Active demethylation in mouse zygotes involves cytosine deamination and base excision repair

Epigenetics & Chromatin

Wendy Dean²  Wolf Reik³  Cristina Rada¹  Heather Burgess³  Julian Peat²  Fátima Santos² 

[1] Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK;Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK;Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK

关键词: TET3;    UNG2;    BER;    AID;    Hydroxymethylation;    DNA methylation;    Epigenetic reprogramming;   

Others  :  805071
DOI  :  10.1186/1756-8935-6-39

 received in 2013-08-22, accepted in 2013-10-30,  发布年份 2013

【 摘 要 】

Background

DNA methylation in mammals is an epigenetic mark necessary for normal embryogenesis. During development active loss of methylation occurs in the male pronucleus during the first cell cycle after fertilisation. This is accompanied by major chromatin remodelling and generates a marked asymmetry between the paternal and maternal genomes. The mechanism(s) by which this is achieved implicate, among others, base excision repair (BER) components and more recently a major role for TET3 hydroxylase. To investigate these methylation dynamics further we have analysed DNA methylation and hydroxymethylation in fertilised mouse oocytes by indirect immunofluorescence (IF) and evaluated the relative contribution of different candidate factors for active demethylation in knock-out zygotes by three-dimensional imaging and IF semi-quantification.

Results

We find two distinct phases of loss of paternal methylation in the zygote, one prior to and another coincident with, but not dependent on, DNA replication. TET3-mediated hydroxymethylation is limited to the replication associated second phase of demethylation. Analysis of cytosine deaminase (AID) null fertilised oocytes revealed a role for this enzyme in the second phase of loss of paternal methylation, which is independent from hydroxymethylation. Investigation into the possible repair pathways involved supports a role for AID-mediated cytosine deamination with subsequent U-G mismatch long-patch BER by UNG2 while no evidence could be found for an involvement of TDG.

Conclusions

There are two observable phases of DNA demethylation in the mouse zygote, before and coincident with DNA replication. TET3 is only involved in the second phase of loss of methylation. Cytosine deamination and long-patch BER mediated by UNG2 appear to independently contribute to this second phase of active demethylation. Further work will be necessary to elucidate the mechanism(s) involved in the first phase of active demethylation that will potentially involve activities required for early sperm chromatin remodelling.

【 授权许可】

   
2013 Santos et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Mayer W, Niveleau A, Walter J, Fundele R, Haaf T: Demethylation of the zygotic paternal genome. Nature 2000, 403:501-502.
• [2]Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, Dean W, Reik W, Walter J: Active demethylation of the paternal genome in the mouse zygote. Curr Biol 2000, 10:475-478.
• [3]Santos F, Hendrich B, Reik W, Dean W: Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol 2002, 241:172-182.
• [4]Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M, Arand J, Nakano T, Reik W, Walter J: 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat Commun 2011, 2:241.
• [5]McLay DW, Clarke HJ: Remodelling the paternal chromatin at fertilization in mammals. Reproduction 2003, 125:625-633.
• [6]van der Heijden GW, Dieker JW, Derijck AA, Muller S, Berden JH, Braat DD, van der Vlag J, de Boer P: Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech Dev 2005, 122:1008-1022.
• [7]Adenot PG, Mercier Y, Renard JP, Thompson EM: Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos. Development 1997, 124:4615-4625.
• [8]Salvaing J, Aguirre-Lavin T, Boulesteix C, Lehmann G, Debey P, Beaujean N: 5-Methylcytosine and 5-hydroxymethylcytosine spatiotemporal profiles in the mouse zygote. PloS one 2012, 7:e38156.
• [9]Santos F, Peters AH, Otte AP, Reik W, Dean W: Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev Biol 2005, 280:225-236.
• [10]Franchini DM, Schmitz KM, Petersen-Mahrt SK: 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu Rev Genet 2012, 46:419-441.
• [11]Gehring M, Reik W, Henikoff S: DNA demethylation by DNA repair. Trends Genet 2009, 25:82-90.
• [12]Ooi SK, Bestor TH: The colorful history of active DNA demethylation. Cell 2008, 133:1145-1148.
• [13]Wu SC, Zhang Y: Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 2010, 11:607-620.
• [14]Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M: A mammalian protein with specific demethylase activity for mCpG DNA. Nature 1999, 397:579-583.
• [15]Zhu JK: Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 2009, 43:143-166.
• [16]Santos F, Dean W: Epigenetic reprogramming during early development in mammals. Reproduction 2004, 127:643-651.
• [17]Wiebauer K, Jiricny J: Mismatch-specific thymine DNA glycosylase and DNA polymerase beta mediate the correction of G.T mispairs in nuclear extracts from human cells. Proc Natl Acad Sci U S A 1990, 87:5842-5845.
• [18]Conticello SG: The AID/APOBEC family of nucleic acid mutators. Genome Biol 2008, 9:229.
• [19]Isobe T, Song SN, Tiwari P, Ito H, Yamaguchi Y, Yoshizaki K: Activation-induced cytidine deaminase auto-activates and triggers aberrant gene expression. FEBS Lett 2013, 587:2487-2492.
• [20]Kumar R, DiMenna L, Schrode N, Liu TC, Franck P, Munoz-Descalzo S, Hadjantonakis AK, Zarrin AA, Chaudhuri J, Elemento O, Evans T: AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes. Nature 2013, 500:89-92.
• [21]Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W: Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 2010, 463:1101-1105.
• [22]Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR: DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 2008, 135:1201-1212.
• [23]Barreto G, Schafer A, Marhold J, Stach D, Swaminathan SK, Handa V, Doderlein G, Maltry N, Wu W, Lyko F, Niehrs C: Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 2007, 445:671-675.
• [24]Niehrs C, Schafer A: Active DNA demethylation by Gadd45 and DNA repair. Trends Cell Biol 2012, 22:220-227.
• [25]Di Noia JM, Neuberger MS: Immunoglobulin gene conversion in chicken DT40 cells largely proceeds through an abasic site intermediate generated by excision of the uracil produced by AID-mediated deoxycytidine deamination. Eur J Immunol 2004, 34:504-508.
• [26]Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T: Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 2000, 102:553-563.
• [27]Petersen-Mahrt S: DNA deamination in immunity. Immunol Rev 2005, 203:80-97.
• [28]Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK: Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem 2004, 279:52353-52360.
• [29]Bestor TH: The DNA methyltransferases of mammals. Hum Mol Genet 2000, 9:2395-2402.
• [30]Kangaspeska S, Stride B, Metivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, Benes V, Gannon F, Reid G: Transient cyclical methylation of promoter DNA. Nature 2008, 452:112-115.
• [31]Li YQ, Zhou PZ, Zheng XD, Walsh CP, Xu GL: Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair. Nucleic Acids Res 2007, 35:390-400.
• [32]Metivier R, Gallais R, Tiffoche C, Le Peron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G: Cyclical DNA methylation of a transcriptionally active promoter. Nature 2008, 452:45-50.
• [33]Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, Iqbal K, Shi YG, Deng Z, Szabo PE, Pfeifer GP, Li J, Xu GL: The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 2011, 477:606-610.
• [34]Wu H, Zhang Y: Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells. Cell Cycle 2011, 10:2428-2436.
• [35]Dean W, Santos F, Stojkovic M, Zakhartchenko V, Walter J, Wolf E, Reik W: Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc Natl Acad Sci USA 2001, 98:13734-13738.
• [36]Inoue A, Zhang Y: Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 2011, 334:194.
• [37]Iqbal K, Jin SG, Pfeifer GP, Szabo PE: Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci USA 2011, 108:3642-3647.
• [38]Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, Sato S, Nakabayashi K, Hata K, Sotomaru Y, Suzuki Y, Kono T: Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet 2012, 8:e1002440.
• [39]Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A: A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 2012, 484:339-344.
• [40]Hajkova P, Jeffries SJ, Lee C, Miller N, Jackson SP, Surani MA: Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 2010, 329:78-82.
• [41]Wossidlo M, Arand J, Sebastiano V, Lepikhov K, Boiani M, Reinhardt R, Scholer H, Walter J: Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes. EMBO J 2010, 29:1877-1888.
• [42]Teperek-Tkacz M, Pasque V, Gentsch G, Ferguson-Smith AC: Epigenetic reprogramming: is deamination key to active DNA demethylation? Reproduction 2011, 142:621-632.
• [43]Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM: Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 2010, 463:1042-1047.
• [44]Schrader CE, Guikema JE, Linehan EK, Selsing E, Stavnezer J: Activation-induced cytidine deaminase-dependent DNA breaks in class switch recombination occur during G1 phase of the cell cycle and depend upon mismatch repair. J Immunol 2007, 179:6064-6071.
• [45]Storck S, Aoufouchi S, Weill JC, Reynaud CA: AID and partners: for better and (not) for worse. Curr Opin Immunol 2011, 23:337-344.
• [46]Clarke HJ: Post-transcriptional control of gene expression during mouse oogenesis. Results Probl Cell Differ 2012, 55:1-21.
• [47]Parsa JY, Ramachandran S, Zaheen A, Nepal RM, Kapelnikov A, Belcheva A, Berru M, Ronai D, Martin A: Negative supercoiling creates single-stranded patches of DNA that are substrates for AID-mediated mutagenesis. PLoS Genet 2012, 8:e1002518.
• [48]Boissonneault G: Chromatin remodeling during spermiogenesis: a possible role for the transition proteins in DNA strand break repair. FEBS Lett 2002, 514:111-114.
• [49]Chahwan R, Wontakal SN, Roa S: Crosstalk between genetic and epigenetic information through cytosine deamination. Trends Genet 2010, 26:443-448.
• [50]Krokan HE, Bjoras M: Base excision repair. Cold Springs Harb Perspect Biol 2013, 5:a012583.
• [51]Rada C, Williams GT, Nilsen H, Barnes DE, Lindahl T, Neuberger MS: Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice. Curr Biol 2002, 12:1748-1755.
• [52]Barnes DE, Lindahl T: Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu Rev Genet 2004, 38:445-476.
• [53]Robertson AB, Klungland A, Rognes T, Leiros I: DNA repair in mammalian cells: Base excision repair: the long and short of it. Cell Mol Life Sci 2009, 66:981-993.
• [54]Cortazar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schar P: Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Nature 2011, 470:419-423.
• [55]Nilsen H, Rosewell I, Robins P, Skjelbred CF, Andersen S, Slupphaug G, Daly G, Krokan HE, Lindahl T, Barnes DE: Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication. Mol Cell 2000, 5:1059-1065.
• [56]Chen CC, Wang KY, Shen CK: DNA 5-methylcytosine demethylation activities of the mammalian DNA methyltransferases. J Biol Chem 2013, 288:9084-9091.
• [57]Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D, Paul YL, Walter J, Cook SJ, Andrews S, Branco MR, Reik W: FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 2013, 13:351-359.
• [58]Kaneda M, Hirasawa R, Chiba H, Okano M, Li E, Sasaki H: Genetic evidence for Dnmt3a-dependent imprinting during oocyte growth obtained by conditional knockout with Zp3-Cre and complete exclusion of Dnmt3b by chimera formation. Genes Cells 2010. [Epub ahead of print]
• [59]Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H: Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 2013, 9:e1003439.
• [60]Wood RD, Mitchell M, Sgouros J, Lindahl T: Human DNA repair genes. Science 2001, 291:1284-1289.
• [61]Derijck A, van der Heijden G, Giele M, Philippens M, de Boer P: DNA double-strand break repair in parental chromatin of mouse zygotes, the first cell cycle as an origin of de novo mutation. Hum Mol Genet 2008, 17:1922-1937.
• [62]Kaneda M, Okano M, Hata K, Sado T, Tsujimoto N, Li E, Sasaki H: Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 2004, 429:900-903.
• [63]Lewandoski M, Wassarman KM, Martin GR: Zp3-cre, a transgenic mouse line for the activation or inactivation of loxP-flanked target genes specifically in the female germ line. Curr Biol 1997, 7:148-151.
• [64]Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A: Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
• [65]Probst AV, Santos F, Reik W, Almouzni G, Dean W: Structural differences in centromeric heterochromatin are spatially reconciled on fertilisation in the mouse zygote. Chromosoma 2007, 116:403-415.
• [66]Patenaude AM, Di Noia JM: The mechanisms regulating the subcellular localization of AID. Nucleus 2010, 1:325-331.