Benutzer:Dirk123456/Baustellenbaustelle 001/Baustelle-2/Baustelle-2.8

aus Wikipedia, der freien Enzyklopädie
Zur Navigation springen Zur Suche springen

Genes 2018, 9(11), 566; doi:10.3390/genes9110566; Review

Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes

Albert Jeltsch, Julian Broche and Pavel Bashtrykov

No. PubMed ID Authors Title Journ. Year Vol. pp.
1. PMID 21203455 Globisch, D.; Münzel, M.; Müller, M.; Michalakis, S.; Wagner, M.; Koch, S.; Brückl, T.; Biel, M.; Carell, T. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 2010 5, e15367.
2. PMID 24260150 Lisanti, S.; Omar, W.A.; Tomaszewski, B.; De Prins, S.; Jacobs, G.; Koppen, G.; Mathers, J.C.; Langie, S.A. Comparison of methods for quantification of global DNA methylation in human cells and tissues. PLoS ONE 2013 8, e79044.
3. PMID 27346641 Allis, C.D.; Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 2016 17, 487–500.
4. PMID 29547264 Noh, K.M.; Allis, C.D.; Li, H. Reading between the lines: “ADD”-ing histone and DNA methylation marks toward a new epigenetic “Sum”. ACS Chem. Biol. 2018 13, 1103.
5. PMID 21941284 Baylin, S.B.; Jones, P.A. A decade of exploring the cancer epigenome—Biological and translational implications. Nat. Rev. Cancer 2011 11, 726–734.
6. PMID 23463312 Bergman, Y.; Cedar, H. DNA methylation dynamics in health and disease. Nat. Struct. Mol. Biol. 2013 20, 274–281.
7. PMID 25406944 Erdmann, A.; Halby, L.; Fahy, J.; Arimondo, P.B. Targeting DNA methylation with small molecules: What’s next? J. Med. Chem. 2015 58, 2569–2583.
8. PMID 27848896 Mirfattah, B.; Herring, J.; Tang, H.; Zhang, K. Probes and targets of DNA methylation and demethylation in drug development. Curr. Top. Med. Chem. 2017 17, 1727–1740.
9. PMID 24947342 Jeltsch, A.; Jurkowska, R.Z. New concepts in DNA methylation. Trends Biochem. Sci. 2014 39, 310–318.
10. PMID 22641018 Jones, P.A. Functions of DNA methylation: Islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 2012 13, 484–492.
11. PMID 24993071 Jeong, M.; Goodell, M.A. New answers to old questions from genome-wide maps of DNA methylation in hematopoietic cells. Exp. Hematol. 2014 42, 609–617.
12. PMID 25592537 Schubeler, D. Function and information content of DNA methylation. Nature 2015 517, 321–326.
13. PMID 29381856 Ye, F.; Kong, X.; Zhang, H.; Liu, Y.; Shao, Z.; Jin, J.; Cai, Y.; Zhang, R.; Li, L.; Zhang, Y.W.; et al. Biochemical studies and molecular dynamic simulations reveal the molecular basis of conformational changes in DNA methyltransferase-1. ACS Chem. Biol. 2018 13, 772–781.
14. PMID 21243710 Jurkowska, R.Z.; Jurkowski, T.P.; Jeltsch, A. Structure and function of mammalian DNA methyltransferases. Chembiochem. 2011 12, 206–222.
15. PMID 27521372 Jeltsch, A.; Jurkowska, R.Z. Allosteric control of mammalian DNA methyltransferases—A new regulatory paradigm. Nucleic Acids Res. 2016 44, 8556–8575.
16. PMID 30154093 Gowher, H.; Jeltsch, A. Mammalian DNA methyltransferases: New discoveries and open questions. Biochem. Soc. Trans. 2018 46, 1191–1202.
17. PMID 20142834 Law, J.A.; Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010 11, 204–220.
18. PMID 26296162 Du, J.; Johnson, L.M.; Jacobsen, S.E.; Patel, D.J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 2015 16, 519–532.
19. PMID 28555658 Wu, X.; Zhang, Y. TET-mediated active DNA demethylation: Mechanism, function and beyond. Nat. Rev. Genet. 2017 18, 517–534.
20. /--/ Jeltsch, A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem. 2002 3, 275–293.
21. PMID 29203910 Verma, N.; Pan, H.; Doré, L.C.; Shukla, A.; Li, Q.V.; Pelham-Webb, B.; Teijeiro, V.; González, F.; Krivtsov, A.; Chang, C.J.; et al. TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells. Nat. Genet. 2018 50, 83–95.
22. PMID 27237052 Von Meyenn, F.; Iurlaro, M.; Habibi, E.; Liu, N.Q.; Salehzadeh-Yazdi, A.; Santos, F.; Petrini, E.; Milagre, I.; Yu, M.; Xie, Z.; et al. Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol. Cell 2016 62, 848–861.
23. PMID 28507606 Gahurova, L.; Tomizawa, S.I.; Smallwood, S.A.; Stewart-Morgan, K.R.; Saadeh, H.; Kim, J.; Andrews, S.R.; Chen, T.; Kelsey, G.; et al. Transcription and chromatin determinants of de novo DNA methylation timing in oocytes. Epigenetics Chromatin 2017 10, 25.
24. PMID 26021671 Bellacosa, A.; Drohat, A.C. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. DNA Repair (Amst) 2015 32, 33–42.
25. PMID 19376112 Illingworth, R.S.; Bird, A.P. CpG islands—‘A rough guide’. FEBS Lett. 2009 583, 1713–1720.
26. PMID 29459678 Rosic, S.; Amouroux, R.; Requena, C.E.; Gomes, A.; Emperle, M.; Beltran, T.; Rane, J.K.; Linnett, S.; Selkirk, M.E.; Schiffer, P.H.; et al. Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity. Nat. Genet. 2018 50, 452–459.
27. PMID 24905787 Shen, L.; Song, C.X.; He, C.; Zhang, Y. Mechanism and function of oxidative reversal of DNA and RNA methylation. Annu. Rev. Biochem. 2014 83, 585–614.
28. PMID 26152727 Fedeles, B.I.; Singh, V.; Delaney, J.C.; Li, D.; Essigmann, J.M. The AlkB Family of Fe(II)/α-ketoglutarate-dependent dioxygenases: Repairing nucleic acid alkylation damage and beyond. J. Biol. Chem. 2015 290, 20734–20742.
29. PMID 23248272 Wojciechowski, M.; Czapinska, H.; Bochtler, M. CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Proc. Natl. Acad. Sci. USA 2013 110, 105–110.
30. PMID 18600261 Meissner, A.; Mikkelsen, T.S.; Gu, H.; Wernig, M.; Hanna, J.; Sivachenko, A.; Zhang, X.; Bernstein, B.E.; Nusbaum, C.; Jaffe, D.B.; et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008 454, 766–770.
31. PMID 19325872 Zhang, Y.; Rohde, C.; Tierling, S.; Jurkowski, T.P.; Bock, C.; Santacruz, D.; Ragozin, S.; Reinhardt, R.; Groth, M.; Walter, J.; et al. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet. 2009 5, e1000438.
32. PMID 29531288 Charlton, J.; Downing, T.L.; Smith, Z.D.; Gu, H.; Clement, K.; Pop, R.; Akopian, V.; Klages, S.; Santos, D.P.; Tsankov, A.M.; et al. Global delay in nascent strand DNA methylation. Nat. Struct. Mol. Biol. 2018 25, 327–332.
33. PMID 24690455 Lokk, K.; Modhukur, V.; Rajashekar, B.; Märtens, K.; Mägi, R.; Kolde, R.; Koltšina, M.; Nilsson, T.K.; Vilo, J.; Salumets, A.; et al. DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biol. 2014 15, r54.
34. PMID 29649096 Pfeifer, G.P. Defining driver DNA methylation changes in human cancer. Int. J. Mol. Sci. 2018 19, 1166.
35. PMID 17334365 Weber, M.; Hellmann, I.; Stadler, M.B.; Ramos, L.; Pääbo, S.; Rebhan, M.; Schübeler, D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 2007 39, 457–466.
36. PMID 23925113 Ziller, M.J.; Gu, H.; Müller, F.; Donaghey, J.; Tsai, L.T.; Kohlbacher, O.; De Jager, P.L.; Rosen, E.D.; Bennett, D.A.; Bernstein, B.E.; et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 2013 500, 477–481.
37. PMID 27084945 Long, H.K.; King, H.W.; Patient, R.K.; Odom, D.T.; Klose, R.J. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res. 2016 44, 6693–6706.
38. PMID 22170606 Stadler, M.B.; Murr, R.; Burger, L.; Ivanek, R.; Lienert, F.; Schöler, A.; van Nimwegen, E.; Wirbelauer, C.; Oakeley, E.J.; Gaidatzis, D.; et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011 480, 490–495.
39. PMID 30139913 Onuchic, V.; Lurie, E.; Carrero, I.; Pawliczek, P.; Patel, R.Y.; Rozowsky, J.; Galeev, T.; Huang, Z.; Altshuler, R.C.; Zhang, Z.; et al. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science 2018 361. /--/
40. PMID 19958531 Zhang, Y.; Rohde, C.; Reinhardt, R.; Voelcker-Rehage, C.; Jeltsch, A. Non-imprinted allele-specific DNA methylation on human autosomes. Genome Biol. 2009 10, R138.
41. PMID 21514197 Xu, Y.; Wu, F.; Tan, L.; Kong, L.; Xiong, L.; Deng, J.; Barbera, A.J.; Zheng, L.; Zhang, H.; Huang, S.; et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol. Cell 2011 42, 451–464.
42. PMID 21552279 Pastor, W.A.; Pape, U.J.; Huang, Y.; Henderson, H.R.; Lister, R.; Ko, M.; McLoughlin, E.M.; Brudno, Y.; Mahapatra, S.; Kapranov, P.; et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011 473, 394–397.
43. PMID 29276034 Xu, C.; Liu, K.; Lei, M.; Yang, A.; Li, Y.; Hughes, T.R.; Min, J. DNA Sequence recognition of human CXXC domains and their structural determinants. Structure 2018 26, 85–95.
44. PMID 23697932 Long, H.K.; Blackledge, N.P.; Klose, R.J. ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection. Biochem. Soc. Trans. 2013 41, 727–740.
45. PMID 24553073 Tanaka, Y.; Umata, T.; Okamoto, K.; Obuse, C.; Tsuneoka, M. CxxC-ZF domain is needed for KDM2A to demethylate histone in rDNA promoter in response to starvation. Cell Struct. Funct. 2014 39, 79–92.
46. PMID 21339843 Hashimoto, H.; Vertino, P.M.; Cheng, X. Molecular coupling of DNA methylation and histone methylation. Epigenomics 2010 2, 657–669.
47. PMID 29556496 Melamed, P.; Yosefzon, Y.; David, C.; Tsukerman, A.; Pnueli, L. TET enzymes, variants, and differential effects on function. Front. Cell Dev. Biol. 2018 6, 22.
48. PMID 18511691 Chahrour, M.; Jung, S.Y.; Shaw, C.; Zhou, X.; Wong, S.T.; Qin, J.; Zoghbi, H.Y. MeCP2, a key contributor to neurological disease, activates and represses transcription. Science 2008 320, 1224–1229.
49. PMID 19369296 Ben-Shachar, S.; Chahrour, M.; Thaller, C.; Shaw, C.A.; Zoghbi, H.Y. Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus. Hum. Mol. Genet. 2009 18, 2431–2442.
50. PMID 25232122 Sugino, K.; Hempel, C.M.; Okaty, B.W.; Arnson, H.A.; Kato, S.; Dani, V.S.; Nelson, S.B. Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes. J. Neurosci. 2014 34, 12877–12883.
51. PMID 30102379 Rajavelu, A.; Lungu, C.; Emperle, M.; Dukatz, M.; Bröhm, A.; Broche, J.; Hanelt, I.; Parsa, E.; Schiffers, S.; Karnik, R.; et al. Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2. Nucleic Acids Res. 2018 46, 9044–9056.
52. PMID 29795194 Reizel, Y.; Sabag, O.; Skversky, Y.; Spiro, A.; Steinberg, B.; Bernstein, D.; Wang, A.; Kieckhaefer, J.; Li, C.; Pikarsky, E.; et al. Postnatal DNA demethylation and its role in tissue maturation. Nat. Commun. 2018 9, 2040.
53. PMID 28473536 Yin, Y.; Morgunova, E.; Jolma, A.; Kaasinen, E.; Sahu, B.; Khund-Sayeed, S.; Das, P.K.; Kivioja, T.; Dave, K.; Zhong, F.; et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 2017 356. /--/
54. PMID 28614722 Kribelbauer, J.F.; Laptenko, O.; Chen, S.; Martini, G.D.; Freed-Pastor, W.A.; Prives, C.; Mann, R.S.; Bussemaker, H.J. Quantitative analysis of the dna methylation sensitivity of transcription factor complexes. Cell Rep. 2017 19, 2383–2395.
55. PMID 26257180 Maurano, M.T.; Wang, H.; John, S.; Shafer, A.; Canfield, T.; Lee, K.; Stamatoyannopoulos, J.A. Role of DNA methylation in modulating transcription factor occupancy. Cell Rep. 2015 12, 1184–1195.
56. PMID 28529057 Hashimoto, H.; Wang, D.; Horton, J.R.; Zhang, X.; Corces, V.G.; Cheng, X. Structural basis for the versatile and methylation-dependent binding of CTCF to DNA. Mol. Cell 2017 66, 711–720.
57. PMID 24614011 Baubec, T.; Schubeler, D. Genomic patterns and context specific interpretation of DNA methylation. Curr. Opin. Genet. Dev. 2014 25, 85–92.
58. PMID 27826844 Shimbo, T.; Wade, P.A. Proteins that read DNA methylation. Adv. Exp. Med. Biol. 2016 945, 303–320.
59. PMID 26700815 Flavahan, W.A.; Drier, Y.; Liau, B.B.; Gillespie, S.M.; Venteicher, A.S.; Stemmer-Rachamimov, A.O.; Suvà, M.L.; Bernstein, B.E. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature 2016 529, 110–114.
60. PMID 29358650 Mayran, A.; Khetchoumian, K.; Hariri, F.; Pastinen, T.; Gauthier, Y.; Balsalobre, A.; Drouin, J. Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate. Nat. Genet. 2018 50, 259–269.
61. PMID 28553926 Wan, J.; Su, Y.; Song, Q.; Tung, B.; Oyinlade, O.; Liu, S.; Ying, M.; Ming, G.L.; Song, H.; Qian, J.; et al. Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration. Elife 2017 6. /--/
62. PMID 27153539 Charlet, J.; Duymich, C.E.; Lay, F.D.; Mundbjerg, K.; Dalsgaard Sørensen, K.; Liang, G.; Jones, P.A. Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol. Cell 2016 62, 422–431.
63. PMID 27476967 Rinaldi, L.; Datta, D.; Serrat, J.; Morey, L.; Solanas, G.; Avgustinova, A.; Blanco, E.; Pons, J.I.; Matallanas, D.; Von Kriegsheim, A.; et al. Dnmt3a and Dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis. Cell Stem Cell 2016 19, 491–501.
64. PMID 26317465 Roulois, D.; Loo Yau, H.; Singhania, R.; Wang, Y.; Danesh, A.; Shen, S.Y.; Han, H.; Liang, G.; Jones, P.A.; Pugh, T.J.; et al. DNA-demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts. Cell 2015 162, 961–973.
65. PMID 28604729 Brocks, D.; Schmidt, C.R.; Daskalakis, M.; Jang, H.S.; Shah, N.M.; Li, D.; Li, J.; Zhang, B.; Hou, Y.; Laudato, S.; et al. DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat. Genet. 2017 49, 1052–1060.
66. PMID 22044633 Su, J.; Shao, X.; Liu, H.; Liu, S.; Wu, Q.; Zhang, Y. Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics 2012 99, 10–17.
67. PMID 29234025 Jurkowska, R.Z.; Qin, S.; Kungulovski, G.; Tempel, W.; Liu, Y.; Bashtrykov, P.; Stiefelmaier, J.; Jurkowski, T.P.; Kudithipudi, S.; Weirich, S.; et al. H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nat. Commun. 2017 8, 2057.
68. PMID 24294107 Lupo, A.; Cesaro, E.; Montano, G.; Zurlo, D.; Izzo, P.; Costanzo, P. KRAB-Zinc finger proteins: A repressor family displaying multiple biological functions. Curr. Genomics 2013 14, 268–278.
69. PMID 25543143 Fasching, L.; Kapopoulou, A.; Sachdeva, R.; Petri, R.; Jönsson, M.E.; Männe, C.; Turelli, P.; Jern, P.; Cammas, F.; Trono, D.; et al. TRIM28 represses transcription of endogenous retroviruses in neural progenitor cells. Cell Rep. 2015 10, 20–28.
70. PMID 16963560 Egger, G.; Jeong, S.; Escobar, S.G.; Cortez, C.C.; Li, T.W.; Saito, Y.; Yoo, C.B.; Jones, P.A.; Liang, G. Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc. Natl. Acad. Sci. USA 2006 103, 14080–14085.
71. PMID 21427766 Siomi, M.C.; Sato, K.; Pezic, D.; Aravin, A.A. PIWI-interacting small RNAs: The vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 2011 12, 246–258.
72. PMID 23664764 Xie, W.; Schultz, M.D.; Lister, R.; Hou, Z.; Rajagopal, N.; Ray, P.; Whitaker, J.W.; Tian, S.; Hawkins, R.D.; Leung, D.; et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 2013 153, 1134–1148.
73. PMID 24270360 Jeong, M.; Sun, D.; Luo, M.; Huang, Y.; Challen, G.A.; Rodriguez, B.; Zhang, X.; Chavez, L.; Wang, H.; Hannah, R.; et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat. Genet. 2014 46, 17–23.
74. PMID 20223770 Zhang, Y.; Jurkowska, R.; Soeroes, S.; Rajavelu, A.; Dhayalan, A.; Bock, I.; Rathert, P.; Brandt, O.; Reinhardt, R.; Fischle, W.; et al. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res. 2010 38, 4246–4253.
75. PMID 26073541 Noh, K.M.; Wang, H.; Kim, H.R.; Wenderski, W.; Fang, F.; Li, C.H.; Dewell, S.; Hughes, S.H.; Melnick, A.M.; Patel, D.J.; et al. Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape and phenotypic features of mouse ESCs. Mol. Cell 2015 59, 89–103.
76. PMID 27179026 Petell, C.J.; Alabdi, L.; He, M.; San Miguel, P.; Rose, R.; Gowher, H. An epigenetic switch regulates de novo DNA methylation at a subset of pluripotency gene enhancers during embryonic stem cell differentiation. Nucleic Acids Res. 2016 44, 7605–7617.
77. PMID 22266761 Wagner, E.J.; Carpenter, P.B. Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell Biol. 2012 13, 115–126.
78. PMID 28386724 McDaniel, S.L.; Strahl, B.D. Shaping the cellular landscape with Set2/SETD2 methylation. Cell. Mol. Life Sci. 2017 74, 3317–3334.
79. PMID 19329998 Ball, M.P.; Li, J.B.; Gao, Y.; Lee, J.H.; LeProust, E.M.; Park, I.H.; Xie, B.; Daley, G.Q.; Church, G.M. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 2009 27, 361–368.
80. PMID 25607372 Baubec, T.; Colombo, D.F.; Wirbelauer, C.; Schmidt, J.; Burger, L.; Krebs, A.R.; Akalin, A.; Schübeler, D. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 2015 520, 243–247.
81. PMID 28225755 Neri, F.; Rapelli, S.; Krepelova, A.; Incarnato, D.; Parlato, C.; Basile, G.; Maldotti, M.; Anselmi, F.; Oliviero, S. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017 543, 72–77.
82. PMID 20613842 Maunakea, A.K.; Nagarajan, R.P.; Bilenky, M.; Ballinger, T.J.; D’Souza, C.; Fouse, S.D.; Johnson, B.E.; Hong, C.; Nielsen, C.; Zhao, Y.; et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010 466, 253–257.
83. PMID 26065575 Qin, W.; Wolf, P.; Liu, N.; Link, S.; Smets, M.; La Mastra, F.; Forné, I.; Pichler, G.; Hörl, D.; Fellinger, K.; et al. DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination. Cell Res. 2015 25, 911–929.
84. PMID 25263941 Yang, X.; Han, H.; De Carvalho, D.D.; Lay, F.D.; Jones, P.A.; Liang, G. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 2014 26, 577–590.
85. PMID 30097071 Su, J.; Huang, Y.H.; Cui, X.; Wang, X.; Zhang, X.; Lei, Y.; Xu, J.; Lin, X.; Chen, K.; Lv, J.; et al. Homeobox oncogene activation by pan-cancer DNA hypermethylation. Genome Biol. 2018 19, 108.
86. PMID 16357870 Vire, E.; Brenner, C.; Deplus, R.; Blanchon, L.; Fraga, M.; Didelot, C.; Morey, L.; Van Eynde, A.; Bernard, D.; Vanderwinden, J.M. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006 439, 871–874.
87. PMID 17200673 Widschwendter, M.; Fiegl, H.; Egle, D.; Mueller-Holzner, E.; Spizzo, G.; Marth, C.; Weisenberger, D.J.; Campan, M.; Young, J.; Jacobs, I.; et al. Epigenetic stem cell signature in cancer. Nat. Genet. 2007 39, 157–158.
88. PMID 17200670 Schlesinger, Y.; Straussman, R.; Keshet, I.; Farkash, S.; Hecht, M.; Zimmerman, J.; Eden, E.; Yakhini, Z.; Ben-Shushan, E.; Reubinoff, B.E.; et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 2007 39, 232–236.
89. PMID 22466170 Brinkman, A.B.; Gu, H.; Bartels, S.J.; Zhang, Y.; Matarese, F.; Simmer, F.; Marks, H.; Bock, C.; Gnirke, A.; Meissner, A.; et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012 22, 1128–1138.
90. PMID 26004255 Galupa, R.; Heard, E. X-chromosome inactivation: New insights into cis and trans regulation. Curr. Opin. Genet. Dev. 2015 31, 57–66.
91. PMID 29058709 Wang, X.; Paucek, R.D.; Gooding, A.R.; Brown, Z.Z.; Ge, E.J.; Muir, T.W.; Cech, T.R. Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA. Nat. Struct. Mol. Biol. 2017 24, 1028–1038.
92. PMID 28483375 Holoch, D.; Margueron, R. Mechanisms Regulating PRC2 Recruitment and Enzymatic Activity. Trends Biochem. Sci. 2017 42, 531–542.
93. PMID 29422066 Li, Y.; Zheng, H.; Wang, Q.; Zhou, C.; Wei, L.; Liu, X.; Zhang, W.; Zhang, Y.; Du, Z.; Wang, X.; et al. Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys. Genome Biol. 2018 19, 18.
94. PMID 11713521 Tamaru, H.; Selker, E.U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 2001 414, 277–283.
95. PMID 22761581 Arand, J.; Spieler, D.; Karius, T.; Branco, M.R.; Meilinger, D.; Meissner, A.; Jenuwein, T.; Xu, G.; Leonhardt, H.; Wolf, V.; et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 2012 8, e1002750.
96. /--/ Lehnertz, B.; Ueda, Y.; Derijck, A.A.; Braunschweig, U.; Perez-Burgos, L.; Kubicek, S.; Chen, T.; Li, E.; Jenuwein, T.; Peters, A.H. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 2003 13, 1192–1200.
97. PMID 23022729 Rothbart, S.B.; Krajewski, K.; Nady, N.; Tempel, W.; Xue, S.; Badeaux, A.I.; Barsyte-Lovejoy, D.; Martinez, J.Y.; Bedford, M.T.; Fuchs, S.M.; et al. Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nat. Struct. Mol. Biol. 2012 19, 1155–1160.
98. PMID 17994007 Sharif, J.; Muto, M.; Takebayashi, S.; Suetake, I.; Iwamatsu, A.; Endo, T.A.; Shinga, J.; Mizutani-Koseki, Y.; Toyoda, T.; Okamura, K.; et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 2007 450, 908–912.
99. PMID 17673620 Bostick, M.; Kim, J.K.; Estève, P.O.; Clark, A.; Pradhan, S.; Jacobsen, S.E. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007 317, 1760–1764.
100. PMID 24253042 Berkyurek, A.C.; Suetake, I.; Arita, K.; Takeshita, K.; Nakagawa, A.; Shirakawa, M.; Tajima, S. The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA. J. Biol. Chem. 2014 289, 379–386.
101. PMID 24532244 Bashtrykov, P.; Rajavelu, A.; Hackner, B.; Ragozin, S.; Carell, T.; Jeltsch, A. Targeted mutagenesis results in an activation of DNA methyltransferase 1 and confirms an autoinhibitory role of its RFTS domain. Chembiochem. 2014 15, 743–748.
102. PMID 22100450 Xie, S.; Jakoncic, J.; Qian, C. UHRF1 double Tudor domain and the adjacent PHD finger act together to recognize K9me3-containing histone H3 tail. J. Mol. Biol. 2012 415, 318–328.
103. PMID 23752590 Rothbart, S.B.; Dickson, B.M.; Ong, M.S.; Krajewski, K.; Houliston, S.; Kireev, D.B.; Arrowsmith, C.H.; Strahl, B.D. Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes Dev. 2013 27, 1288–1298.
104. PMID 21489993 Nady, N.; Lemak, A.; Walker, J.R.; Avvakumov, G.V.; Kareta, M.S.; Achour, M.; Xue, S.; Duan, S.; Allali-Hassani, A.; Zuo, X.; et al. Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J. Biol. Chem. 2011 286, 24300–24311.
105. PMID 27554592 Zhao, Q.; Zhang, J.; Chen, R.; Wang, L.; Li, B.; Cheng, H.; Duan, X.; Zhu, H.; Wei, W.; Li, J.; et al. Dissecting the precise role of H3K9 methylation in crosstalk with DNA maintenance methylation in mammals. Nat. Commun. 2016 7, 12464.
106. PMID 29262320 Veland, N.; Hardikar, S.; Zhong, Y.; Gayatri, S.; Dan, J.; Strahl, B.D.; Rothbart, S.B.; Bedford, M.T.; Chen, T. The arginine methyltransferase PRMT6 regulates DNA methylation and contributes to global DNA hypomethylation in cancer. Cell Rep. 2017 21, 3390–3397.
107. PMID 23345616 Jorgensen, S.; Schotta, G.; Sorensen, C.S. Histone H4 lysine 20 methylation: Key player in epigenetic regulation of genomic integrity. Nucleic Acids Res. 2013 41, 2797–2806.
108. PMID 16395332 Zhu, H.; Geiman, T.M.; Xi, S.; Jiang, Q.; Schmidtmann, A.; Chen, T.; Li, E.; Muegge, K. Lsh is involved in de novo methylation of DNA. EMBO J. 2006 25, 335–345.
109. PMID 25170028 Yu, W.; McIntosh, C.; Lister, R.; Zhu, I.; Han, Y.; Ren, J.; Landsman, D.; Lee, E.; Briones, V.; Terashima, M.; et al. Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Res. 2014 24, 1613–1623.
110. PMID 25823553 Lungu, C.; Muegge, K.; Jeltsch, A.; Jurkowska, R.Z. An ATPase-deficient variant of the SNF2 family member HELLS shows altered dynamics at pericentromeric heterochromatin. J. Mol. Biol. 2015 427, 1903–1915.
111. PMID 25578963 Ren, J.; Briones, V.; Barbour, S.; Yu, W.; Han, Y.; Terashima, M.; Muegge, K. The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences. Nucleic Acids Res. 2015 43, 1444–1455.
112. PMID 22323818 Song, J.; Teplova, M.; Ishibe-Murakami, S.; Patel, D.J. Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 2012 335, 709–712.
113. PMID 29414941 Zhang, Z.M.; Lu, R.; Wang, P.; Yu, Y.; Chen, D.; Gao, L.; Liu, S.; Ji, D.; Rothbart, S.B.; Wang, Y.; et al. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 2018 554, 387–391.
114. PMID 14578347 Okuwaki, M.; Verreault, A. Maintenance DNA methylation of nucleosome core particles. J. Biol. Chem. 2004 279, 2904–2912.
115. PMID 16026162 Gowher, H.; Stockdale, C.J.; Goyal, R.; Ferreira, H.; Owen-Hughes, T.; Jeltsch, A. De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases. Biochemistry 2005 44, 9899–9904.
116. PMID 16567415 Takeshima, H.; Suetake, I.; Shimahara, H.; Ura, K.; Tate, S.; Tajima, S. Distinct DNA methylation activity of Dnmt3a and Dnmt3b towards naked and nucleosomal DNA. J. Biochem. 2006 139, 503–515.
117. PMID 21622955 Felle, M.; Hoffmeister, H.; Rothammer, J.; Fuchs, A.; Exler, J.H.; Längst, G. Nucleosomes protect DNA from DNA methylation in vivo and in vitro. Nucleic Acids Res. 2011 39, 6956–6969.
118. PMID 26496704 Schrader, A.; et al. Characterization of Dnmt1 binding and DNA methylation on nucleosomes and nucleosomal arrays. PLoS ONE 2015 10, e0140076.
119. PMID 10647011 Xu, G.L.; Bestor, T.H.; Bourc’his, D.; Hsieh, C.L.; Tommerup, N.; Bugge, M.; Hulten, M.; Qu, X.; Russo, J.J.; Viegas-Péquignot, E. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 1999 402, 187–191.
120. /--/ Okano, M.; Bell, D.W.; Haber, D.A.; Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999 99, 247–257.
121. PMID 21596365 De Greef, J.C.; Wang, J.; Balog, J.; den Dunnen, J.T.; Frants, R.R.; Straasheijm, K.R.; Aytekin, C.; van der Burg, M.; Duprez, L.; Ferster, A.; et al. Mutations in ZBTB24 are associated with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2. Am. J. Hum. Genet. 2011 88, 796–804.
122. PMID 26216346 Thijssen, P.E.; Ito, Y.; Grillo, G.; Wang, J.; Velasco, G.; Nitta, H.; Unoki, M.; Yoshihara, M.; Suyama, M.; Sun, Y.; et al. Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome. Nat. Commun. 2015 6, 7870.
123. PMID 27027282 Wu, T.P.; Wang, T.; Seetin, M.G.; Lai, Y.; Zhu, S.; Lin, K.; Liu, Y.; Byrum, S.D.; Mackintosh, S.G.; Zhong, M.; et al. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature 2016 532, 329–333.
124. PMID 29339483 Jenness, C.; Giunta, S.; Müller, M.M.; Kimura, H.; Muir, T.W.; Funabiki, H. HELLS and CDCA7 comprise a bipartite nucleosome remodeling complex defective in ICF syndrome. Proc. Natl. Acad. Sci. USA 2018 115, E876–E885.
125. PMID 22641038 Bashtrykov, P.; Ragozin, S.; Jeltsch, A. Mechanistic details of the DNA recognition by the Dnmt1 DNA methyltransferase. FEBS Lett. 2012 586, 1821–1823.
126. PMID 26077819 He, Y.; Ecker, J.R. Non-CG methylation in the human genome. Annu. Rev. Genomics Hum. Genet. 2015 16, 55–77.
127. PMID 28900200 Lee, J.H.; Park, S.J.; Nakai, K. Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s. Sci. Rep. 2017 7, 11295.
128. PMID 25739960 Kinde, B.; Gabel, H.W.; Gilbert, C.S.; Griffith, E.C.; Greenberg, M.E. Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2. Proc. Natl. Acad. Sci. USA 2015 112, 6800–6806.
129. PMID 27965390 Kinde, B.; Wu, D.Y.; Greenberg, M.E.; Gabel, H.W. DNA methylation in the gene body influences MeCP2-mediated gene repression. Proc. Natl. Acad. Sci. USA 2016 113, 15114–15119.
130. PMID 25960197 Cheng, J.; Yang, H.; Fang, J.; Ma, L.; Gong, R.; Wang, P.; Li, Z.; Xu, Y. Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation. Nat. Commun. 2015 6, 7023.
131. PMID 28320934 Keown, C.L.; Berletch, J.B.; Castanon, R.; Nery, J.R.; Disteche, C.M.; Ecker, J.R.; Mukamel, E.A. Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. Proc. Natl. Acad. Sci. USA 2017 114, E2882–E2890.
132. PMID 27826841 O’Brown, Z.K.; Greer, E.L. N6-Methyladenine: A conserved and dynamic DNA mark. Adv. Exp. Med. Biol. 2016 945, 213–246.
133. PMID 25936839 Greer, E.L.; Blanco, M.A.; Gu, L.; Sendinc, E.; Liu, J.; Aristizábal-Corrales, D.; Hsu, C.H.; Aravind, L.; He, C.; Shi, Y. DNA methylation on N6-Adenine in C. elegans. Cell 2015 161, 868–878.
134. PMID 25936838 Zhang, G.; Huang, H.; Liu, D.; Cheng, Y.; Liu, X.; Zhang, W.; Yin, R.; Zhang, D.; Zhang, P.; Liu, J.; et al. N6-methyladenine DNA modification in Drosophila. Cell 2015 161, 893–906.
135. PMID 26689968 Koziol, M.J.; Bradshaw, C.R.; Allen, G.E.; Costa, A.S.H.; Frezza, C.; Gurdon, J.B. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat. Struct. Mol. Biol. 2016 23, 24–30.
136. PMID 30017583 Xiao, C.L.; Zhu, S.; He, M.; Chen, D.; Zhang, Q.; Chen, Y.; Yu, G.; Liu, J.; Xie, S.Q.; Luo, F.; et al. N6-methyladenine DNA modification in the human genome. Mol. Cell 2018 71, 306–318.
137. PMID 28371147 Schiffers, S.; Ebert, C.; Rahimoff, R.; Kosmatchev, O.; Steinbacher, J.; Bohne, A.V.; Spada, F.; Michalakis, S.; Nickelsen, J.; Müller, M.; et al. Quantitative LC-MS provides no evidence for m6 dA or m4 dC in the genome of mouse embryonic stem cells and tissues. Angew. Chem. Int. Ed. Engl. 2017 56, 11268–11271.
138. PMID 25891224 Van der Wijst, M.G.; Rots, M.G. Mitochondrial epigenetics: An overlooked layer of regulation? Trends Genet. 2015 31, 353–356.
139. PMID 28484249 Saini, S.K.; Mangalhara, K.C.; Prakasam, G.; Bamezai, R.N.K. DNA Methyltransferase1 (DNMT1) Isoform3 methylates mitochondrial genome and modulates its biology. Sci. Rep. 2017 7, 1525.
140. PMID 28282966 Van der Wijst, M.G.; van Tilburg, A.Y.; Ruiters, M.H.; Rots, M.G. Experimental mitochondria-targeted DNA methylation identifies GpC methylation, not CpG methylation, as potential regulator of mitochondrial gene expression. Sci. Rep. 2017 7, 177.
141. PMID 26996456 Liu, B.; Du, Q.; Chen, L.; Fu, G.; Li, S.; Fu, L.; Zhang, X.; Ma, C.; Bin, C. CpG methylation patterns of human mitochondrial DNA. Sci. Rep. 2016 6, 23421.
142. PMID 29163634 Mechta, M.; Ingerslev, L.R.; Fabre, O.; Picard, M.; Barrès, R. Evidence suggesting absence of mitochondrial DNA methylation. Front. Genet. 2017 8, 166.
143. PMID 26732754 Kungulovski, G.; Jeltsch, A. Epigenome editing: State of the art, concepts, and perspectives. Trends Genet. 2016 32, 101–113.
144. PMID 29524127 Rots, M.G.; Jeltsch, A. Editing the epigenome: Overview, open questions, and directions of future development. Methods Mol. Biol. 2018 1767, 3–18.
Abgerufen von „https://de.wikipedia.org/w/index.php?title=Benutzer:Dirk123456/Baustellenbaustelle_001/Baustelle-2/Baustelle-2.8&oldid=183670631“