A permissive chromatin structure is adopted prior to site-specific DNA demethylation of developmentally expressed genes involved in macronuclear differentiation

Epigenetics and Chromatin

Volumn 6, Issue 1, 2013, Pages

  Bulic, Aneta ^a   Postberg, Jan ^a   Fischer, Andreas ^b   Jönsson, Franziska ^a   Reuter, Günter ^b   Lipps, Hans J ^a  

^a UNIVERSITY OF WITTEN HERDECKE   (Germany)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

Chromatin structure; Ciliates; Cytosine methylation; Demethylation; Macronucleus

Indexed keywords

BETA TUBULIN; CYTOSINE; HISTONE; HISTONE ACETYLTRANSFERASE; HISTONE H3; PIWI PROTEIN;

ARTICLE; CELL CYCLE; CELL DIFFERENTIATION; CHROMATIN STRUCTURE; CHROMOSOME; CILIATE; DEVELOPMENTAL GENE; DNA METHYLATION; DROSOPHILA; FUNGUS; GENE ACTIVATION; GENE ACTIVITY; GENE EXPRESSION; GENE EXPRESSION REGULATION; MACRONUCLEUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN PROCESSING; REPRODUCTION; STYLONYCHIA LEMNAE;

CILIOPHORA; EUKARYOTA; FUNGI; STYLONYCHIA LEMNAE;

EID: 84874490139     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-5     Document Type: Article

References (34)

1. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Bogdanovic O, Veenstra GJ, Chromosoma 2009 118 549 565 10.1007/s00412-009-0221-9 19506892
2. Regulation of chromatin by histone modifications. Bannister AJ, Kouzarides T, Cell Res 2011 21 381 395 10.1038/cr.2011.22 21321607
3. Nucleosome dynamics and histone variants. Ray-Gallet D, Almouzni G, Essays Biochem 2010 48 75 87 10.1042/bse0480075 20822487
4. Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Berdasco M, Esteller M, Dev Cell 2010 19 698 711 10.1016/j.devcel.2010.10.005 21074720
5. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Nat Genet 2009 41 1350 1353 10.1038/ng.471 19881528
6. Non-CpG cytosine methylation of p53 exon 5 in non-small cell lung carcinoma. Kouidou S, Agidou T, Kyrkou A, Andreou A, Katopodi T, Georgiou E, Krikelis D, Dimitriadou A, Spanos P, Tsilikas C, Lung Cancer 2005 50 299 307 10.1016/j.lungcan.2005.06.012 16125822
7. Human DNA methylomes at base resolution show widespread epigenomic differences. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Nature 2009 462 315 322 10.1038/nature08514 19829295
8. DNA methylation landscapes: provocative insights from epigenomics. Suzuki MM, Bird A, Nat Rev Genet 2008 9 465 476 18463664 (Pubitemid 351693975)
9. Higher-order structures of chromatin: the elusive 30 nm fiber. Tremethick DJ, Cell 2007 128 651 654 10.1016/j.cell.2007.02.008 17320503 (Pubitemid 46290574)
10. The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T, J Biol Chem 2003 278 4035 4040 10.1074/jbc.M210256200 12427740 (Pubitemid 36801137)
11. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP, Nat Genet 1998 19 187 191 10.1038/561 9620779 (Pubitemid 28248804)
12. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A, Nature 1998 393 386 389 10.1038/30764 9620804 (Pubitemid 28269714)
13. Substitutions in the amino-terminal tail of Neurospora histone H3 have varied effects on DNA methylation. Adhvaryu KK, Berge E, Tamaru H, Freitag M, Selker EU, PLoS Genet 2011 7 1002423 10.1371/journal.pgen.1002423 22242002
14. Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Honda S, Selker EU, Mol Cell Biol 2008 28 6044 6055 10.1128/MCB.00823-08 18678653
15. Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells. Ikegami K, Iwatani M, Suzuki M, Tachibana M, Shinkai Y, Tanaka S, Greally JM, Yagi S, Hattori N, Shiota K, Genes Cells 2007 12 1 11 10.1111/j.1365-2443.2006.01029.x 17212651 (Pubitemid 44971094)
16. Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, Grewal SI, Allis CD, Cheng X, Selker EU, Nat Genet 2003 34 75 79 10.1038/ng1143 12679815 (Pubitemid 36548794)
17. The Polycomb group protein EZH2 directly controls DNA methylation. Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, Nature 2006 439 871 874 10.1038/nature04431 16357870 (Pubitemid 43255707)
18. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Science 2012 336 1445 1448 10.1126/science.1219416 22700931
19. New insights into the macronuclear development in ciliates. Juranek SA, Lipps HJ, Int Rev Cytol 2007 262 219 251 17631190 (Pubitemid 47031310)
20. Spatial and temporal plasticity of chromatin during programmed DNA-reorganization in Stylonychia macronuclear development. Postberg J, Heyse K, Cremer M, Cremer T, Lipps HJ, Epigenetics & chromatin 2008 1 3 10.1186/1756-8935-1-3 23520280
21. The unusual way to make a genetically active nucleus. Jonsson F, Postberg J, Lipps HJ, DNA Cell Biol 2009 28 71 78 10.1089/dna.2008.0806 19196049
22. A microarray analysis of developmentally regulated genes during macronuclear differentiation in the stichotrichous ciliate Stylonychia lemnae. Paschka AG, Horejschi V, Jonsson F, Lindecke A, Weier G, Kaltschmidt C, Lipps HJ, Gene 2005 359 81 90 16150557 (Pubitemid 41341401)
23. Histone modifications are specifically relocated during gene activation and nuclear differentiation. Heyse KS, Weber SE, Lipps HJ, BMC Genomics 2009 10 554 10.1186/1471-2164-10-554 19930675
24. De novo cytosine methylation in the differentiating macronucleus of the stichotrichous ciliate Stylonychia lemnae. Juranek S, Wieden HJ, Lipps HJ, Nucleic Acids Res 2003 31 1387 1391 10.1093/nar/gkg233 12595545 (Pubitemid 36304899)
25. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Bracht JR, Perlman DH, Landweber LF, Genome Biol 2012 13 99 10.1186/gb-2012-13-10-r99 23075511
26. A PIWI homolog is one of the proteins expressed exclusively during macronuclear development in the ciliate Stylonychia lemnae. Fetzer CP, Hogan DJ, Lipps HJ, Nucleic Acids Res 2002 30 4380 4386 10.1093/nar/gkf579 12384584 (Pubitemid 35277248)
27. Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery. Mani J, Guttinger A, Schimanski B, Heller M, Acosta-Serrano A, Pescher P, Spath G, Roditi I, PLoS One 2011 6 22463 10.1371/journal.pone.0022463 21811616
28. A specific CpG site demethylation in the human interleukin 2 gene promoter is an epigenetic memory. Murayama A, Sakura K, Nakama M, Yasuzawa-Tanaka K, Fujita E, Tateishi Y, Wang Y, Ushijima T, Baba T, Shibuya K, EMBO J 2006 25 1081 1092 10.1038/sj.emboj.7601012 16498406 (Pubitemid 43372121)
29. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Liu Y, Taverna SD, Muratore TL, Shabanowitz J, Hunt DF, Allis CD, Genes Dev 2007 21 1530 1545 10.1101/gad.1544207 17575054 (Pubitemid 46955725)
30. Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H, Chem Biol 2010 17 471 482 10.1016/j.chembiol.2010.03.006 20534345
31. snRNA and heterochromatin formation are involved in DNA excision during macronuclear development in stichotrichous ciliates. Juranek SA, Rupprecht S, Postberg J, Lipps HJ, Eukaryot Cell 2005 4 1934 1941 10.1128/EC.4.11.1934-1941. 2005 16278460 (Pubitemid 41636885)
32. The development of the macronucleus in the ciliated protozoan Stylonychia mytilus. Ammermann D, Steinbruck G, von Berger L, Hennig W, Chromosoma 1974 45 401 429 4209692
33. DNA methylation in Drosophila-a critical evaluation. Krauss V, Reuter G, Prog Mol Biol Transl Sci 2011 101 177 191 21507351
34. The methylated component of the Neurospora crassa genome. Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, Bird AP, Freitag M, Nature 2003 422 893 897 10.1038/nature01564 12712205 (Pubitemid 36520041)