Genomic determinants in the phenotypic variability of Down syndrome

Progress in Brain Research

Volumn 197, Issue , 2012, Pages 15-28

  Letourneau, Audrey ^a   Antonarakis, Stylianos E ^a  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

Author keywords

Down syndrome; Gene expression; Genomic variability; Human chromosome 21; Phenotypic variability; Trisomy 21

Indexed keywords

ARTICLE; CHROMOSOME 21; CHROMOSOME SIZE; DOWN SYNDROME; GENETIC CODE; GENETIC MARKER; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME; HUMAN; MOLECULAR GENETICS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DEGRADATION; SIGNAL TRANSDUCTION; TRISOMY 21;

EID: 84860324473     PISSN: 00796123     EISSN: 18757855     Source Type: Book Series    
DOI: 10.1016/B978-0-444-54299-1.00002-9     Document Type: Chapter

References (78)

1. Adams M.D., et al. The genome sequence of Drosophila melanogaster. Science 2000, 287(5461):2185-2195.
2. Ait Yahya-Graison E., et al. Classification of human chromosome 21 gene-expression variations in Down syndrome: Impact on disease phenotypes. The American Journal of Human Genetics 2007, 81(3):475-491.
3. Altug-Teber O., et al. Specific transcriptional changes in human fetuses with autosomal trisomies. Cytogenetic and Genome Research 2007, 119(3-4):171-184.
4. Antonarakis S.E., et al. Chromosome 21 and Down syndrome: From genomics to pathophysiology. Nature Reviews. Genetics 2004, 5(10):725-738.
5. Bamburg J.R., Bloom G.S. Cytoskeletal pathologies of Alzheimer disease. Cell Motility and the Cytoskeleton 2009, 66(8):635-649.
6. Beattie R.B., Manson I.W., Whittle M.J. Identical twins with trisomy 21 discordant for exomphalos. Prenatal Diagnosis 1993, 13(11):1067-1070.
7. Beckmann J.S., Estivill X., Antonarakis S.E. Copy number variants and genetic traits: Closer to the resolution of phenotypic to genotypic variability. Nature Reviews. Genetics 2007, 8(8):639-646.
8. Chapman R.S., Hesketh L.J. Language, cognition, and short-term memory in individuals with Down syndrome. Down's Syndrome, Research and Practice: The Journal of the Sarah Duffen Centre/University of Portsmouth 2001, 7(1):1-7.
9. Chapman R.S., et al. Language skills of children and adolescents with Down syndrome: II. Production deficits. Journal of Speech, Language, and Hearing Research 1998, 41(4):861-873.
10. Cheon M.S., et al. Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain: Challenging the gene dosage effect hypothesis (Part II). Amino Acids 2003, 24(1-2):119-125.
11. Cheon M.S., et al. Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain: Challenging the gene dosage effect hypothesis (Part III). Amino Acids 2003, 24(1-2):127-134.
12. Cheon M.S., et al. Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain: Challenging the gene dosage effect hypothesis (Part I). Amino Acids 2003, 24(1-2):111-117.
13. Cheon M.S., et al. Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain: Challenging the gene dosage effect hypothesis (Part IV). Amino Acids 2003, 25(1):41-47.
14. Cheon M.S., et al. Protein expression of BACE1, BACE2 and APP in Down syndrome brains. Amino Acids 2008, 35(2):339-343.
15. Chrast R., et al. Mice trisomic for a bacterial artificial chromosome with the single-minded 2 gene (Sim2) show phenotypes similar to some of those present in the partial trisomy 16 mouse models of Down syndrome. Human Molecular Genetics 2000, 9(12):1853-1864.
16. Conti A., et al. Altered expression of mitochondrial and extracellular matrix genes in the heart of human fetuses with chromosome 21 trisomy. BMC Genomics 2007, 8:268.
17. Costa V., et al. Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21. PLoS One 2011, 6(4):e18493.
18. de Smith A., Trewick A., Blakemore A. Implications of copy number variation in people with chromosomal abnormalities: Potential for greater variation in copy number state may contribute to variability of phenotype. The HUGO Journal 2010, 4(1):1-9.
19. De Vita S., et al. Trisomic dose of several chromosome 21 genes perturbs haematopoietic stem and progenitor cell differentiation in Down's syndrome. Oncogene 2010, 29(46):6102-6114.
20. Delabar J.M., et al. Molecular mapping of twenty-four features of Down syndrome on chromosome 21. European Journal of Human Genetics 1993, 1(2):114-124.
21. Dermitzakis E.T., et al. Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature 2002, 420(6915):578-582.
22. Draheim C.C., McCubbin J.A., Williams D.P. Differences in cardiovascular disease risk between nondiabetic adults with mental retardation with and without Down syndrome. American Journal of Mental Retardation 2002, 107(3):201-211.
23. Faghihi M.A., et al. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nature Medicine 2008, 14(7):723-730.
24. Feng X., et al. Allele-specific silencing of Alzheimer's disease genes: The amyloid precursor protein genes with Swedish or London mutations. Gene 2006, 371(1):68-74.
25. Ferrando-Miguel R., Cheon M.S., Lubec G. Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain (Part V): Overexpression of phosphatidyl-inositol-glycan class P protein (DSCR5). Amino Acids 2004, 26(3):255-261.
26. Ferrando-Miguel R., et al. Overexpression of transcription factor BACH1 in fetal Down syndrome brain. Journal of Neural Transmission. Supplementum 2003, 67:193-205.
27. Gardiner K. Transcriptional dysregulation in Down syndrome: Predictions for altered protein complex stoichiometries and post-translational modifications, and consequences for learning/behavior genes ELK, CREB, and the estrogen and glucocorticoid receptors. Behavior Genetics 2006, 36(3):439-453.
28. Gardiner K., Davisson M. The sequence of human chromosome 21 and implications for research into Down syndrome. Genome Biology 2000, 1(2). REVIEWS0002.
29. Gardiner-Garden M., Frommer M. CpG islands in vertebrate genomes. Journal of Molecular Biology 1987, 196(2):261-282.
30. Grynberg M., et al. Prenatal diagnosis in monozygotic twins with Down syndrome who had different phenotypes. Prenatal Diagnosis 2007, 27(6):552-554.
31. Gupta R.A., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464(7291):1071-1076.
32. Gusev A., et al. Whole population, genome-wide mapping of hidden relatedness. Genome Research 2009, 19(2):318-326.
33. Harrow J., et al. GENCODE: Producing a reference annotation for ENCODE. Genome Biology 2006, 7(Suppl. 1):S41-S49.
34. Hattori M., et al. The DNA sequence of human chromosome 21. Nature 2000, 405(6784):311-319.
35. Kahlem P., et al. Transcript level alterations reflect gene dosage effects across multiple tissues in a mouse model of Down syndrome. Genome Research 2004, 14(7):1258-1267.
36. Kerkel K., et al. Altered DNA methylation in leukocytes with trisomy 21. PLoS Genetics 2010, 6(11):e1001212.
37. Kocerha J., Kauppinen S., Wahlestedt C. microRNAs in CNS disorders. Neuromolecular Medicine 2009, 11(3):162-172.
38. Korbel J.O., et al. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proceedings of the National Academy of Sciences of the United States of America 2009, 106(29):12031-12036.
39. Korenberg J.R., et al. Molecular definition of a region of chromosome 21 that causes features of the Down syndrome phenotype. The American Journal of Human Genetics 1990, 47(2):236-246.
40. Korenberg J.R., et al. Down syndrome phenotypes: The consequences of chromosomal imbalance. Proceedings of the National Academy of Sciences of the United States of America 1994, 91(11):4997-5001.
41. Kuhn D.E., et al. Human chromosome 21-derived miRNAs are overexpressed in Down syndrome brains and hearts. Biochemical and Biophysical Research Communications 2008, 370(3):473-477.
42. Li C.M., et al. Cell type-specific over-expression of chromosome 21 genes in fibroblasts and fetal hearts with trisomy 21. BMC Medical Genetics 2006, 7:24.
43. Ligon K.L., et al. Olig gene function in CNS development and disease. Glia 2006, 54(1):1-10.
44. Lockstone H.E., et al. Gene expression profiling in the adult Down syndrome brain. Genomics 2007, 90(6):647-660.
45. Lyle R., et al. Gene expression from the aneuploid chromosome in a trisomy mouse model of Down syndrome. Genome Research 2004, 14(7):1268-1274.
46. Lyle R., et al. Genotype-phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21. European Journal of Human Genetics 2009, 17(4):454-466.
47. Mao R., et al. Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart. Genome Biology 2005, 6(13):R107.
48. McKernan K.J., et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research 2009, 19(9):1527-1541.
49. Morrison R.A., et al. Low blood pressure in Down's syndrome, a link with Alzheimer's disease?. Hypertension 1996, 28(4):569-575.
50. Nadel L. Down's syndrome: A genetic disorder in biobehavioral perspective. Genes, Brain, and Behavior 2003, 2(3):156-166.
51. O'Leary D.A., et al. Tissue-specific overexpression of the HSA21 gene GABPalpha: Implications for DS. Biochimica et Biophysica Acta 2004, 1739(1):81-87.
52. Olson L.E., et al. A chromosome 21 critical region does not cause specific Down syndrome phenotypes. Science 2004, 306(5696):687-690.
53. Olson L.E., et al. Trisomy for the Down syndrome 'critical region' is necessary but not sufficient for brain phenotypes of trisomic mice. Human Molecular Genetics 2007, 16(7):774-782.
54. Osato M., Ito Y. Increased dosage of the RUNX1/AML1 gene: A third mode of RUNX leukemia?. Critical Reviews in Eukaryotic Gene Expression 2005, 15(3):217-228.
55. Patel A., et al. Association of variants within APOE, SORL1, RUNX1, BACE1 and ALDH18A1 with dementia in Alzheimer's disease in subjects with Down syndrome. Neuroscience Letters 2011, 487(2):144-148.
56. Pennacchio L.A., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444(7118):499-502.
57. Prandini P., et al. Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance. The American Journal of Human Genetics 2007, 81(2):252-263.
58. Pritchard M.A., Kola I. The "gene dosage effect" hypothesis versus the "amplified developmental instability" hypothesis in Down syndrome. Journal of Neural Transmission. Supplementum 1999, 57:293-303.
59. Pulsifer M.B. The neuropsychology of mental retardation. Journal of the International Neuropsychological Society 1996, 2(2):159-176.
60. Rachidi M., Lopes C. Mental retardation in Down syndrome: From gene dosage imbalance to molecular and cellular mechanisms. Neuroscience Research 2007, 59(4):349-369.
61. Rachidi M., et al. Spatial and temporal localization during embryonic and fetal human development of the transcription factor SIM2 in brain regions altered in Down syndrome. International Journal of Developmental Neuroscience 2005, 23(5):475-484.
62. Rachidi M., et al. A quantitative assessment of gene expression (QAGE) reveals differential overexpression of DOPEY2, a candidate gene for mental retardation, in Down syndrome brain regions. International Journal of Developmental Neuroscience 2009, 27(4):393-398.
63. Robyr D., et al. Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One 2011, 6(3):e17634.
64. Roizen N.J., Patterson D. Down's syndrome. Lancet 2003, 361(9365):1281-1289.
65. Sethupathy P., et al. Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: A mechanism for functional single-nucleotide polymorphisms related to phenotypes. The American Journal of Human Genetics 2007, 81(2):405-413.
66. Shim K.S., Ferrando-Miguel R., Lubec G. Aberrant protein expression of transcription factors BACH1 and ERG, both encoded on chromosome 21, in brains of patients with Down syndrome and Alzheimer's disease. Journal of Neural Transmission. Supplementum 2003, 67:39-49.
67. Silverman W. Down syndrome: Cognitive phenotype. Mental Retardation and Developmental Disabilities Research Reviews 2007, 13(3):228-236.
68. Sommer C.A., et al. Identification of dysregulated genes in lymphocytes from children with Down syndrome. Genome 2008, 51(1):19-29.
69. Stranger B.E., et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315(5813):848-853.
70. Sturgeon X., Gardiner K.J. Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions. Mammalian Genome 2011, 22(5-6):261-271.
71. Sultan M., et al. Gene expression variation in Down's syndrome mice allows prioritization of candidate genes. Genome Biology 2007, 8(5):R91.
72. Takai D., Jones P.A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(6):3740-3745.
73. Telfer M.A., Baker D., Bergman M. Twins, probably monozygotic, displaying Down's syndrome, physical and functional mirror-imaging, and discordance for congenital heart disease. American Journal of Mental Deficiency 1972, 76(4):391-396.
74. Terry R.D. The cytoskeleton in Alzheimer disease. Journal of Neural Transmission. Supplementum 1998, 53:141-145.
75. van Bilsen P.H., et al. Identification and allele-specific silencing of the mutant huntingtin allele in Huntington's disease patient-derived fibroblasts. Human Gene Therapy 2008, 19(7):710-719.
76. Wang J., et al. The diploid genome sequence of an Asian individual. Nature 2008, 456(7218):60-65.
77. Zigman W.B., Lott I.T. Alzheimer's disease in Down syndrome: Neurobiology and risk. Mental Retardation and Developmental Disabilities Research Reviews 2007, 13(3):237-246.
78. Zigman W.B., et al. Alzheimer's disease in adults with Down syndrome. International Review of Research in Mental Retardation 2008, 36:103-145.