| [1] |
Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. |
| [2] |
Liu X, Nisa KU, Kong W, Lang Z, Niu Q. 2025. DNA methylation and histone modifications: conserved, divergent, and synergistic epigenetic regulation across plants and animals. |
| [3] |
Meza-Menchaca T, Giancarlo VM, Melgar-Lalanne G, Ricaño-Rodríguez J, Aguirre-von-Wobeser E. 2025. Reframing epigenetics: three dimensions in the post-genomic era. |
| [4] |
Wyatt GR. 1951. Recognition and estimation of 5-methylcytosine in nucleic acids. |
| [5] |
Dostal V, Churchill MEA. 2019. Cytosine methylation of mitochondrial DNA at CpG sequences impacts transcription factor A DNA binding and transcription. |
| [6] |
Widagdo J, Anggono V. 2018. The m6A-epitranscriptomic signature in neurobiology: from neurodevelopment to brain plasticity. |
| [7] |
Smith ZD, Hetzel S, Meissner A. 2025. DNA methylation in mammalian development and disease. |
| [8] |
Mulholland CB, Nishiyama A. 2025. Molecular mechanisms of maintenance DNA methylation. |
| [9] |
Bronner C, Alhosin M, Hamiche A, Mousli M. 2019. Coordinated dialogue between UHRF1 and DNMT1 to ensure faithful inheritance of methylated DNA patterns. |
| [10] |
Anderson CM, Gillespie SL, Thiele DK, Ralph JL, Ohm JE. 2018. Effects of maternal vitamin D supplementation on the maternal and infant epigenome. |
| [11] |
Masser DR, Hadad N, Porter H, Stout MB, Unnikrishnan A, et al. 2018. Analysis of DNA modifications in aging research. |
| [12] |
Jeltsch A, Broche J, Bashtrykov P. 2018. Molecular processes connecting DNA methylation patterns with DNA methyltransferases and histone modifications in mammalian genomes. |
| [13] |
Zhang H, Liu H, Chen Y, Yang X, Wang P, et al. 2016. A cell cycle-dependent BRCA1–UHRF1 cascade regulates DNA double-strand break repair pathway choice. |
| [14] |
Almalki NAR, Sabir JSM, Ibrahim A, Alhosin M, Asseri AH, et al. 2024. UHRF1 poly-auto-ubiquitination induced by the anti-cancer drug, thymoquinone, is involved in the DNA repair machinery recruitment. |
| [15] |
Feng L, Lou J. 2018. DNA methylation analysis. Nanotoxicity. New York, NY: Springer New York: 181−227 doi: 10.1007/978-1-4939-8916-4_12 |
| [16] |
Hermann A, Gowher H, Jeltsch A. 2004. Biochemistry and biology of mammalian DNA methyltransferases. |
| [17] |
Jeltsch A, Jurkowska RZ. 2016. Allosteric control of mammalian DNA methyltransferases–a new regulatory paradigm. |
| [18] |
Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, et al. 2006. Computational prediction of methylation status in human genomic sequences. |
| [19] |
Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, et al. 2006. Large-scale structure of genomic methylation patterns. |
| [20] |
Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, et al. 2014. Gene body methylation can alter gene expression and is a therapeutic target in cancer. |
| [21] |
Illingworth R, Kerr A, DeSousa D, Jørgensen H, Ellis P, et al. 2008. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. |
| [22] |
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, et al. 2010. Dynamic changes in the human methylome during differentiation. |
| [23] |
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. |
| [24] |
Nazarenko T, Vavourakis CD, Jones A, Evans I, Schreiberhuber L, et al. 2024. Technical and biological sources of unreliability of Infinium probes on Illumina methylation microarrays. |
| [25] |
Šestáková Š, Šálek C, Remešová H. 2019. DNA methylation validation methods: a coherent review with practical comparison. |
| [26] |
Lövkvist C, Dodd IB, Sneppen K, Haerter JO. 2016. DNA methylation in human epigenomes depends on local topology of CpG sites. |
| [27] |
Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, et al. 2011. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. |
| [28] |
Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, et al. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. |
| [29] |
Portela A, Esteller M. 2010. Epigenetic modifications and human disease. |
| [30] |
Alhosin M, Sharif T, Mousli M, Etienne-Selloum N, Fuhrmann G, et al. 2011. Down-regulation of UHRF1 associated with re-expression of tumor suppressor genes, is a common feature of natural compounds exhibiting anti-cancer properties. |
| [31] |
Alhosin M, Omran Z, Zamzami MA, Al-Malki AL, Choudhry H, et al. 2016. Signalling pathways in UHRF1-dependent regulation of tumor suppressor genes in cancer. |
| [32] |
Xie S, Hagen D, Becker GM, Davenport KM, Shira KA, et al. 2025. Analyzing the relationship of RNA and DNA methylation with gene expression. |
| [33] |
Neri F, Incarnato D, Krepelova A, Rapelli S, Anselmi F, et al. 2015. Single-base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals promoter DNA methylation dynamics. |
| [34] |
Yu M, Hon GC, Szulwach KE, Song CX, Jin P, et al. 2012. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. |
| [35] |
Bronner C, Achour M, ARIMA Y, Chataigneau T, Saya H, et al. 2007. The UHRF family: Oncogenes that are drugable targets for cancer therapy in the near future? |
| [36] |
Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PWTC, et al. 2013. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. |
| [37] |
Schoenfelder S, Fraser P. 2019. Long-range enhancer–promoter contacts in gene expression control. |
| [38] |
Choudalakis M, Kungulovski G, Mauser R, Bashtrykov P, Jeltsch A. 2023. Refined read-out: The hUHRF1Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3. |
| [39] |
Choudalakis M, Bashtrykov P, Jeltsch A. 2024. RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats. |
| [40] |
Swanberg SE, Nagarajan RP, Peddada S, Yasui DH, LaSalle JM. 2009. Reciprocal co-regulation of EGR2 and MECP2 is disrupted in Rett syndrome and autism. |
| [41] |
Flam EL, Danilova L, Kelley DZ, Stavrovskaya E, Guo T, et al. 2019. Differentially methylated super-enhancers regulate target gene expression in human cancer. |
| [42] |
Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, et al. 2013. Master transcription factors and mediator establish super-enhancers at key cell identity genes. |
| [43] |
Pang P, Chen J, Li Q, Su Z, Lin J, et al. 2026. UHRF1-mediated DNA 5-mC modification drives super-enhancer redistribution and impedes osteogenesis via TGM2-regulated autophagic flux in senile osteoporosis. |
| [44] |
Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, et al. 2013. Global epigenomic reconfiguration during mammalian brain development. |
| [45] |
Hahn O, Grönke S, Stubbs TM, Ficz G, Hendrich O, et al. 2017. Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. |
| [46] |
Pérez RF, Santamarina P, Tejedor JR, Urdinguio RG, Álvarez-Pitti J, et al. 2019. Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes. |
| [47] |
Terekhova M, Swain A, Bohacova P, Aladyeva E, Arthur L, et al. 2023. Single-cell atlas of healthy human blood unveils age-related loss of NKG2C+GZMB−CD8+ memory T cells and accumulation of type 2 memory T cells. |
| [48] |
Kim KY, Tanaka Y, Su J, Cakir B, Xiang Y, et al. 2018. Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. |
| [49] |
Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, et al. 2024. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. |
| [50] |
Papin C, Ibrahim A, Sabir JSM, Le Gras S, Stoll I, et al. 2023. MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density. |
| [51] |
Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, et al. 2020. Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase. |
| [52] |
Kikuchi A, Arita K. 2025. A comprehensive review of structural insights into DNA methylation maintenance. |
| [53] |
Han M, Li J, Cao Y, Huang Y, Li W, et al. 2020. A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1 chromatin association. |
| [54] |
Dong Q, Gong C, Jiang Q, Liu Y, Hu Y, et al. 2024. Identification of differentially expressed tumour-related genes regulated by UHRF1-driven DNA methylation. |
| [55] |
Holliday R, Pugh JE. 1975. DNA modification mechanisms and gene activity during development. |
| [56] |
Mattei AL, Bailly N, Meissner A. 2022. DNA methylation: a historical perspective. |
| [57] |
Bernstein C. 2022. DNA methylation and establishing memory. |
| [58] |
Buck-Koehntop BA, Defossez PA. 2013. On how mammalian transcription factors recognize methylated DNA. |
| [59] |
Bronner C, Fuhrmann G, Chédin FL, Macaluso M, Dhe-Paganon S. 2009. UHRF1 links the histone code and DNA methylation to ensure faithful epigenetic memory inheritance. |
| [60] |
Maleknia M, Ahmadirad N, Golab F, Katebi Y, Haj Mohamad Ebrahim Ketabforoush A. 2023. DNA methylation in cancer: epigenetic view of dietary and lifestyle factors. |
| [61] |
Jones PA, Issa JJ, Baylin S. 2016. Targeting the cancer epigenome for therapy. |
| [62] |
Bochtler M, Kolano A, Xu GL. 2017. DNA demethylation pathways: Additional players and regulators. |
| [63] |
Markiewicz E, Idowu OC. 2019. DNA damage in human skin and the capacities of natural compounds to modulate the bystander signalling. |
| [64] |
Vito AF, Boesch DJ, Hammons AM, Freudenthal BD, Weaver TM. 2025. Base excision repair in chromatin: a tug-of-war for DNA damage. |
| [65] |
Zhou W, Jing X, Hang R, Liu Z, Cao L, et al. 2025. Base excision repair in human cancer: Emerging diagnostic and therapeutic target. |
| [66] |
Sjolund AB, Senejani AG, Sweasy JB. 2013. MBD4 and TDG: Multifaceted DNA glycosylases with ever expanding biological roles. |
| [67] |
Bellacosa A, Cicchillitti L, Schepis F, Riccio A, Yeung AT, et al. 1999. MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. |
| [68] |
Koliadenko V, Wilanowski T. 2020. Additional functions of selected proteins involved in DNA repair. |
| [69] |
Hashimoto H, Zhang X, Cheng X. 2012. Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. |
| [70] |
Cortellino S, Turner D, Masciullo V, Schepis F, Albino D, et al. 2003. The base excision repair enzyme MED1 mediates DNA damage response to antitumor drugs and is associated with mismatch repair system integrity. |
| [71] |
Branch P, Hampson R, Karran P. 1995. DNA mismatch binding defects, DNA damage tolerance, and mutator phenotypes in human colorectal carcinoma cell lines. |
| [72] |
Hopfner R, Mousli M, Jeltsch JM, Voulgaris A, Lutz Y, et al. 2000. ICBP90, a novel human CCAAT binding protein, involved in the regulation of topoisomerase IIalpha expression. |
| [73] |
Achour M, Jacq X, Rondé P, Alhosin M, Charlot C, et al. 2008. The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. |
| [74] |
Bostick M, Kim JK, Estève PO, Clark A, Pradhan S, et al. 2007. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. |
| [75] |
Sharif J, Muto M, Takebayashi SI, Suetake I, Iwamatsu A, et al. 2007. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. |
| [76] |
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, et al. 2008. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. |
| [77] |
Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, et al. 2008. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1. |
| [78] |
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M. 2008. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. |
| [79] |
Yamaguchi K, Chen X, Rodgers B, Miura F, Bashtrykov P, et al. 2024. Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells. |
| [80] |
Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, et al. 2011. Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. |
| [81] |
Bronner C, Chataigneau T, Schini-Kerth V, Landry Y. 2007. The "epigenetic code replication machinery", ECREM: a promising drugable target of the epigenetic cell memory. |
| [82] |
Tauber M, Fischle W. 2015. Conserved linker regions and their regulation determine multiple chromatin-binding modes of UHRF1. |
| [83] |
Sidhu H, Capalash N. 2017. UHRF1: The key regulator of epigenetics and molecular target for cancer therapeutics. |
| [84] |
Polepalli S, George SM, Valli Sri Vidya R, Rodrigues GS, Ramachandra L, et al. 2019. Role of UHRF1 in malignancy and its function as a therapeutic target for molecular docking towards the SRA domain. |
| [85] |
Xue B, Zhao J, Feng P, Xing J, Wu H, et al. 2019. Epigenetic mechanism and target therapy of UHRF1 protein complex in malignancies. |
| [86] |
Xie S, Qian C. 2018. The growing complexity of UHRF1-mediated maintenance DNA methylation. |
| [87] |
Mancini M, Magnani E, Macchi F, Bonapace IM. 2021. The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity. |
| [88] |
Kim A, Benavente CA. 2024. Oncogenic roles of UHRF1 in cancer. |
| [89] |
Gu L, Fu Y, Li X. 2024. Roles of post-translational modifications of UHRF1 in cancer. |
| [90] |
Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, et al. 2024. Oncogenes and tumor suppressor genes: functions and roles in cancers. |
| [91] |
Valcárcel G, Lazarenkov A, López-Rubio AV, Berenguer C, Calafell-Segura J, et al. 2025. Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing. |
| [92] |
Ashraf W, Ahmad T, Reynoird N, Hamiche A, Mély Y, et al. 2023. Natural and synthetic anticancer epidrugs targeting the epigenetic integrator UHRF1. |
| [93] |
Zhuo H, Tang J, Lin Z, Jiang R, Zhang X, et al. 2016. The aberrant expression of MEG3 regulated by UHRF1 predicts the prognosis of hepatocellular carcinoma. |
| [94] |
Ashraf W, Ibrahim A, Alhosin M, Zaayter L, Ouararhni K, et al. 2017. The epigenetic integrator UHRF1: on the road to become a universal biomarker for cancer. |
| [95] |
Kostyrko K, Román M, Lee AG, Simpson DR, Dinh PT, et al. 2023. UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma. |
| [96] |
Pacaud R, Brocard E, Lalier L, Hervouet E, Vallette FM, et al. 2014. The DNMT1/PCNA/UHRF1 disruption induces tumorigenesis characterized by similar genetic and epigenetic signatures. |
| [97] |
Jeanblanc M, Mousli M, Hopfner R, Bathami K, Martinet N, et al. 2005. The retinoblastoma gene and its product are targeted by ICBP90 a key mechanism in the G1/S transition during the cell cycle. |
| [98] |
Ashraf W, Bronner C, Zaayter L, Ahmad T, Richert L, et al. 2017. Interaction of the epigenetic integrator UHRF1 with the MYST domain of TIP60 inside the cell. |
| [99] |
Achour M, Fuhrmann G, Alhosin M, Rondé P, Chataigneau T, et al. 2009. UHRF1 recruits the histone acetyltransferase Tip60 and controls its expression and activity. |
| [100] |
Arima Y, Hirota T, Bronner C, Mousli M, Fujiwara T, et al. 2004. Down-regulation of nuclear protein ICBP90 by p53/p21Cip1/WAF1-dependent DNA-damage checkpoint signals contributes to cell cycle arrest at G1/S transition. |
| [101] |
Abusnina A, Alhosin M, Keravis T, Muller CD, Fuhrmann G, et al. 2011. Down-regulation of cyclic nucleotide phosphodiesterase PDE1A is the key event of p73 and UHRF1 deregulation in thymoquinone-induced acute lymphoblastic leukemia cell apoptosis. |
| [102] |
Alhosin M, Abusnina A, Achour M, Sharif T, Muller C, et al. 2010. Induction of apoptosis by thymoquinone in lymphoblastic leukemia Jurkat cells is mediated by a p73-dependent pathway which targets the epigenetic integrator UHRF1. |
| [103] |
Hervouet E, Lalier L, Debien E, Cheray M, Geairon A, et al. 2010. Disruption of Dnmt1/PCNA/UHRF1 interactions promotes tumorigenesis from human and mice glial cells. |
| [104] |
Chen J, Wang D, Wu G, Xiong F, Liu W, et al. 2024. STUB1-mediated K63-linked ubiquitination of UHRF1 promotes the progression of cholangiocarcinoma by maintaining DNA hypermethylation of PLA2G2A. |
| [105] |
Unoki M, Sasaki H. 2022. The UHRF protein family in epigenetics, development, and carcinogenesis. |
| [106] |
Ren Y. 2022. Regulatory mechanism and biological function of UHRF1–DNMT1-mediated DNA methylation. |
| [107] |
Kondo E, Gu Z, Horii A, Fukushige S. 2005. The thymine DNA glycosylase MBD4 represses transcription and is associated with Methylated p16INK4a and hMLH1 Genes. |
| [108] |
Unoki M, Nishidate T, Nakamura Y. 2004. ICBP90, an E2F-1 target, recruits HDAC1 and binds to methyl-CpG through its SRA domain. |
| [109] |
Thillainadesan G, Chitilian JM, Isovic M, Ablack JNG, Mymryk JS, et al. 2012. TGF-β-dependent active demethylation and expression of the p15ink4b tumor suppressor are impaired by the ZNF217/CoREST complex. |
| [110] |
Jia CY, Xiang W, Liu JB, Jiang GX, Sun F, et al. 2021. miR-9-1 suppresses cell proliferation and promotes apoptosis by targeting UHRF1 in lung cancer. |
| [111] |
Meng H, Harrison DJ, Meehan RR. 2015. MBD4 interacts with and recruits USP7 to heterochromatic foci. |
| [112] |
Silveira AB, Houy A, Ganier O, Özemek B, Vanhuele S, et al. 2024. Base-excision repair pathway shapes 5-methylcytosine deamination signatures in pan-cancer genomes. |
| [113] |
Ibrahim A, Alhosin M, Papin C, Ouararhni K, Omran Z, et al. 2018. Thymoquinone challenges UHRF1 to commit auto-ubiquitination: a key event for apoptosis induction in cancer cells. |
| [114] |
Ruzov A, Shorning B, Mortusewicz O, Dunican DS, Leonhardt H, et al. 2009. MBD4 and MLH1 are required for apoptotic induction in xDNMT1-depleted embryos. |
| [115] |
Yang Y, Liu G, Qin L, Ye L, Zhu F, et al. 2019. Overexpression of UHRF1 and its potential role in the development of invasive ductal breast cancer validated by integrative bioinformatics and immunohistochemistry analyses. |
| [116] |
Choudhry H, Zamzami M, Omran Z, Wu W, Mousli M, et al. 2017. Targeting microRNA/UHRF1 pathways as a novel strategy for cancer therapy (Review). |
| [117] |
The Human Protein Atlas. www.proteinatlas.org/ENSG00000129071-MBD4/cancer |
| [118] |
Tien AL, Senbanerjee S, Kulkarni A, Mudbhary R, Goudreau B, et al. 2011. UHRF1 depletion causes a G2/M arrest, activation of DNA damage response and apoptosis. |
| [119] |
Zastko L. 2025. Genetic regulation of DNA double-strand breaks and repair pathways. |
| [120] |
Mistry H, Tamblyn L, Butt H, Sisgoreo D, Gracias A, et al. 2010. UHRF1 is a genome caretaker that facilitates the DNA damage response to γ-irradiation. |
| [121] |
DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, et al. 2018. A bifunctional role for the UHRF1 UBL domain in the control of hemi-methylated DNA-dependent histone ubiquitylation. |
| [122] |
Ciaco S, Mazzoleni V, Javed A, Eiler S, Ruff M, et al. 2023. Inhibitors of UHRF1 base flipping activity showing cytotoxicity against cancer cells. |
| [123] |
Kamel EM, Ali MAM, Allam AA, Ahmed NA, Abalkhail A, et al. 2025. Disrupting the epigenetic alliance: structural insights and therapeutic strategies targeting DNMT1–UHRF1. |
| [124] |
Fu Y, Jiang L, Xie G, Peng Y, Fu Y, et al. 2025. A Hybrid compound H93 treats prostate cancer by directly binding UHRF1 and promoting protein dimerization. |
| [125] |
Akrani I, Driva D, Tsakalidis E, Mozumdar N, Mavridi D, et al. 2025. Discovery and characterization of uracil derivatives targeting the set-and-ring domain of UHRF1. |
| [126] |
Giovinazzo H, Walker D, Wyhs N, Liu J, Esopi DM, et al. 2019. A high-throughput screen of pharmacologically active compounds for inhibitors of UHRF1 reveals epigenetic activity of anthracycline derivative chemotherapeutic drugs. |
| [127] |
Bellacosa A, Drohat AC. 2015. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. |
| [128] |
Screaton RA, Kiessling S, Sansom OJ, Millar CB, Maddison K, et al. 2003. Fas-associated death domain protein interacts with methyl-CpG binding domain protein 4: a potential link between genome surveillance and apoptosis. |