Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin

Epigenetics

Volumn 8, Issue 9, 2013, Pages 899-906

  Hirose, Kentaro ^a   Shimoda, Nobuyoshi ^b   Kikuchi, Yutaka ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

^b NATIONAL CENTER FOR GERIATRICS AND GERONTOLOGY   (Japan)

Author keywords

5 hydroxymethylcytosine; 5 methylcytosine; Active DNA demethylation; Fin regeneration; Zebrafish

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; ACTIVATION INDUCED CYTIDINE DEAMINASE; GROWTH ARREST AND DNA DAMAGE INDUCIBLE PROTEIN 45; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1; THYMINE DNA GLYCOSYLASE;

AMPUTATION; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL DEDIFFERENTIATION; CELL PROLIFERATION; CONTROLLED STUDY; DEMETHYLATION; DNA DEMETHYLATION; DNA REPAIR; DOT HYBRIDIZATION; EMBRYO; FIN (ORGAN); GEL ELECTROPHORESIS; GENE EXPRESSION; IMMUNOHISTOCHEMISTRY; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; REGENERATION; WESTERN BLOTTING; ZEBRA FISH;

AMPHIBIA; DANIO RERIO;

5-HYDROXYMETHYLCYTOSINE; 5-METHYLCYTOSINE; ACTIVE DNA DEMETHYLATION; FIN REGENERATION; ZEBRAFISH;

5-METHYLCYTOSINE; ANIMAL FINS; ANIMALS; ANIMALS, GENETICALLY MODIFIED; CELL DEDIFFERENTIATION; CYTOSINE; DNA METHYLATION; DNA REPAIR; EMBRYO, NONMAMMALIAN; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, DEVELOPMENTAL; REGENERATION; ZEBRAFISH;

EID: 84883527566     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.25653     Document Type: Article

References (29)

1. Wu SC, Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 2010; 11:607-20; PMID:20683471; http://dx.doi. org/10.1038/nrm2950
2. Cedar H, Bergman Y. Programming of DNA methylation patterns. Annu Rev Biochem 2012; 81:97-117; PMID:22404632; http://dx.doi.org/10.1146/annurevbiochem-052610-091920
3. Franchini DM, Schmitz KM, Petersen-Mahrt SK. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu Rev Genet 2012; 46:419-41; PMID:22974304; http://dx.doi.org/10.1146/annurevgenet-110711-155451
4. Goll MG, Bestor TH. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 2005; 74:481-514; PMID:15952895; http://dx.doi.org/10.1146/annurev. biochem.74.010904.153721
5. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13:484-92; PMID:22641018; http://dx.doi. org/10.1038/nrg3230
6. Zhu JK. Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 2009; 43:143-66; PMID:19659441; http://dx.doi.org/10.1146/annurevgenet-102108-134205
7. Niehrs C, Schäfer A. Active DNA demethylation by Gadd45 and DNA repair. Trends Cell Biol 2012; 22:220-7; PMID:22341196; http://dx.doi. org/10.1016/j.tcb.2012.01.002
8. Branco MR, Ficz G, Reik W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 2012; 13:7-13; PMID:22083101
9. Williams K, Christensen J, Helin K. DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep 2011; 13:28-35; PMID:22157888; http://dx.doi. org/10.1038/embor.2011.233
10. Tan L, Shi YG. Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development 2012; 139:1895-902; PMID:22569552; http://dx.doi. org/10.1242/dev.070771
11. Akimenko MA, Marí-Beffa M, Becerra J, Géraudie J. Old questions, new tools, and some answers to the mystery of fin regeneration. Dev Dyn 2003; 226:190-201; PMID:12557198; http://dx.doi.org/10.1002/ dvdy.10248
12. Poss KD, Keating MT, Nechiporuk A. Tales of regeneration in zebrafish. Dev Dyn 2003; 226:202-10; PMID:12557199; http://dx.doi.org/10.1002/ dvdy.10220
13. Tanaka EM, Reddien PW. The cellular basis for animal regeneration. Dev Cell 2011; 21:172-85; PMID:21763617; http://dx.doi.org/10.1016/j.devcel. 2011.06.016
14. Slack JM. Amphibian muscle regeneration--dedifferentiation or satellite cells? Trends Cell Biol 2006; 16:273-5; PMID:16697200; http://dx.doi.org/10.1016/j. tcb.2006.04.007
15. Barrero MJ, Izpisua Belmonte JC. Regenerating the epigenome. EMBO Rep 2011; 12:208-15; PMID:21311559; http://dx.doi.org/10.1038/ embor.2011.10
16. Katsuyama T, Paro R. Epigenetic reprogramming during tissue regeneration. FEBS Lett 2011; 585:1617-24; PMID:21569771; http://dx.doi.org/10.1016/j.febslet. 2011.05.010 methylation: TET proteins-guardians of CpG islands? EMBO Rep 2011; 13:28-35; PMID:22157888; http://dx.doi. org/10.1038/embor.2011.233
17. Thummel R, Burket CT, Hyde DR. Two different transgenes to study gene silencing and re-expression during zebrafish caudal fin and retinal regeneration. ScientificWorldJournal 2006; 6(Suppl 1):65-81; PMID:17205188; http://dx.doi.org/10.1100/ tsw.2006.328
18. Yakushiji N, Suzuki M, Satoh A, Sagai T, Shiroishi T, Kobayashi H, et al. Correlation between Shh expression and DNA methylation status of the limb-specific Shh enhancer region during limb regeneration in amphibians. Dev Biol 2007; 312:171-82; PMID:17961537; http://dx.doi.org/10.1016/j.ydbio.2007.09.022
19. Martin CC, Laforest L, Akimenko MA, Ekker M. A role for DNA methylation in gastrulation and somite patterning. Dev Biol 1999; 206:189-205; PMID:9986732; http://dx.doi.org/10.1006/ dbio.1998.9105
20. Mhanni AA, McGowan RA. Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev Genes Evol 2004; 214:412-7; PMID:15309635; http://dx.doi.org/10.1007/s00427-004-0418-0
21. MacKay AB, Mhanni AA, McGowan RA, Krone PH. Immunological detection of changes in genomic DNA methylation during early zebrafish development. Genome 2007; 50:778-85; PMID:17893737; http:// dx.doi.org/10.1139/G07-055
22. Almeida RD, Loose M, Sottile V, Matsa E, Denning C, Young L, et al. 5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development. Epigenetics 2012; 7:383-9; PMID:22419071; http://dx.doi.org/10.4161/ epi.19375
23. Urasaki A, Morvan G, Kawakami K. Functional dissection of the Tol2 transposable element identified the minimal cis-sequence and a highly repetitive sequence in the subterminal region essential for transposition. Genetics 2006; 174:639-49; PMID:16959904; http:// dx.doi.org/10.1534/genetics.106.060244
24. Woods AL, Hall PA, Shepherd NA, Hanby AM, Waseem NH, Lane DP, et al. The assessment of proliferating cell nuclear antigen (PCNA) immunostaining in primary gastrointestinal lymphomas and its relationship to histological grade, S+G2+M phase fraction (flow cytometric analysis) and prognosis. Histopathology 1991; 19:21-7; PMID:1680784; http://dx.doi. org/10.1111/j.1365-2559.1991.tb00890.x
25. Powell C, Elsaeidi F, Goldman D. Injury-dependent Müller glia and ganglion cell reprogramming during tissue regeneration requires Apobec2a and Apobec2b. J Neurosci 2012; 32:1096-109; PMID:22262907; http:// dx.doi.org/10.1523/JNEUROSCI.5603-11.2012
26. Poleo G, Brown CW, Laforest L, Akimenko MA. Cell proliferation and movement during early fin regeneration in zebrafish. Dev Dyn 2001; 221:380-90; PMID:11500975; http://dx.doi.org/10.1002/ dvdy.1152
27. Tittle RK, Sze R, Ng A, Nuckels RJ, Swartz ME, Anderson RM, et al. Uhrf1 and Dnmt1 are required for development and maintenance of the zebrafish lens. Dev Biol 2011; 350:50-63; PMID:21126517; http:// dx.doi.org/10.1016/j.ydbio.2010.11.009
28. MacKay AB, Mhanni AA, McGowan RA, Krone PH. Immunological detection of changes in genomic DNA methylation during early zebrafish development. Genome 2007; 50:778-85; PMID:17893737; http:// dx.doi.org/10.1139/G07-055
29. Nechiporuk A, Keating MT. A proliferation gradient between proximal and msxb-expressing distal blastema directs zebrafish fin regeneration. Development 2002; 129:2607-17; PMID:12015289