Duplications on human chromosome 22 reveal a novel Ret finger protein-like gene family with sense and endogenous antisense transcripts

Genome Research

Volumn 9, Issue 9, 1999, Pages 803-814

  Seroussi, Eyal ^a   Kedra, Darek ^a   Pan, Hua Qin ^b   Peyrard, Myriam ^a   Schwartz, Charles ^c   Scambler, Peter ^d   Donnai, Dian ^e   Roe, Bruce A ^b   Dumanski, Jan P ^a  

^a KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^b UNIVERSITY OF OKLAHOMA   (United States)

^c GREENWOOD GENETIC CENTER   (United States)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

^e ST MARY S HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; COMPLEMENTARY RNA; MESSENGER RNA;

ARTICLE; AUTOSOMAL DOMINANT INHERITANCE; CHROMOSOME 22Q; CHROMOSOME 6; CHROMOSOME DUPLICATION; GENE EXPRESSION REGULATION; GENETIC LINKAGE; GENETIC POLYMORPHISM; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PSEUDOGENE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ADAPTOR PROTEIN COMPLEX 1; ADAPTOR PROTEIN COMPLEX BETA SUBUNITS; AMINO ACID SEQUENCE; BASE SEQUENCE; CARRIER PROTEINS; CHROMOSOMES, HUMAN, PAIR 22; CONTIG MAPPING; DNA, ANTISENSE; FEMALE; GENE DUPLICATION; HUMANS; MALE; MEMBRANE PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PEDIGREE; POLYMORPHISM, GENETIC; PSEUDOGENES; SEQUENCE HOMOLOGY, AMINO ACID; SYNDROME; TISSUE DISTRIBUTION; TRANSCRIPTION, GENETIC;

EID: 0032856327     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.9.9.803     Document Type: Article

References (55)

1. Ando, H., N. Mizuki, M. Ota, M. Yamazaki, S. Ohno, K. Goto, Y. Miyata, K. Wakisaka, S. Bahram, and H. Inoko. 1997. Allelic variants of the human MHC class I chain-related B gene (MICB). Immunogenetics 46: 499-508.
2. Bodenteich, A., S. Chissoe, Y.F. Wang, and B.A. Roe. 1994. Shotgun cloning as the strategy of choice to generate templates for high-throughput dideoxynucleotide sequencing. In Automated DNA sequencing and analysis techniques (ed. C. Venter), pp. 42-50. Academic Press, London, UK.
3. Borden, K.L. and P.S. Freemont. 1996. The RING finger domain: A recent example of a sequence-structure family. Curr. Opin. Struct. Biol. 6: 395-401.
4. Borden, K.L., J.M. Lally, S.R. Martin, N.J. O'Reilly, E. Solomon, and P.S. Freemont. 1996. In vivo and in vitro characterization of the B1 and B2 zinc-binding domains from the acute promyelocytic leukemia protooncoprotein PML. Proc. Natl. Acad. Sci. 93: 1601-1606.
5. Bruder, C.E.G., K. Ichimura, E. Blennow, T. Ikeuchi, T. Yamaguchi, Y. Yuasa, V.P. Collins, and J.P. Dumanski. 1999. Severe phenotype of the neurofibromatosis type 2 in a patient with a 7.4 Mbp constitutional deletion on chromosome 22; possible localization of a neurofibromatosis type 2 modifier gene? Genes, Chromosomes, Cancer 25: 184-1900.
6. Cao, T., E. Duprez, K.L. Borden, P.S. Freemont, and L.D. Etkin. 1998. Ret finger protein is a normal component of PML nuclear bodies and interacts directly with PML. J. Cell Sci. 111: 1319-1329.
7. Caudevilla, C., D. Serra, A. Miliar, C. Codony, G. Asins, M. Bach, and F.G. Hegardt. 1998. Natural trans-splicing in carnitine octanoyltransferase pre-mRNAs in rat liver. Proc. Natl. Acad. Sci. 95: 12185-12190.
8. Chissoe, S.L., Y.F. Wang, S.W. Clifton, N.T. Ma, H.J. Sun, J.S. Lobsinger, S.M. Kenton, J.D. White, and B.R. Roe. 1991. Strategies for rapid and accurate DNA sequencing. Methods Companion Methods Enzymol. 3: 55-65.
9. Collins, J.E., C.G. Cole, L.J. Smink, C.L. Garrett, M.A. Leversha, C.A. Soderlund, G.L. Maslen, L.A. Everett, K.M. Rice, A.J. Coffey et al. 1995. A high resolution integrated yeast artificial chromosome clone map of human chromosome 22. Nature 377: 367-379.
10. Collins, J.E., A.J. Mungall, K.L. Badcock, J.M. Fay, and I. Dunham. 1997. The organization of the gamma-glutamyl transferase genes and other low copy repeats in human chromosome 22q11. Genome Res. 7: 522-531.
11. Dandekar, T. and P.R. Sibbald. 1990. Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates. Nucleic Acids Res. 18: 4719-4725.
12. Delattre, O., J. Zuckman, B. Plougastel, C. Desmaze, T. Melot, M. Peter, H. Kovar, I. Joubert, P. de Jong, G. Rouleau, A. Aurias, and G. Thomas. 1992. Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours. Nature 359: 162-165.
13. Deutscher, S.L., J.B. Harley, and J.D. Keene. 1988. Molecular analysis of the 60-kDa human Ro ribonucleoprotein. Proc. Natl. Acad. Sci. 85: 9479-9483.
14. Dolnick, B.J. 1997. Naturally occurring antisense RNA. Pharmacol. Therap. 75: 179-184.
15. Farndon, P.A. and D. Donnai. 1983. Male to male transmission of the G syndrome. Clin. Genet. 24: 446-448.
16. Feinberg, A.P. and B. Vogelstein. 1984. A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Addendum. Anal. Biochem. 137: 266-267.
17. Halford, S., E. Lindsay, M. Nayudu, A.H. Carey, A. Baldini, and P.J. Scambler. 1993. Low-copy-number repeat sequences flank the DiGeorge/velo-cardio-facial syndrome loci at 22q11. Hum. Mol. Genet. 2: 191-196.
18. Henry, J., M. Ribouchon, D. Depetris, M. Mattei, C. Offer, R. Tazi-Ahnini, and P. Pontarotti. 1997. Cloning, structural analysis, and mapping of the B30 and B7 multigenic families to the major histocompatibility complex (MHC) and other chromosomal regions. Immunogenetics 46: 383-395.
19. Kedra, D., E. Seroussi, I. Fransson, J. Trifunovic, M. Clark, J. Lagercrantz, E. Blennow, H. Mehlin, and J.P. Dumanski. 1997. The germinal center kinase gene and a novel CDC25-like gene are located in the vicinity of PYGM gene on 11q13. Hum. Genet. 100: 611-619.
20. Kimelman, D. and M.W. Kirschner. 1989. An antisense mRNA directs the covalent modification of the transcript encoding fibroblast growth factor in Xenopus oocytes. Cell 59: 687-696.
21. Knee, R.S., S.E. Pitcher, and P.R. Murphy. 1994. Basic fibroblast growth factor sense (FGF) and antisense (gfg) RNA transcripts are expressed in unfertilized human oocytes and in differentiated adult tissues. Biochem. Biophys. Res. Cumm. 205: 577-583.
22. Konarska, M.M., R.A. Padgett, and P.A. Sharp. 1985. Trans splicing of mRNA precursors in vitro. Cell 42: 165-171.
23. Kozak, M. 1996. Interpreting cDNA sequences: Some insights from studies on translation. Mamm. Genome 7: 563-574.
24. Krystal, G.W., B.C. Armstrong, and J.F. Battey. 1990. N-myc mRNA forms an RNA-RNA duplex with endogenous antisense transcripts. Mol. Cell. Biol. 10: 4180-4191.
25. Lacassie, Y. and M.I. Arriaza. 1996. Opitz GBBB syndrome and the 22q11.2 deletion. Am. J. Med. Genet. 62: 3180.
26. Lee, R.C., R.L. Feinbaum, and V. Ambros. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
27. Lees, J.F., P.S. Shneidman, S.F. Skuntz, M.J. Carden, and R.A. Lazzarini. 1988. The structure and organization of the human heavy neurofilament subunit (NF-H) and the gene encoding it. EMBO J. 7: 1947-1955.
28. Lupas, A., D.M. Van, and J. Stock. 1991. Predicting coiled coils from protein sequences. Science 252: 1162-1164.
29. Mazoyer, S., A.M. Dunning, O. Serova, J. Dearden, N. Puget, C.S. Healey, S.A. Gayther, J. Mangion, M.R. Stratton, H.T. Lynch et al. 1996. A polymorphic stop codon in BRCA2. Nat. Genet. 14: 253-254.
30. Mazzarella, R. and D. Schlessinger. 1997. Duplication and distribution of repetitive elements and non-unique regions in the human genome. Gene 205: 29-38.
31. McDonald-McGinn, D.M., D.A. Driscoll, L. Bason, K. Christensen, D. Lynch, K. Sullivan, D. Canning, W. Zavod, N. Quinn, J. Rome et al. 1995. Autosomal dominant "Opitz" GBBB syndrome due to a 22q11.2 deletion. Am. J. Med. Genet. 59: 103-113.
32. Peyrard, M., I. Fransson, Y.-G. Xie, F.-Y. Han, M.H. Ruttledge, S. Swahn, J.E. Collins, I. Dunham, V.P. Collins, and J.P. Dumanski. 1994. Characterization of a new member of the human β-adaptin gene family from chromosome 22q12, a candidate meningioma gene. Hum. Mol. Genet. 3: 1393-1399.
33. Peyrard, M., H.Q. Pan, D. Kedra, I. Fransson, S. Swahn, K. Hartman, S.W. Clifton, B.A. Roe, and J.P. Dumanski. 1996. Structure of the promoter and genomic organization of the human beta′-adaptin gene (BAM22) from chromosome 22q12. Genomics 36: 112-117.
34. Pruijn, G.J., F.H. Simons, and W.J. van Venrooij. 1997. Intracellular localization and nucleocytoplasmic transport of Ro RNP components. Eur. J. Cell Biol. 74: 123-132.
35. Puech, A., B. Saint-Jore, B. Funke, D.J. Gilbert, H. Sirotkin, N.G. Copeland, N.A. Jenkins, R. Kucherlapati, B. Morrow, and A.I. Skoultchi. 1997. Comparative mapping of the human 22q11 chromosomal region and the orthologous region in mice reveals complex changes in gene organization. Proc. Natl. Acad. Sci. 94: 14608-14613.
36. Quaderi, N.A., S. Schweiger, K. Gaudenz, B. Franco, E.I. Rugarli, W. Berger, G.J. Feldman, M. Volta, G. Andolfi, S. Gilgenkrantz et al. 1997. Opitz g/bbb syndrome, a defect of midline development, is due to mutations in a new ring finger gene on Xp22. Nat. Genet. 17: 285-291.
37. Robertson, N.G., R.J. Pomponio, G.L. Mutter, and C.C. Morton. 1991. Testis-specific expression of the human MYCL2 gene. Nucleic Acids Res. 19: 3129-3137.
38. Robin, N.H., G.J. Feldman, A.L. Aronson, H.F. Mitchell, R. Weksberg, C.O. Leonard, B.K. Burton, K.D. Josephson, R. Laxova, K.A. Aleck et al. 1995. Opitz syndrome is genetically heterogeneous, with one locus on Xp22, and a second locus on 22q11.2. Nat. Genet. 11: 459-461.
39. Ruddy, D.A., G.S. Kronmal, V.K. Lee, G.A. Mintier, L. Quintana, R.J. Domingo, N.C. Meyer, A. Irrinki, E.E. McClelland, A. Fullan et al. 1997. A 1.1-Mb transcript map of the hereditary hemochromatosis locus. Genome Res. 7: 441-456.
40. Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
41. Sanson, M., C. Marineau, C. Desmaze, M. Luthman, M. Ruttledge, C. Baron, S. Narod, O. Delattre, G. Lenoir, G. Thomas et al. 1993. Germline deletion in a neurofibromatosis type 2 kindred inactivates the NF2 gene and a candidate meningioma locus. Hum. Mol. Genet. 2: 1215-1220.
42. Scambler, P.J. 1993. Deletions of human chromosome 22 and associated birth defects. Curr. Opin. Genet. Dev. 3: 432-437.
43. Seroussi, E., H.-Q. Pan, D. Kedra, B. Roe, and J.P. Dumanski. 1998. Characterization of the human NIPSNAP1 gene from 22q12: A member of a novel gene family. Gene 212: 13-20.
44. Staden, R., Ed. 1994. The Staden package. Methods in molecular biology. Humana Press, Totawa, NJ.
45. Takahashi, M., Y. Inaguma, H. Hiai, and F. Hirose. 1988. Developmentally regulated expression of a human "finger"-containing gene encoded by the 5′ half of the ret transforming gene. Mol. Cell. Biol. 8: 1853-1856.
46. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The CLUSTAL:X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Adds Res. 25: 4876-4882.
47. +/glucose cotransporter gene SGLT1 to chromosome 22q13.1. Genomics 17: 752-754.
48. Vanhee-Brossollet, C. and C. Vaquero. 1998. Do natural antisense transcripts make sense in eukaryotes? Gene 211: 1-9.
49. Vernet, C., J. Boretto, M.G. Mattei, M. Takahashi, L.J. Jack, I.H. Mather, S. Rouquier, and P. Pontarotti. 1993. Evolutionary study of multigenic families mapping close to the human MHC class I region. J. Mol. Evol. 37: 600-612.
50. Wagner, E.G. and R.W. Simons. 1994. Antisense RNA control in bacteria, phages, and plasmids. Ann. Rev. Microbiol. 48: 713-742.
51. Watson, C.J., L. Gaunt, G. Evans, K. Patel, R. Harris, and T. Strachan. 1993. A disease associated germline deletion maps the type 2 neurofibromatosis (NF2) gene between the Ewing sarcoma region and the leukemia inhibitory factor locus. Hum. Mol. Genet. 2: 701-704.
52. Wightman, B., I. Ha, and G. Ruvkun. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
53. Wolf, E., P.S. Kim, and B. Berger. 1997. MultiCoil: A program for predicting two- and three-stranded coiled coils. Protein Sci. 6: 1179-1189.
54. Xie, Y.-G., F.-Y. Han, M. Peyrard, M.H. Ruttledge, I. Fransson, P. DeJong, J. Collins, I. Dunham, M. Nordenskjöld, and J.P. Dumanski. 1993. Cloning of a novel, anonymous gene from a megabase-range YAC and cosmid contig in the neurofibromatosis type 2/meningioma region on human chromosome 22q12. Hum. Mol. Genet. 2: 1361-1368.
55. Zucman-Rossi, J., P. Legoix, and G. Thomas. 1996. Identification of new members of the gas2 and ras families in the 22q12 chromosome region. Genomics 38: 247-254.