Juxta-centromeric region of human chromosome 21 is enriched for pseudogenes and gene fragments

Gene

Volumn 239, Issue 1, 1999, Pages 55-64

  Ruault, Myriam ^a   Trichet, Valérie ^a   Gimenez, Sylvie ^a   Boyle, Shelagh ^b   Gardiner, Kathleen ^c   Rolland, Morgane ^a   Roizès, Gérard ^a   De Sario, Albertina ^a  

^a INSTITUTE OF HUMAN GENETICS   (France)

^b WESTERN GENERAL HOSPITAL   (United Kingdom)

^c UNIVERSITY OF DENVER   (United States)

Author keywords

BACs; cDNAs; Pericentric duplication; Pseudogenes

Indexed keywords

COMPLEMENTARY DNA; DNA FRAGMENT;

ARTICLE; CHROMOSOME 21; CHROMOSOME MAP; DNA LIBRARY; GENETIC ANALYSIS; HUMAN; NORMAL HUMAN; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PSEUDOGENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ANIMALS; BASE COMPOSITION; BLOTTING, SOUTHERN; CACO-2 CELLS; CELL LINE; CENTROMERE; CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; CHROMOSOMES, HUMAN, PAIR 21; CONTIG MAPPING; CPG ISLANDS; CYTOSINE; DNA; DNA, COMPLEMENTARY; GENES; GUANINE; HELA CELLS; HUMANS; HYBRID CELLS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICE; POLYMERASE CHAIN REACTION; PSEUDOGENES; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TUMOR CELLS, CULTURED;

EID: 0032830318     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(99)00381-9     Document Type: Article

References (30)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic Local Alignment Search Tool. J. Mol. Biol. 215:1990;403-410.
2. Antonarakis S.E. 10 years of genomics, chromosome 21 and Down Syndrome. Genomics. 51:1998;1-16.
3. Bailey L.C., Fischer S., Schug J., Crabtree J., Gibson M., Overton C. GAIA: framework annotation of genomic sequence. Genome Res. 8:1998;234-250.
4. Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:1997;78-94.
5. Chen H., Chrast R., Rossier C., Morris M.A., Lalioti M.D., Antonarakis S.E. Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping. Genome Res. 6:1996;747-760.
6. Chumakov I., et al. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature. 359:1992;380-387.
7. Collins J.E., Mungall A.J., Badcock K.L., Fay J.M., Dunham I. The organization of the γ-glutamyl transferase genes and other low copy repeats in human chromosome 22q11. Genome Res. 7:1997;522-531.
8. De Sario A., Roizès G., Allegre N., Bernardi G. A compositional map of the cen-q21 region of human chromosome 21. Gene. 194:1997;107-113.
9. Dubois B.L., Naylor S. Characterization of NIGMS human/rodent somatic cell hybrid mapping panel 2 by PCR. Genomics. 16:1993;315-319.
10. Dutriaux A., Rossier J., Van Hul W., Nizetic D., Theophille D., Delabar J.M., Van Broeckhoven C., Potier M.C. Cloning and characterization of a 135- to 500-kb region of homology on the long arm of human chromosome 21. Genomics. 22:1994;472-477.
11. Eichler E.E. Masquerading repeats: paralogous pitfalls of the human genome. Genome Res. 8:1998;758-762.
12. Fantes J.A., Bickmore W.A., Fletcher J.M., Ballesta F., Hanson I.M., van Heyningen V. Submicroscopic deletions at the WAGR locus, revealed by nonradioactive in situ hybridization. Am. J. Hum. Genet. 51:1992;1286-1294.
13. Flint J., Thomas K., Micklem G., Raynham H., Clark K., Doggett N.A., King A., Higgs D.R. The relationship between chromosome structure and function at a human telomeric region. Nat. Genet. 15:1997;252-257.
14. Gardiner K., Graw S., Ichikawa H., Ohki M., Joetham A., Gervy P., Chumakov I., Patterson D. YAC analysis and minimal tiling path construction for chromosome 21q. Somat. Cell Mol. Genet. 21:1995;399-414.
15. Gardiner K. Clonability and gene distribution on human chromosome 21: reflections of junk DNA content? Gene. 205:1997;39-46.
16. Groet J., Ives J.H., South A.P., Baptista P.R., Jones T.A., Yaspo M.L., Lehrach H., Potier M.C., Van Broeckhoven C., Nizetic D. Bacterial contig map of the 21q11 region associated with Alzheimer's disease and abnormal myelopoiesis in Down Syndrome. Genome Res. 8:1998;385-398.
17. Jackson M., Rocchi M., Thompson G., Hearn T., Crosier M., Guy J., Kirk D., Mulligan L., Ricco A., Piccininni S., Marzella R., Viggiano L., Archidiacono N. Sequences flanking the centromere of human chromosome 10 are a complex patchwork of arm-specific sequences, stable duplications and unstable sequences with homologies to telomeric and other centromeric locations. Hum. Mol. Genet. 8:1999;205-215.
18. Jurka J., Klonowski P., Dagman V., Pelton P. CENSOR a program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 20:1996;119-122.
19. Korenberg J.R., et al. Down syndrome phenotypes: the consequences of chromosome imbalance. Proc. Natl. Acad. Sci. USA. 91:1994;4997-5001.
20. Korenberg J.R., Chen X.N., Mitchell S., Fannin S., Gerwehr S., Cohen D., Chumakov I. A high-fidelity physical map of human chromosome 21q in Yeast Artificial Chromosomes. Genome Res. 5:1995;427-443.
21. Puechberty J., Laurent A.M., Gimenez S., Billault A., Brun M.E., Calenda A., Marçais B., Prades C., Ioannou P., Yurov Y., Roizès G. Genetic and physical analyses of the centromeric and pericentromeric regions of human chromosome 5: recombination across 5cen. Genomics. 5:1999;274-287.
22. Regnier V., Meddeb M., Lecointre G., Richard F., Duvergner A., Nguyen V., Dutrillaux B., Danglot G. Emergence and scattering of multiple neurofibromatosis (NF1)-related sequences during hominoid evolution suggest a process of pericentromeric interchromosomal transposition. Hum. Mol. Genet. 6:1997;9-16.
23. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edition :1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
24. Saupe S., Roizès G., Peter M., Boyle S., Gardiner K., De Sario A. Molecular cloning of a human cDNA IGSF3 encoding an Immunoglobulin-like membrane protein: expression and mapping to chromosome 1p13. Genomics. 52:1998;305-311.
25. Soriano P., Meunier-Rotival M., Bernardi G. The distribution of interspersed repeats is non uniform and conserved in the mouse and human genomes. Proc. Natl. Acad. Sci. USA. 80:1983;1816-1820.
26. Tassone F., Xu H., Burkin H., Weissman S., Gardiner K. cDNA selection from 10 Mb of chromosome 21 DNA: efficiency in transcriptional mapping and reflections of genome organization. Hum. Mol. Genet. 4:1995;1509-1518.
27. Trowell H., Nagy A., Vissel K.H., Choo A. Long-range analyses of the centromeric regions of human chromosomes 13, 14 and 21: identification of a narrow domain containing two key centromeric DNA elements. Hum. Mol. Genet. 2:1993;1639-1649.
28. Uberbacher E.C., Mural R. Locating protein coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA. 88:1991;11261-11265.
29. Xu H., Wei H., Tassone F., Graw S., Gardiner K., Weissman S.M. A search for genes from the dark band regions of human chromosome 21. Genomics. 27:1995;1-8.
30. Zimonjic D.B., Kelley M.J., Rubin J.S., Aaronson S.A., Popescu N.C. Fluorescence in situ hybridization analysis of keratinocyte growth factor gene amplification and dispersion in evolution of great apes and humans. Proc. Natl. Acad. Sci. USA. 21:1997;11461-11465.