Chromosome 21: From sequence to applications

Current Opinion in Genetics and Development

Volumn 11, Issue 3, 2001, Pages 241-246

  Antonarakis, Stylianos E ^a  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENE PRODUCT;

BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME 21; CHROMOSOME 22; CHROMOSOME ARM; DNA FLANKING REGION; DOWN SYNDROME; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENE SEQUENCE; HUMAN; MONOGENIC DISORDER; NONHUMAN; OPEN READING FRAME; PATHOPHYSIOLOGY; PHENOTYPE; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TRISOMY 21;

BACTERIA (MICROORGANISMS);

EID: 0035371176     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(00)00185-4     Document Type: Review

References (58)

1. Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.S., Toyoda A., Ishii K., Totoki Y., Choi D.K., et al. The DNA sequence of human chromosome 21. The chromosome 21 mapping and sequencing consortium. Nature. 405:2000;311-319. In this paper, the (almost) entire sequence of the long arm of human chromosome 21 is described. The sequence is of high quality, covers 33.55 Mb, and includes a gene catalogue of 127 known and 98 predicted genes. This landmark publication is the result of an international collaboration, and concludes intensive efforts carried out over about 5 years. The sequence will provide the infrastructure for many discoveries in the next decade.
2. Lejeune J., Gautier M., Turpin R. Etude des chromosomes somatiques de neuf enfants mongoliens. CR Acad Sci. 248:1959;1721-1722.
3. Lieman-Hurwitz J., Dafni N., Lavie V., Groner Y. Human cytoplasmic superoxide dismutase cDNA clone: a probe for studying the molecular biology of Down syndrome. Proc Natl Acad Sci USA. 79:1982;2808-2811.
4. Kishimoto T.K., O'Conner K., Springer T.A. Leukocyte adhesion deficiency. Aberrant splicing of a conserved integrin sequence causes a moderate deficiency phenotype. J Biol Chem. 264:1989;3588-3595.
5. Warren A.C., Slaugenhaupt S.A., Lewis J.G., Chakravarti A., Antonarakis S.E. A genetic linkage map of 17 markers on human chromosome 21. Genomics. 4:1989;579-591.
6. Chumakov I., Rigault P., Guillou S., Ougen P., Billaut A., Guasconi G., Gervy P., Legall I., Soularue P., Grinas L. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature. 359:1992;380-387.
7. Dunham I., Shimizu N., Roe B.A., Chissoe S., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., et al. The DNA sequence of human chromosome 22. Nature. 402:1999;489-495. This paper describes for the first time the (almost) complete sequence of a human chromosome. This achievement of international collaboration marks the new era of post-sequence medicine. The sequence obtained consists of 12 contiguous segments spanning 33.4 Mb, and comprises at least 545 genes and 134 pseudogenes.
8. Gardiner K., Davisson M.T. The sequence of human chromosome 21 and implications for research in Down syndrome. Genome Biol. 1:2000;2.1-2.9.
9. Deloukas P., Schuler G.D., Gyapay G., Beasley E.M., Soderlund C., Rodriguez-Tome P., Hui L., Matise T.C., McKusick K.B., Beckmann J.S., et al. A physical map of 30 000 human genes. Science. 282:1998;744-746.
10. Ji Y., Eichler E.E., Schwartz S., Nicholls R.D. Structure of chromosomal duplicons and their role in mediating human genomic disorders. Genome Res. 10:2000;597-610.
11. Lynn A., Kashuk C., Petersen M.B., Bailey J.A., Cox D.R., Antonarakis S.E., Chakravarti A. Patterns of meiotic recombination on the long arm of human chromosome 21. Genome Res. 10:2000;1319-1332.
12. Halushka M.K., Fan J.B., Bentley K., Hsie L., Shen N., Weder A., Cooper R., Lipshutz R., Chakravarti A. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet. 22:1999;239-247.
13. Deutsch S., Iseli C., Bucher P., Antonarakis S.E., Scott H.S. A cSNP map and database for human chromosome 21. Genome Res. 11:2001;300-307.
14. Altshuler D., Pollara V.J., Cowles C.R., Van etten W.J., Baldwin J., Linton L., Lander E.S. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature. 407:2000;513-516.
15. Schork N.J., Fallin D., Lanchbury J.S. Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet. 58:2000;250-264.
16. Liu H.X., Cartegni L., Zhang M.Q., Krainer A.R. A mechanism for exon skipping caused by nonsense or missense mutations in BRCA1 and other genes. Nat Genet. 27:2001;55-58. This study describes how missense and silent nucleotide substitutions may cause exon skipping if they occur in splicing enhancer sequences. Every sequence variant is a candidate for causing a differential RNA splicing.
17. Delabar J.M., Theophile D., Rahmani Z., Chettouh Z., Blouin J.L., Prieur M., Noel B., Sinet P.M. Molecular mapping of twenty-four features of Down syndrome on chromosome 21. Eur J Hum Genet. 1:1993;114-124.
18. Brown P.O., Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 21:1999;33-37. A review paper that describes the advantages and the potential uses of the analysis of the transcriptome by cDNA microarrays.
19. Velculescu V.E., Zhang L., Vogelstein B., Kinzler K.W. Serial analysis of gene expression. Science. 270:1995;484-487.
20. Chrast R., Scott H.S., Papasavvas M.P., Rossier C., Antonarakis E.S., Barras C., Davisson M.T., Schmidt C., Estivill X., Dierssen M., Pritchard M., Antonarakis S.E. The mouse brain transcriptome by SAGE: differences in gene expression between P30 brains of the partial trisomy 16 mouse model of down syndrome (Ts65Dn) and normals. Genome Res. 10:2000;2006-2021.
21. Yates J.R. Mass spectrometry. From genomics to proteomics. Trends Genet. 16:2000;5-8.
22. Pandey A., Mann M. Proteomics to study genes and genomes. Nature. 405:2000;837-846. Comprehensive review of the different methods for large-scale analysis of proteins.
23. Macbeath G., Schreiber S.L. Printing proteins as microarrays for high-throughput function determination. Science. 289:2000;1760-1763.
24. Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D., Collins C., Kuo W.L., Chen C., Zhai Y., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 20:1998;207-211.
25. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 409:2001;953-958.
26. Reeves R.H., Irving N.G., Moran T.H., Wohn A., Kitt C., Sisodia S.S., Schmidt C., Bronson R.T., Davisson M.T. A mouse model for Down syndrome exhibits learning and behaviour deficits. Nat Genet. 11:1995;177-184.
27. Baxter L.L., Moran T.H., Richtsmeier J.T., Troncoso J., Reeves R.H. Discovery and genetic localization of Down syndrome cerebellar phenotypes using the Ts65Dn mouse. Hum Mol Genet. 9:2000;195-202.
28. Costa A.C., Walsh K., Davisson M.T. Motor dysfunction in a mouse model for Down syndrome. Physiol Behav. 68:1999;211-220.
29. Escorihuela R.M., Vallina I.F., Martinez-Cue C., Baamonde C., Dierssen M., Tobena A., Florez J., Fernandez-Teruel A. Impaired short- and long-term memory in Ts65Dn mice, a model for short and long-term memory in Ts65Dn mice, a model for Down syndrome. Neurosci Lett. 247:1998;171-174.
30. Sago H., Carlson E.J., Smith D.J., Kilbridge J., Rubin E.M., Mobley W.C., Epstein C.J., Huang T.T. Ts1Cje, a partial trisomy 16 mouse model for Down syndrome, exhibits learning and behavioral abnormalities. Proc Natl Acad Sci USA. 95:1998;6256-6261.
31. Sago H., Carlson E.J., Smith D.J., Rubin E.M., Crnic L.S., Huang T.T., Epstein C.J. Genetic dissection of region associated with behavioral abnormalities in mouse models for down syndrome. Pediatr Res. 48:2000;606-613.
32. Herault Y., Rassoulzadegan M., Cuzin F., Duboule D. Engineering chromosomes in mice through targeted meiotic recombination (TAMERE). Nat Genet. 20:1998;381-384.
33. Zheng B., Sage M., Sheppeard E.A., Jurecic V., Bradley A. Engineering mouse chromosomes with Cre-loxP: range, efficiency, and somatic applications. Mol Cell Biol. 20:2000;648-655.
34. Maroun L.E., Heffernan T.N., Hallam D.M. Partial IFN-alpha/beta and IFN-γ receptor knockout trisomy 16 mouse fetuses show improved growth and cultured neuron viability. J Interferon Cytokine Res. 20:2000;197-203.
35. Chrast R., Scott H.S., Madani R., Huber L., Wolfer D.P., Prinz M., Aguzzi A., Lipp H.P., Antonarakis S.E. 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. Hum Mol Genet. 9:2000;1853-1864. Using BAC clones, the authors create single-gene transgenic mice with well-controlled overexpression from one extra copy of the transgene. Their method results in the physiological overexpression of the transgene.
36. Epstein C.J., Avraham K.B., Lovett M., Smith S., Elroy-Stein O., Rotman G., Bry C., Groner Y. Transgenic mice with increased Cu/Zn-superoxide dismutase activity: animal model of dosage effects in Down syndrome. Proc Natl Acad Sci USA. 84:1987;8044-8048.
37. Sumarsono S.H., Wilson T.J., Tymms M.J., Venter D.J., Corrick C.M., Kola R., Lahoud M.H., Papas T.S., Seth A., Kola I. Down's syndrome-like skeletal abnormalities in Ets2 transgenic mice. Nature. 379:1996;534-537.
38. Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides S.E.P.G., Scherer P.W., Li R.A., Hoskins G.A.L.L.E. R.F., et al. The genome sequence of Drosophila melanogaster. Science. 287:2000;2185-2195. The gene catalogue of Drosophila described in this landmark paper (~13 600 genes) will advance the functional characterization of human gene products that are homologous to the flyproteins.
39. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 282:1998;2012-2018.
40. Anonymous. The yeast genome directory. Nature. 387:1997;5.
41. Gonczy P., Echeverri G., Oegema K., Coulson A., Jones S.J., Copley R.R., Duperon J., Oegema J., Brehm M., Cassin E., et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature. 408:2000;331-336. The studies described in 41••, 42•• provide a large-scale functional analysis of C. elegans proteins using double-stranded RNA interference. Approximately 90% of the predicted genes on chromosomes I and III of the worm have been investigated.
42. Fraser A.G., Kamath R.S., Zipperlen P., Martinez-Campos M., Sohrmann M., Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 408:2000;325-330. See annotation for Gonczy et al. 41••.
43. Ross-MacDonald P., Coelho P.S., Roemer T., Agarwal S., Kumar A., Jansen R., Cheung K.H., Sheehan A., Symoniatis D., Umansky L., Heidtman M., et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 402:1999;413-418. This study describes the functional characteristics of systematic gene description in yeast, and provides a way to understand the cellular consequences of the gene deletions of homologous human genes.
44. Pennacchio L.A., Lehesjoki A.E., Stone N.E., Willour V.L., Virtaneva K., Miao J., D'Amato E., Ramirez L., Faham M., Koskiniemi M., et al. Mutations in the gene encoding cystatin B in progressive myoclonus epilepsy (EPM1). Science. 271:1996;1731-1734.
45. Nagamine K., Peterson P., Scott H.S., Kudoh J., Minoshima S., Heino M., Krohn K.J., Lalioti M.D., Mullis P.E., Antonarakis S.E., et al. Positional cloning of the APECED gene. Nat Genet. 17:1997;393-398.
46. Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy: An autoimmune disease, APECED, caused by mutations in a novel gene featuring two PHD-type zinc-finger domains. Nat Genet. 17:1997;399-403.
47. Song W.J., Sullivan M.G., Legare R.D., Hutchings S., Tan X., Kufrin D., Ratajczak J., Resende I.C., Haworth C., Hock R., et al. Haploinsufficiency of CBFA2 causes familial thrombocytopenia with propensity to develop acute myelogenous leukaemia. Nat Genet. 23:1999;166-175.
48. Sertie A.L., Sossi V., Camargo A.A., Zatz M., Brahe C., Passos-Bueno M.R. Collagen XVIII, containing an endogenous inhibitor of angiogenesis and tumor growth, plays a critical role in the maintenance of retinal structure and in neural tube closure (Knobloch syndrome). Hum Mol Genet. 9:2000;2051-2058.
49. Scott H.S., Kudoh J., Wattenhofer M., Shibuya K., Berry A., Chrast R., Guipponi M., Wang J., Kawasaki K., Asakawa S., et al. Insertion of beta-satellite repeats identifies a transmembrane protease causing both congenital and childhood onset autosomal recessive deafness. Nat Genet. 27:2001;59-63.
50. Wilcox E.R., Burton Q.L., Naz S., Riazuddin S., Smith T.N., Ploplis B., Belyatseva I., Ben-Yosef T., Liburd N.A., Morell R.J., et al. Mutations in the gene encoding tight junction claudin-14 cause recessive deafness DFNB29. Cell. 104:2001;165-172.
51. Straub R.E., Lehner T., Luo Y., Loth J.E., Shao W., Sharpe L., Alexander J.R., Das K., Simon R., Fieve R.R. A possible vulnerability locus for bipolar affective disorder on chromosome 21q22.3. Nat Genet. 8:1994;291-296.
52. Pajukanta P., Terwilliger J.D., Perola M., Hiekkalinna T., Nuotio I., Ellonen P., Parkkonen M., Hartiala J., Ylitalo K., Pihlajamaki J., et al. Genomewide scan for familial combined hyperlipidemia genes in finnish families, suggesting multiple susceptibility loci influencing triglyceride, cholesterol, and apolipoprotein B levels. Am J Hum Genet. 64:1999;1453-1463.
53. Zipursky A., Brown E.J., Christensen H., Doyle J. Transient myeloproliferative disorder (transient leukemia) and hematologic manifestations of Down syndrome. Clin Lab Med. 19:1999;157-167.
54. Iselius L., Jacobs P., Morton N. Leukaemia and transient leukaemia in Down syndrome. Hum Genet. 85:1990;477-485.
55. Hasle H., Clemmensen I.H., Mikkelsen M. Risks of leukaemia and solid tumours in individuals with Down's syndrome. Lancet. 355:2000;165-169.
56. Risch N.J. Searching for genetic determinants in the new millennium. Nature. 405:2000;847-856. Thesec two papers 56•, 57• comprehensively review the theory and practice of using the nucleotide variation of the human genome to detect functionally important determinants of common complex human phenotypes.
57. Weiss K.M., Terwilliger J.D. How many diseases does it take to map a gene with SNPs? Nat Genet. 26:2000;151-157. See annotation for Risch 56•.
58. Horikawa Y., Oda N., Cox N.J., Li X., Orho-Melander M., Hara M., Hinokio Y., Lindner T.H., Mashima H., Schwarz P.E., et al. Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet. 26:2000;163-175. An example of the discovery of functional polymorphic variants associated with type 2 diabetes mellitus.