Association of modified cytosines and the methylated DNA-binding protein MeCP2 with distinctive structural domains of lampbrush chromatin

Chromosome Research

Volumn 20, Issue 8, 2012, Pages 925-942

  Morgan, Garry T ^a   Jones, Peter ^b   Bellini, Michel ^c  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b BOSTON BIOMEDICAL RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

5 hydroxymethylcytosine; Lampbrush chromosomes; Methylation; Oocyte; Transcription unit

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; CYTOSINE; DNA; DNA BINDING PROTEIN; METHYL CPG BINDING PROTEIN 2; RNA POLYMERASE II;

AMPHIBIA; ANIMAL CELL; ARTICLE; CHROMATIN; CHROMOSOME; DNA METHYLATION; GENE REPRESSION; IMMUNOBLOTTING; IMMUNOHISTOCHEMISTRY; LAMPBRUSH CHROMATIN; MULTIGENE FAMILY; NONHUMAN; OOCYTE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN STRUCTURE; RETT SYNDROME; XENOPUS LAEVIS;

5-METHYLCYTOSINE; ANIMALS; CHROMATIN; CHROMOSOMES; CYTOSINE; DNA; DNA METHYLATION; GENE EXPRESSION REGULATION; HUMANS; IMMUNOBLOTTING; METHYL-CPG-BINDING PROTEIN 2; MUTATION; OOCYTES; RNA POLYMERASE II; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC; XENOPUS LAEVIS;

AMBYSTOMA MEXICANUM; AMPHIBIA; XENOPUS LAEVIS;

EID: 84877576210     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-012-9324-x     Document Type: Article

References (64)

1. Andrulis ED, Neiman AM, Zapulla DC, Sternglanz R (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394:592-595 (Pubitemid 28366836)
2. Angelier N, Bonnanfant-Jaïs ML, Moreau N, Gounon P, Lavaud A (1986) DNA methylation and RNA transcriptional activity in amphibian lampbrush chromosomes. Chromosoma 94:169-182
3. Austin C, Novikova N, Guacci V, Bellini M (2009) Lampbrush chromosomes enable study of cohesin dynamics. Chromosom Res 17:165-184
4. Ballestar E, Yusufzai TM, Wolffe A (2000) Effects of Rett syndrome mutations of the methyl-CpG binding domain of the transcriptional repressor MeCP2 on selectivity for association with methylated DNA. Biochemistry 39:7100-7106 (Pubitemid 30413098)
5. Beenders B, Watrin E, Legagneux V, Kireev I, Bellini M (2003) Distribution of XCAP-E and XCAP-D2 in the Xenopus oocyte nucleus. Chromosom Res 11:549-564 (Pubitemid 37056157)
6. Beenders B, Jones PL, Bellini M (2007) The tripartite motif of nuclear factor 7 is required for its association with transcriptional units. Mol Cell Biol 27:2615-2624 (Pubitemid 46581352)
7. Bhutani N, Burns DM, Blau HM (2011) DNA demethylation dynamics. Cell 146:866-872
8. Bouvet P, Dimitrov S, Wolffe AP (1994) Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1. Genes Dev 8:1147-1159 (Pubitemid 24163443)
9. Buhrmester H, von Kries JP, Strätling WH (1995) Nuclear matrix protein ARBP recognizes a novel DNA sequence motif with high affinity. Biochemistry 34:4108-4117
10. Bustin M, Catez F, Lim JH (2005) The dynamics of histone H1 function in chromatin. Mol Cell 17:617-620 (Pubitemid 40320912)
11. Callan HG (1966) Chromosomes and nucleoli of the axolotl, Ambystoma mexicanum. J Cell Sci 1:85-108
12. Callan HG (1986) Lampbrush chromosomes. Springer, Berlin
13. Chahrour M, Jung SY, Shaw C, Zhou X,Wong STC, Qin J, Zoghbi HY (2008) MeCP2, a key contributor to neurological disease, activates and represses transcription. Science 320:1224-1229 (Pubitemid 351929512)
14. Davidson EH (1986) Gene activity in early development, 3rd edn. Academic, Orlando
15. Dawid IB, Brown DD, Reeder RH (1970) Composition and structure of chromosomal and amplified ribosomal DNA's of Xenopus laevis. J Mol Biol 51:341-360
16. Gaginskaya E, Kulikova T, Krasikova A (2009) Avian lampbrush chromosomes: a powerful tool for exploration of genome expression. Cytogenet Genome Res 124:251-267
17. Gall J (1998) Spread preparation of Xenopus germinal vesicle contents. In: Spector D, Goldman R, Leinwand L (eds) Cells: a laboratory manual, vol 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 52.51-52.54
18. Gall JG, Wu Z (2010) Examining the contents of isolated Xenopus germinal vesicles. Methods 51:45-51
19. Gall JG,Bellini M,Wu Z,Murphy C (1999) Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes. Mol Biol Cell 10:4385-4402
20. Habib M, Fares F, Bourgeois CA et al (1999) DNA global hypomethylation in EBV-transformed interphase nuclei. Exp Cell Res 249:46-53 (Pubitemid 29394023)
21. Hock R, Moorman A, Fischer D, Scheer U (1993) Absence of somatic histone H1 in oocytes and preblastula embryos of Xenopus laevis. Dev Biol 158:510-522 (Pubitemid 23243908)
22. Hock R, Carl M, Lieb B, Gebauer D, Scheer U (1996) A monoclonal antibody against DNA topoisomerase II labels the axial granules of Pleurodeles lampbrush chromosomes. Chromosoma 104:358-366 (Pubitemid 26047628)
23. Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T (2005) Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett Syndrome. Nat Genet 37:31-40 (Pubitemid 40070937)
24. Howe L, Ranalli TA, Allis CD, Ausio J (1998) Transcriptionally active Xenopus laevis somatic 5 S ribosomal RNA genes are packaged with hyperacetylated histone H4, whereas transcriptionally silent oocyte genes are not. J Biol Chem 273:20693-20696 (Pubitemid 28385343)
25. Ishibashi T, Thambirajah AA, Ausió J (2008) MeCP2 preferentially bidns to methylated linker DNA in the absence of the terminal tail of histone H3 and independently of histone acetylation. FEBS Lett 582:1157-1162
26. Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genetics 13:484-492
27. Jones PL,Veenstra GJ,Wade PA,VermaakD, Kass SU, Landsberger N, Strouboulis J, Wolffe AP (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nature Genet 19:187-191 (Pubitemid 28248804)
28. Jullien J, Pasque V, Halley-Stott RP, Miyamoto K, Gurdon JB (2011) Mechanisms of nuclear reprogramming by eggs and oocytes: a deterministic process? Nat Rev Mol Cell Biol 12:453-459
29. Kaludov NK, Wolffe AP (2000) MeCP2 driven transcriptional repression in vitro: selectivity for methylated DNA, action at a distance and contacts with the basal transcription machinery. Nucleic Acid Res 28:1921-1928 (Pubitemid 30229657)
30. Klose RJ, Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31:89-97 (Pubitemid 43221841)
31. Korner U, Bustin M, Scheer U, Hock R (2003) Developmental role of HMGN proteins in Xenopus laevis. Mech Dev 120:1177-1192 (Pubitemid 37272224)
32. Krasikova A, Daks A, Zlotina A, Gaginskaya E (2009) Polymorphic heterochromatic segments in Japanese quail microchromosomes. Cytogenet Genome Res 126:148-155
33. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5- hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929-930
34. Kumar A,Kamboj S, MaloneBM,Kudo S,Twiss JL,CzymmekKJ, LaSalle JM, Schanen NC (2008) Analysis of protein domains and Rett syndrome mutations indicate that multiple regions influence chromatin-binding dynamics of the chromatin-associated protein MECP2 in vivo. J Cell Sci 121:1128-1137 (Pubitemid 351639431)
35. Lewis JD, Meehan RR, Henzel WJ et al (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69:905-914
36. Miller OL Jr, Hamkalo BA (1972) Visualization of RNA synthesis on chromosomes. Int Rev Cytol 33:1-25
37. Miller JR, Cartwright EM, Brownlee GG, Fedoroff NV, Brown DD (1978) The nucleotide sequence of oocyte 5S DNA in Xenopus laevis. II. The GC-rich region. Cell 13:717-725 (Pubitemid 8312227)
38. Morgan GT (2002) Lampbrush chromosomes and associated bodies: new insights into principles of nuclear structure and function. Chromosom Res 10:177-200 (Pubitemid 34553493)
39. Morgan GT (2008)Working with oocyte nuclei: cytological preparations of active chromatin and nuclear bodies from amphibian germinal vesicles. Methods Mol Biol 463:55-66
40. Murphy C, Wang Z, Roeder RG, Gall JG (2002) RNA Polymerase III in Cajal bodies and lampbrush chromosomes of the Xenopus oocyte nucleus. Mol Biol Cell 13:3466-3476 (Pubitemid 35191368)
41. Nan X, Ng HH, Johnson CA, et al. (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386-389 (Pubitemid 28269714)
42. Pukkila PJ (1975) Identification of the lampbrush chromosome loops which transcribe 5S ribosomal RNA in Notophthalmus (Triturus) viridescens. Chromosoma 53:71-89
43. Reynaud C, Bruno C, Boullanger P, Grange J, Barbesti S, Niveleau A (1992) Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies. Cancer Lett 61:255-262
44. Scheer U (1978) Changes of nucleosome frequency in nucleolar and non-nucleolar chromatin as a function of transcription: an electron microscopic study. Cell 13:535-549
45. Scheer U (1987) Structure of lampbrush chromosome loops during different states of transcriptional activity as visualised in the presence of physiological salt concentrations. Biol Cell 59:33-42
46. Singh J, Saxena A, Christodoulou J, Ravine D (2008) MECP2 genomic structure and function: insights from ENCODE. Nucleic Acid Res 36:6035-6047
47. Skene PJ, Illingworth RS,Webb S et al (2010) Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol Cell 37:457-468
48. Smallwood SA, Tomizawa S, Krueger F et al (2011) Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 43:811-814
49. Smith RC, Dworkin-Rastl E, Dworkin MB (1988) Expression of a histone H1-like protein is restricted to early Xenopus development. Genes Dev 2:1284-1295
50. Smith AJ, Ling Y, Morgan GT (2003) Subnuclear localization and Cajal body targeting of transcription elongation factor TFIIS in amphibian oocytes. Mol Biol Cell 14:1255-1267 (Pubitemid 36337467)
51. Sommerville J, Baird J, Turner BM (1993) Histone H4 acetylation and transcription in amphibian chromatin. J Cell Biol 120:277-290 (Pubitemid 23040069)
52. Stewart MD, Sommerville J,Wong J (2006) Dynamic regulation of histone modifications in Xenopus oocytes through histone exchange. Mol Cell Biol 26:6890-6901 (Pubitemid 44387638)
53. Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE (2011) 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol 12:R54
54. Stutz F, Gouilloud E, Clarkson SG (1989) Oocyte and somatic tyrosine tRNA genes in Xenopus laevis. Genes Dev 3:1190-1198
55. Tahiliani M, Koh KP, Shen Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930-935
56. Tan L, Shi YG (2012) Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development 139:1895-1902
57. Van den Eynde H, Mazabraud A, Denis H (1989) Biochemical research on oogenesis. RNA accumulation in the oocytes of the newt Pleurodeles waltl. Development 106:11-16 (Pubitemid 19150666)
58. Warren SL, Landolfi AS, Curtis C, Morrow JSW (1992) Cytostellin: a novel, highly conserved protein that undergoes continuous redistribution during the cell cycle. J Cell Sci 103:381-388
59. Weitzel JM, Buhrmester H, Strätling WH (1997) Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG-binding protein MeCP2. Mol Cell Biol 17:5656-5666 (Pubitemid 27357662)
60. White RJ (2011) Transcription by RNA polymerase III: more complex than we thought. Nat Rev Genetics 12:459-463
61. Wolffe AP, Brown DD (1988) Developmental regulation of two 5S ribosomal RNA genes. Science 241:1626-1632
62. Woodcock CL, Skoultchi AI, Fan Y (2006) Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosom Res 14:17-25
63. Yasui DH, Peddada S, Bleda MC, Vallero RO, Hogart A, Nagarajan R, Thatcher KN, Farnham PJ, LaSalle JM (2007) Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Nat Acad Sci 104:19416-19421
64. Yu F, Thiesen J, Stratling WH (2000) Histone deacetylase-independent transcriptional repression by methyl-CpG-binding protein 2. Nucleic Acid Res 28:2201-2206 (Pubitemid 30255545)