Expression profiling of clonal lymphocyte cell cultures from Rett syndrome patients

BMC Medical Genetics

Volumn 7, Issue , 2006, Pages

  Delgado, Ivan J ^a,c   Kim, Dong Sun ^a,d   Thatcher, Karen N ^b   LaSalle, Janine M ^b   Van den Veyver, Ignantia B ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c Identigene Inc   (United States)

^d Kyungpook National University School of Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

METHYL CPG BINDING PROTEIN 2; OLIGONUCLEOTIDE;

ALLELE; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DOWN REGULATION; EMBRYO; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MUTATION; HUMAN; HUMAN CELL; LYMPHOCYTE CULTURE; MICROARRAY ANALYSIS; MOLECULAR CLONING; MOSAICISM; MOUSE; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; RETT SYNDROME; T LYMPHOCYTE; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE; UPREGULATION; WILD TYPE;

ANIMALS; CELLS, CULTURED; CLONE CELLS; DISEASE MODELS, ANIMAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; LYMPHOCYTES; METHYL-CPG-BINDING PROTEIN 2; MICE; MICROARRAY ANALYSIS; MUTANT PROTEINS; PROTEOGLYCANS; RETT SYNDROME; RNA, MESSENGER;

EID: 33748892622     PISSN: 14712350     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-7-61     Document Type: Article

References (58)

1. Akesson HO, Hagberg B, Wahlstrom J: Rett syndrome, classical and atypical: genealogical support for common origin. J Med Genet 1996, 33(9):764-766.
2. Hagberg B, Hagberg G: Rett syndrome: epidemiology and geographical variability. Eur Child Adolesc Psychiatry 1997, 6(Suppl 1):5-7.
3. Armstrong DD: Review of Rett syndrome. J Neuropathol Exp Neurol 1997, 56(8):843-849.
4. Weaving LS, Ellaway CJ, Gecz J, Christodoulou J: Rett syndrome: clinical review and genetic update. J Med Genet 2005, 42(1):1-7.
5. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY: Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl- CpG-binding protein 2. Nat Genet 1999, 23(2):185-188.
6. Miltenberger-Miltenyi G, Laccone F: Mutations and polymorphisms in the human methyl CpG-binding protein MECP2. Hum Mutat 2003, 22(2):107-115.
7. Van den Veyver IB, Zoghbi HY: Methyl-CpG-binding protein 2 mutations in Rett syndrome. Curr Opin Genet Dev 2000, 10(3):275-279.
8. Van den Veyver IB, Zoghbi HY: Genetic basis of Rett syndrome. Ment Retard Dev Disabil Res Rev 2002, 8(2):82-86.
9. Amir RE, Fang P, Yu Z, Glaze DG, Percy AK, Zoghbi HY, Roa BB, Van den Veyver IB: Mutations in exon 1 of MECP2 are a rare cause of Rett Syndrome. J Med Genet 2005, 42(2):e15.
10. Laccone F, Junemann I, Whatley S, Morgan R, Butler R, Huppke P, Ravine D: Large deletions of the MECP2 gene detected by gene dosage analysis in patients with Rett syndrome. Hum Mutat 2004, 23(3):234-244.
11. Archer HL, Whatley SD, Evans JC, Ravine D, Huppke P, Kerr A, Bunyan D, Kerr B, Sweeney E, Davies SJ, Reardon W, Horn J, Macdermot KD, Smith RA, Magee A, Donaldson A, Crow Y, Hermon G, Miedzybrodzka Z, Cooper DN, Lazarou L, Butler R, Sampson J, Pilz DT, Laccone F, Clarke AJ: Gross rearrangements of the MECP2 gene are found in both classical and atypical Rett syndrome patients. J Med Genet 2006, 43(5):451-456.
12. Shi J, Shibayama A, Liu Q, Nguyen VQ, Feng J, Santos M, Temudo T, Maciel P, Sommer SS: Detection of heterozygous deletions and duplications in the MECP2 gene in Rett syndrome by Robust Dosage PCR (RD-PCR). Hum Mutat 200S, 25(5):505.
13. Kriaucionis S, Bird A: The major form of MeCP2 has a novel N-terminus generated by alternative splicing. Nucleic Acids Res 2004, 32(5):1818-1823.
14. Mnatzakanian GN, Lohi H, Munteanu I, Alfred SE, Yamada T, MacLeod PJ, Jones JR, Scherer SW, Schanen NC, Friez MJ, Vincent JB, Minassian BA: A previously unidentified MECP2 open reading frame defines a new protein isoform relevant to Rett syndrome. Nat Genet 2004, 36(4):339-341.
15. Philippe C, Villard L, De Roux N, Raynaud M, Bonnefond JP, Pasquier L, Lesca G, Mancini J, Jonveaux P, Moncla A, Chelly J, Bienvenu T: Spectrum and distribution of MECP2 mutations in 424 Rett syndrome patients: a molecular update. Eur J Med Genet 2006, 49(1):9-18.
16. Evans JC, Archer HL, Whatley SD, Kerr A, Clarke A, Butler R: Variation in exon 1 coding region and promoter of MECP2 in Rett syndrome and controls. Eur J Hum Genet 2005, 13(1):124-126.
17. Nan X, Meehan RR, Bird A: Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 1993, 21(21):4886-4892.
18. Nan X, Campoy FJ, Bird A: MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 1997, 88(4):471-481.
19. Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP: Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 1998, 19(2):187-191.
20. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A: Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998, 393(6683):386-389.
21. Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T: The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 2003, 278(6):4035-4040.
22. Kimura H, Shiota K: Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmtl. J Biol Chem 2003, 278(7):4806-4812.
23. Harikrishnan KN, Chow MZ, Baker EK, Pal S, Bassal S, Brasacchio D, Wang L, Craig JM, Jones PL, Sif S, El-Osta A: Brahma links the SWI/SNF chromatin-remodeling complex with MeCP2-dependent transcriptional silencing. Nat Genet 2005, 37(3):254-264.
24. Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF, Kang D, Richman R, Johnson JM, Berget S, Zoghbi HY: Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2. Proc Natl Acad Sci USA 2005, 102(49):17551-17558.
25. Chen WG, Chang Q, Lin Y, Meissner A, West AE, Griffith EC, Jaenisch R, Greenberg ME: Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2. Science 2003, 302(5646):885-889.
26. Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y, Fan G, Sun YE: DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 2003, 302(5646):890-893.
27. Chang Q, Khare G, Dani V, Nelson S, Jaenisch R: The disease progression of Mecp2 mutant mice is affected by the level of BDNF expression. Neuron 2006, 49(3):341-348.
28. Stancheva I, Collins AL, Van den Veyver IB, Zoghbi H, Meehan RR: A mutant form of MeCP2 protein associated with human Rett syndrome cannot be displaced from methylated DNA by notch in Xenopus embryos. Mol Cell 2003, 12(2):425-435.
29. Traynor J, Agarwal P, Laizeroni L, Francke U: Gene expression patterns vary in clonal cell cultures from Rett syndrome females with eight different MECP2 mutations. BMC Med Genet 2002, 3:12.
30. Tudor M, Akbarian S, Chen RZ, Jaenisch R: Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci USA 2002, 99(24):15536-15541.
31. Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V, Hoffman EP, Kaufmann WE, Naidu S, Pevsner J: Gene expression profiling in postmortem Rett Syndrome brain: differential gene expression and patient classification. Neurobiol Dis 2001, 8(5):847-865.
32. Pescucci C, Meloni I, Renieri A: Is Rett syndrome a loss-of-imprinting disorder? Nat Genet 2005, 37(1):10-11.
33. Klose R, Bird A: Molecular biology. MeCP2 repression goes nonglobal. Science 2003, 302(5646):793-795.
34. Horike S, Cai S, Miyano M, Cheng JF, Kohwi-Shigematsu T: Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome. Nat Genet 2005, 37(1):31-40.
35. Balmer D, LaSalle JM: Clonal maintenance of imprinted expression of SNRPN and IPW in normal lymphocytes: correlation with allele-specific methylation of SNRPN intron 1 but not intron 7. Hum Genet 2001, 108(2):116-122.
36. LaSalle JM, Ritchie RJ, Glatt H, Lalande M: Clonall heterogeneity at allelic methylation sites diagnostic for Prader-Willi and Angelman syndromes. Proc Natl Acad Sci USA 1998, 95(4):1675-1680.
37. Balmer D, Arredondo J, Samaco RC, LaSalle JM: MECP2 mutations in Rett syndrome adversely affect lymphocyte growth, but do not affect imprinted gene expression in blood or brain. Hum Genet 2002, 110(6):545-552.
38. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5(10):R80.
39. Bioconductor [http://www.bioconductor.org]
40. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oilgonucleotide army probe level data. Biostatistics 2003, 4(2):249-264.
41. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193.
42. Wu Z, Irizarry RA, Gentleman R, Martinez Murillo F, Spencer F: A model based background adjustment for oligonucleotide expression arrays. Johns Hopkins Dept of Biostatistics Working Papers 2004. (paper 1).
43. Shahbazian MD, Young YI, Yuva-Paylor LA, Spencer CM, Antalffy BA, Noebels JL, Armstrong DL, Paylor R, Zoghbi HY: Mice with Truncated MeCP2 Recapitulate Many Rett Syndrome Features and Display Hyperacetylation of Histone H3. Neuron 2002, 35:243-254.
44. Ballestar E, Ropero S, Alaminos M, Armstrong J, Setien F, Agrelo R, Fraga MF, Herranz M, Avila S, Pineda M, Monros E, Esteller M: The impact of MECP2 mutations in the expression patterns of Rett syndrome patients. Hum Genet 2005, 116(1-2):91-104.
45. National Center for Biotechnoology Information Entrez Gene [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene]
46. Applied Biosystems user bulletin #2: ABI PRISM 7700 Sequence Detection System [http://docs.appliedbiosystems.com/pebiodocs/04303859.pdf]
47. Alvarez E, Zhou W, Witta SE, Freed CR: Characterization of the Bex gene family in humans, mice, and rats. Gene 2005, 357(1):18-28.
48. Phan J, Reue K: Lipin, a lipodystrophy and obesity gene. Cell Metab 2005, 1(1):73-83.
49. Suviolahti E, Reue K, Cantor RM, Phan J, Gentile M, Naukkarinen J, Soro-Paavonen A, Oksanen L, Kaprio J, Rissanen A, Salomaa V, Kontula K, Taskinen MR, Pajukanta P, Peltonen L: Cross-species analyses implicate Lipin 1 involvement in human glucose metabolism. Hum Mol Genet 2006, 15(3):377-386.
50. Alliel PM, Perin JP, Jolles P, Bonnet FJ: Testican, a multidomain testicular proteoglycan resembling modulators of cell social behaviour. Eur J Biochem 1993, 214(1):347-350.
51. Marr HS, Basalamah MA, Bouldin TW, Duncan AW, Edgell CJ: Distribution of testican expression in human brain. Cell Tissue Res 2000, 302(2):139-144.
52. Charbonnier F, Chanoine C, Cifuentes-Diaz C, Gallien CL, Rieger F, Alliell PM, Perin JP: Expression of the proteoglycan SPOCK during mouse embryo development. Mech Dev 2000, 90(2):317-321.
53. Marr HS, Edgell CS: Testican-1 inhibits attachment of Neuro-2a cells. Matrix Biology 2003, 22:259-266.
54. Bonnet F, Perin JP, Charbonnier F, Camuzat A, Roussel G, Nussbaum JL, Alliel PM: Structure and cellular distribution of mouse brain testican. Association with the postsynaptic area of hippocampus pyramidal cells. J Biol Chem 1996, 271(8):4373-4380.
55. Shahbazian MD, Sun Y, Zoghbi HY: Balanced X chromosome inactivation patterns in the Rett syndrome brain. Am J Med Genet 2002, 111(2):164-168.
56. Amir RE, Zoghbi HY: Rett syndrome: methyl-CpG-binding protein 2 mutations and phenotype-genotype correlations. Am J Med Genet 2000, 97(2):147-152.
57. BaSalamah MA, Marr HS, Duncan AW, Edgell CJ: Testican in human blood. Biochem Biophys Res Commun 2001, 283(5):1083-1090.
58. Bocock JP, Edgell CJ, Marr HS, Erickson AH: Human proteoglycan testican-1 inhibits the lysosomal cysteine protease cathepsin L. Eur J Biochem 2003, 270(19):4008-4015.