SAHA in cutaneous T-cell lymphoma cells: relevance to mechanism of therapeutic action. J Invest Dermatol 125:1045–1052
Zhang Y, Wu K, Shao Y, Sui F, Yang Q, Shi B, Hou P, Ji M (2016) Decreased 5-Hydroxymethylcytosine (5-hmC) predicts poor prognosis in early-stage laryngeal squamous cell carcinoma. Am J Cancer Res 6:1089–1098
Zhang P, Wu W, Chen Q, Chen M (2019a) Non-coding RNAs and their integrated networks. J Integr Bioinform 16:20190027
Zhang Q, Han Q, Zi J, Ma J, Song H, Tian Y, McGrath M, Song C, Ge Z (2019b) Mutations in EZH2 are associated with poor prognosis for patients with myeloid neoplasms. Genes Dis 6:276–281
Zhang MM, Bahal R, Rasmussen TP, Manautou JE, Zhong XB (2021a) The growth of siRNA-based therapeutics: updated clinical studies. Biochem Pharmacol 189:114432
Zhang Y, Geng X, Xu J, Li Q, Hao L, Zeng Z, Xiao M, Song J, Liu F, Fang C, Wang H (2021b) Identification and characterization of N6-methyladenosine modification of circRNAs in glioblastoma. J Cell Mol Med 25:7204–7217
Zhao Z, Han L (2009) CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun 382:643–645
Zhou J, Fan JY, Rangasamy D, Tremethick DJ (2007) The nucleosome surface regulates chromatin compaction and couples it with transcriptional repression. Nat Struct Mol Biol 14:1070–1076
Zhu ZM, Huo FC, Pei DS (2020) Function and evolution of RNA N6-methyladenosine modification. Int J Biol Sci 16:1929–1940
Zou C, He Q, Feng Y, Chen M, Zhang D (2022) A m(6)Avalue predictive of prostate cancer stemness, tumor immune landscape and immunotherapy response. NAR. Cancer 4:zcac010
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Stein, R.A., Deverakonda, A.N. (2022). Epigenetics in Cancer Biology. In: Rezaei, N. (eds) Cancer Research: An Interdisciplinary Approach. Interdisciplinary Cancer Research, vol 1. Springer, Cham. https://doi.org/10.1007/16833_2022_86
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