Intergenic transcripts in genes with phase I introns

Genomics

Volumn 85, Issue 4, 2005, Pages 431-440

  Královičová, Jana ^a   Vořechovský, Igor ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

Exon; HLA; Intergenic; Lymphocytes; MHC; mRNA; RNA surveillance; Splicing

Indexed keywords

CHIMERIC PROTEIN; COMPLEMENTARY DNA; HLA ANTIGEN CLASS 2; MESSENGER RNA; POLYADENYLIC ACID; RNA DIRECTED DNA POLYMERASE; SPACER DNA; TAQ POLYMERASE;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA TEMPLATE; EXON; GENE; GENETIC TRANSCRIPTION; HLA SYSTEM; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; IN VIVO STUDY; LYMPHOCYTE; PLASMID; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 15244338515     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2004.12.001     Document Type: Article

References (50)

1. E.S. Lander Initial sequencing and analysis of the human genome Nature 409 2001 860 921
2. J.C. Venter The sequence of the human genome Science 291 2001 1304 1351
3. D.L. Black Protein diversity from alternative splicing: a challenge for bioinformatics and postgenome biology Cell 103 2000 367 370
4. J.M. Nigro Scrambled exons Cell 64 1991 607 613
5. C. Cocquerelle, P. Daubersies, M.A. Majerus, J.P. Kerckaert, and B. Bailleul Splicing with inverted order of exons occurs proximal to large introns EMBO J. 11 1992 1095 1098
6. J. Crawford The PISSLRE gene: structure, exon skipping, and exclusion as tumor suppressor in breast cancer Genomics 56 1999 90 97
7. G. Flouriot, H. Brand, B. Seraphin, and F. Gannon Natural trans-spliced mRNAs are generated from the human estrogen receptor-alpha (hERalpha) gene J. Biol. Chem. 277 2002 26244 26251
8. C. Caudevilla Natural trans-splicing in carnitine octanoyltransferase pre-mRNAs in rat liver Proc. Natl. Acad. Sci. U.S.A. 95 1998 12185 12190
9. R. Rigatti, J.H. Jia, N.J. Samani, and I.C. Eperon Exon repetition: a major pathway for processing mRNA of some genes is allele-specific Nucleic. Acids Res. 32 2004 441 446
10. M. Labrador Protein encoding by both DNA strands Nature 409 2001 1000
11. B. Lehner, G. Williams, R.D. Campbell, and C.M. Sanderson Antisense transcripts in the human genome Trends Genet. 18 2002 63 65
12. S. Fears Intergenic splicing of MDS1 and EVI1 occurs in normal tissues as well as in myeloid leukemia and produces a new member of the PR domain family Proc. Natl. Acad. Sci. U.S.A. 93 1996 1642 1647
13. T.K. Chatterjee, and R.A. Fisher Novel alternative splicing and nuclear localization of human RGS12 gene products J. Biol. Chem. 275 2000 29660 29671
14. C. Finta, and P.G. Zaphiropoulos Intergenic mRNA molecules resulting from trans-splicing J. Biol. Chem. 277 2002 5882 5890
15. B. Tasic Promoter choice determines splice site selection in protocadherin alpha and gamma pre-mRNA splicing Mol. Cell 10 2002 21 33
16. T. Horiuchi, E. Giniger, and T. Aigaki Alternative trans-splicing of constant and variable exons of a Drosophila axon guidance gene, lola Genes Dev. 17 2003 2496 2501
17. F. Magrangeas Cotranscription and intergenic splicing of human galactose-1-phosphate uridylyltransferase and interleukin-11 receptor alpha-chain genes generate a fusion mRNA in normal cells: implication for the production of multidomain proteins during evolution J. Biol. Chem. 273 1998 16005 16010
18. R.C. Moore Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel J. Mol. Biol. 292 1999 797 817
19. J.K. Millar, S. Christie, C.A. Semple, and D.J. Porteous Chromosomal location and genomic structure of the human translin-associated factor X gene (TRAX; TSNAX) revealed by intergenic splicing to DISC1, a gene disrupted by a translocation segregating with schizophrenia Genomics 67 2000 69 77
20. D. Communi, N. Suarez-Huerta, D. Dussossoy, P. Savi, and J.M. Boeynaems Cotranscription and intergenic splicing of human P2Y11 and SSF1 genes J. Biol. Chem. 276 2001 16561 16566
21. F. Poulin, A. Brueschke, and N. Sonenberg Gene fusion and overlapping reading frames in the mammalian genes for 4E-BP3 and MASK J. Biol. Chem. 278 2003 52290 52297
22. J. Eul, M. Graessmann, and A. Graessmann Experimental evidence for RNA trans-splicing in mammalian cells EMBO J. 14 1995 3226 3235
23. R. Dorn, G. Reuter, and A. Loewendorf Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila Proc. Natl. Acad. Sci. U.S.A. 98 2001 9724 9729
24. J. Eul, M. Graessmann, and A. Graessmann In vitro synthesized SV40 cRNA is trans-spliced after microinjection into the nuclei of mammalian cells FEBS Lett. 394 1996 227 232
25. X.C. Zeng, and S.X. Wang Evidence that BmTXK beta-BmKCT cDNA from Chinese scorpion Buthus martensii Karsch is an artifact generated in the reverse transcription process FEBS Lett. 520 2002 183 185
26. J. Trowsdale "Both man & bird & beast": comparative organization of MHC genes Immunogenetics 41 1995 1 17
27. J. Robinson IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex Nucleic Acids Res. 31 2003 311 314
28. G.X. Luo, and J. Taylor Template switching by reverse transcriptase during DNA synthesis J. Virol. 64 1990 4321 4328
29. S. Paabo, D.M. Irwin, and A.C. Wilson DNA damage promotes jumping between templates during enzymatic amplification J. Biol. Chem. 265 1990 4718 4721
30. A.K. Arvidsson Characterization of three separated exons in the HLA class II DR region of the human major histocompatibility complex Hum. Immunol. 42 1995 254 264
31. C. Biernaux, M. Loos, A. Sels, G. Huez, and P. Stryckmans Detection of major bcr-abl gene expression at a very low level in blood cells of some healthy individuals Blood 86 1995 3118 3122
32. A.B. Chetverin, H.V. Chetverina, A.A. Demidenko, and V.I. Ugarov Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure Cell 88 1997 503 513
33. A.N. Akopian Trans-splicing of a voltage-gated sodium channel is regulated by nerve growth factor FEBS Lett. 445 1999 177 182
34. T. Takahara, S.I. Kanazu, S. Yanagisawa, and H. Akanuma Heterogeneous Sp1 mRNAs in human HepG2 cells include a product of homotypic trans-splicing J. Biol. Chem. 275 2000 38067 38072
35. Z. Pasman, and M.A. Garcia-Blanco The 5′ and 3′ splice sites come together via a three dimensional diffusion mechanism Nucleic Acids Res. 24 1996 1638 1645
36. A.B. Chetverin The puzzle of RNA recombination FEBS Lett. 460 1999 1 5
37. A. Romani, E. Guerra, M. Trerotola, and S. Alberti Detection and analysis of spliced chimeric mRNAs in sequence databanks Nucleic Acids Res. 31 2003 E17-E17
38. X. Wang, H. Su, and A. Bradley Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model Genes Dev. 16 2002 1890 1905
39. V.E. Velculescu Analysis of human transcriptomes Nat. Genet. 23 1999 387 388
40. T.M. Thomson Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene Genome Res. 10 2000 1743 1756
41. B. Lawrence TPM3-ALK and TPM4-ALK oncogenes in inflammatory myofibroblastic tumors Am. J. Pathol. 157 2000 377 384
42. T. Kikumori, G.J. Cote, and R.F. Gagel Naturally occurring heterologous trans-splicing of adenovirus RNA with host cellular transcripts during infection FEBS Lett. 522 2002 41 46
43. S.J. Kim, D. Mitra, J.R. Salerno, and R.S. Hegde Signal sequences control gating of the protein translocation channel in a substrate-specific manner Dev. Cell 2 2002 207 217
44. B. Malissen, N. Shastri, M. Pierres, and L. Hood Cotransfer of the Ad alpha and Ad beta genes into L cells results in the surface expression of a functional mixed-isotype Ia molecule Proc. Natl. Acad. Sci. U.S.A. 83 1986 3958 3962
45. G. Ruberti Presentation of antigen by mixed isotype class II molecules in normal H-2d mice J. Exp. Med. 175 1992 157 162
46. I. Vořechovský Short tandem repeat (STR) haplotypes in HLA: an integrated 50-kb STR/linkage disequilibrium/gene map between the RING3 and HLA-B genes and identification of STR haplotype diversification in the class III region Eur. J. Hum. Genet. 9 2001 590 598
47. J. Královičová, L. Hammarstrom, A. Plebani, A.D. Webster, and I. Vořechovský Fine-scale mapping at IGAD1 and genome-wide genetic linkage analysis implicate HLA-DQ/DR as a major susceptibility locus in selective IgA deficiency and common variable immunodeficiency J. Immunol. 170 2003 2765 2775
48. I. Vořechovský Clustering of missense mutations in the ataxia-telangiectasia gene in a sporadic T-cell leukaemia Nat. Genet. 17 1997 96 99
49. J. Královičová, S. Houngninou-Molango, A. Kramer, and I. Vořechovský Branch sites haplotypes that control alternative splicing Hum. Mol. Genet. 13 2004 3189 3202
50. S. Senju Allele-specific expression of the cytoplasmic exon of HLA-DQB1 gene Immunogenetics 36 1992 319 325