Comparative study of methyl-CpG-binding domain proteins

BMC Genomics

Volumn 4, Issue , 2003, Pages

  Roloff, Tim C ^a,b   Ropers, H Hilger ^a   Nuber, Ulrike A ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; METHYL CPG BINDING PROTEIN 2; POLYPEPTIDE;

AMINO ACID SEQUENCE; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; METHYLATION; MOUSE; NONHUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN MOTIF; TRANSCRIPTION REGULATION;

VERTEBRATA;

EID: 9144246375     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-4-1     Document Type: Article

References (52)

1. Bird A The essentials of DNA methylation. Cell 1992, 70:5-8
2. Singal R and Ginder GD DNA methylation. Blood 1999, 93:4059-4070
3. El Osta A and Wolffe AP DNA methylation and histone deacetylation in the control of gene expression: basic biochemistry to human development and disease. Gene Expr 2000, 9:63-75
4. Ohki I, Shimotake N, Fujita N, Nakao M and Shirakawa M Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1. EMBO J 1999, 18:6653-6661
5. Wakefield RI, Smith BO, Nan X, Free A, Soteriou A, Uhrin D, Bird AP and Barlow PN The solution structure of the domain from MeCP2 that binds to methylated DNA. J Mol Biol 1999, 291: 055-1065
6. Ballestar E and Wolffe AP Methyl-CpG-binding proteins. Targeting specific gene repression. Eur J Biochem 2001, 268: -6
7. Nan X, Meehan RR and Bird A Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 1993, 21:4886-4892
8. Daniel JM and Reynolds AB The catenin p120(ctn) interacts with Kaiso, a novel BTB/POZ domain zinc finger transcription factor. Mol Cell Biol 1999, 19:3614-3623
9. Prokhortchouk A, Hendrich B, Jorgensen H, Ruzov A, Wilm M, Georgiev G, Bird A and Prokhortchouk E The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev 2001, 15:1613-1618
10. Wade PA Methyl CpG-binding proteins and transcriptional repression. Bioessays 2001, 23:1131-1137
11. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN and Bird A Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393:386-389
12. Ng HH, Zhang Y, Hendrich B, Johnson CA, Turner BM, Erdjument-Bromage H, Tempst P, Reinberg D and Bird A MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat Genet 1999, 23:58-61
13. Ng HH, Jeppesen P and Bird A Active repression of methylated genes by the chromosomal protein MBD1. Mol Cell Biol 2000, 20:1394-1406
14. Amir RE, Van dV I, Wan M, Tran CQ, Francke U and Zoghbi HY Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 1999, 23:185-188
15. Percy AK Rett syndrome: clinical correlates of the newly discovered gene. Brain Dev 2001, 23(Suppl 1):S202-S205
16. Yusufzai TM and Wolffe AP Functional consequences of Rett syndrome mutations on human MeCP2. Nucleic Acids Res 2000, 28:4172-4179
17. Kudo S, Nomura Y, Segawa M, Fujita N, Nakao M, Dragich J, Schanen C and Tamura M Functional analyses of MeCP2 mutations associated with Rett syndrome using transient expression systems. Brain Dev 2001, 23(Suppl 1):S165-S173
18. Nan X and Bird A The biological functions of the methyl-CpG-binding protein MeCP2 and its implication in Rett syndrome. Brain Dev 2001, 23(Suppl 1):S32-S37
19. Guy J, Hendrich B, Holmes M, Martin JE and Bird A A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. Nat Genet 2001, 27:322-326
20. Chen RZ, Akbarian S, Tudor M and Jaenisch R Deficiency of methyl-CpG binding protein-2 in CNS neurons results in a Rett-like phenotype in mice. Nat Genet 2001, 27:327-331
21. Shahbazian M, Young J, Yuva-Paylor L, Spencer C, Antalffy B, Noebels J, Armstrong D, Paylor R and Zoghbi H Mice with truncated MeCP2 recapitulate many Rett syndrome features and display hyperacetylation of histone H3. Neuron 2002, 35:243-254
22. Mabuchi H, Fujii H, Calin G, Alder H, Negrini M, Rassenti L, Kipps TJ, Bullrich F and Croce CM Cloning and characterization of CLLD6, CLLD7, and CLLD8, novel candidate genes for leukemogenesis at chromosome 13q14, a region commonly deleted in B-cell chronic lymphocytic leukemia. Cancer Res 2001, 61:2870-2877
23. Schultz DC, Ayyanathan K, Negorev D, Maul GG and Rauscher FJ III SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 2002, 16:919-932
24. Strohner R, Nemeth A, Jansa P, Hofmann-Rohrer U, Santoro R, Langst G and Grummt I NoRC - a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J 2001, 20:4892-4900
25. Kanehisa M, Goto S, Kawashima S and Nakaya A The KEGG databases at GenomeNet. Nucleic Acids Res 2002, 30:42-46
26. Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F and Bird A Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 1992, 69:905-914
27. Hendrich B and Bird A Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 1998, 18:6538-6547
28. Bird A DNA methylation patterns and epigenetic memory. Genes Dev 2002, 16:6-21
29. Hendrich B, Hardeland U, Ng HH, Jiricny J and Bird A The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 1999, 401:301-304
30. Petronzelli F, Riccio A, Markham GD, Seeholzer SH, Genuardi M, Karbowski M, Yeung AT, Matsumoto Y and Bellacosa A Investigation of the substrate spectrum of the human mismatch-specific DNA N-glycosylase MED1 (MBD4): fundamental role of the catalytic domain. J Cell Physiol 2000, 185:473-480
31. Saito M and Ishikawa F The mCpG-binding domain of human MBD3 does not bind to mCpG but interacts with NuRD/Mi2 components HDAC1 and MTA2. J Biol Chem 2002, 277:35434-35439
32. Vacca M, Filippini F, Budillon A, Rossi V, Mercadante G, Manzati E, Gualandi F, Bigoni S, Trabanelli C and Pini G Mutation analysis of the MECP2 gene in British and Italian Rett syndrome females. J Mol Med 2001, 78:648-655
33. Santoro R, Li J and Grummt I The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet 2002, 32:393-396
34. Schultz DC, Friedman JR and Rauscher FJ III Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD. Genes Dev 2001, 15: 28-443
35. Doerks T, Copley R and Bork P DDT - a novel domain in different transcription and chromosome remodeling factors. Trends Biochem Sci 2001, 26:145-146
36. Yang L, Mei Q, Zielinska-Kwiatkowska A, Matsui Y, Blackburn ML, Benedetti D, Krumm A, Taborsky GJ Jr and Chansky HA An ERG (ets-related gene)-associated histone methyltransferase interacts with histone deacetylases 1/2 and mSin3 transcription corepressors mSin3A /B. Biochem J 2002, Pt:
37. Wang H, Cao R, Xia L, Erdjument-Bromage H, Borchers C, Tempst P and Zhang Y Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol Cell 2001, 8:1207-1217
38. Tachibana M, Sugimoto K, Fukushima T and Shinkai Y Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 2001, 276: 5309-25317
39. Stec I, Wright TJ, van Ommen GJ, de Boer PA, van Haeringen A, Moorman AF, Altherr MR and den Dunnen JT WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma. Hum Mol Genet 1998, 7:1071-1082
40. Qiu C, Sawada K, Zhang X and Cheng X The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol 2002, 9:217-224
41. Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP and Kouzarides T The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 2002,
42. Hendrich B, Abbott C, McQueen H, Chambers D, Cross S and Bird A Genomic structure and chromosomal mapping of the murine and human Mbd1, Mbd2, Mbd3, and Mbd4 genes. Mamm Genome 1999, 10: 06-912
43. Quaderi NA, Meehan RR, Tate PH, Cross SH, Bird AP, Chatterjee A, Herman GE and Brown SD Genetic and physical mapping of a gene encoding a methyl CpG binding protein, Mecp2, to the mouse X chromosome. Genomics 1994, 22:648-651
44. D'Esposito M, Quaderi NA, Ciccodicola A, Bruni P, Esposito T, D'Urso M and Brown SD Isolation, physical mapping, and northern analysis of the X-linked human gene encoding methyl CpG-binding protein, MECP2. Mamm Genome 1996, 7:533-535
45. Nagase T, Kikuno R and Ohara O Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. DNA Res 2001, 8:179-187
46. Jones MH, Hamana N, Nezu J and Shimane M A novel family of bromodomain genes. Genomics 2000, 63:40-45
47. Shahbazian MD, Antalffy B, Armstrong DL and Zoghbi HY Insight into Rett syndrome: MeCP2 levels display tissue- and cellspecific differences and correlate with neuronal maturation. Hum Mol Genet 2002, 11:115-124
48. LaSalle JM, Goldstine J, Balmer D and Greco CM Quantitative localization of heterogeneous methyl-CpG-binding protein 2 (MeCP2) expression phenotypes in normal and Rett syndrome brain by laser scanning cytometry. Hum Mol Genet 2001, 10:1729-1740
49. Tudor M, Akbarian S, Chen RZ and Jaenisch R Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci U S A 2002, 99:15536-15541
50. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F and Higgins DG The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882
51. Coy JF, Sedlacek Z, Bachner D, Delius H and Poustka A A complex pattern of evolutionary conservation and alternative polyadenylation within the long 3″-untranslated region of the methyl-CpG-binding protein 2 gene (MeCP2) suggests a regulatory role in gene expression. Hum Mol Genet 1999, 8:1253-1262
52. Nomura N, Nagase T, Miyajima N, Sazuka T, Tanaka A, Sato S, Seki N, Kawarabayasi Y, Ishikawa K and Tabata S Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1 (supplement). DNA Res 1994, 1:251-262