Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism

BMC Molecular Biology

Volumn 9, Issue , 2008, Pages

  Calvanese, Vincenzo ^a,e   Mallya, Meera ^b,d   Campbell, R Duncan ^b,c   Aguado, Begoña ^a,b  

^a CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

^b MRC Rosalind Franklin Centre for Genomics Research   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e Structural Biology and Biocomputing Programme   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ACTIN; CASEIN KINASE; CYCLOHEXIMIDE; DACTINOMYCIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; IMMUNOGLOBULIN; LUCIFERASE; LYMPHOCYTE ANTIGEN; LYMPHOCYTE ANTIGEN 6; PUROMYCIN; RNA; UNCLASSIFIED DRUG; CHIMERIC PROTEIN; LY ANTIGEN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CELL LINE; CELL STRAIN HEK293; CELL STRAIN K 562; CELL STRAIN U937; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HELA CELL; HUMAN; HUMAN CELL; INTRON; LEUKEMIA CELL LINE; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PLASMID; POLYMERASE CHAIN REACTION; PROTEIN DOMAIN; QUANTITATIVE ANALYSIS; RAJI CELL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; SEQUENCE DATABASE; STOP CODON; TRANSLATION REGULATION; ALTERNATIVE RNA SPLICING; ANTIBODY SPECIFICITY; BIOSYNTHESIS; GENETICS; RNA STABILITY;

ALTERNATIVE SPLICING; ANTIGENS, LY; CELL LINE; CODON, NONSENSE; GENE EXPRESSION REGULATION; HUMANS; INTRONS; MUTANT CHIMERIC PROTEINS; ORGAN SPECIFICITY; RNA STABILITY;

EID: 53549097370     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-9-81     Document Type: Article

References (35)

1. Blencowe BJ Alternative splicing: New insights from global analyses Cell 2006, 126:37-47 10.1016/j.cell.2006.06.023 16839875
2. Stamm S Ben-Ari S Rafalska I Tang Y Zhang Z Toiber D Thanaraj TA Soreq H Function of alternative splicing Gene 2005, 344:1-20 10.1016/ j.gene.2004.10.022 15656968
3. Hanke J Brett D Zastrow I Aydin A Delbruck S Lehmann G Luft F Reich J Bork P Alternative splicing of human genes: More the rule than the exception? Trends Genet 1999, 15:389-390 10.1016/S0168-9525(99)01830-2 10498933
4. Caceres JF Kornblihtt AR Alternative splicing: Multiple control mechanisms and involvement in human disease Trends Genet 2002, 18:186-193 10.1016/S0168-9525(01)02626-9 11932019
5. Buratti E Baralle M Baralle FE Defective splicing, disease and therapy: searching for master checkpoints in exon definition Nucleic Acids Res 2006, 34:3494-3510 1524908 16855287 10.1093/nar/gkl498
6. Wang GS Cooper TA Splicing in disease: Disruption of the splicing code and the decoding machinery Nat Rev Genet 2007, 8:749-761 10.1038/nrg2164 17726481
7. Garcia-Blanco MA Baraniak AP Lasda EL Alternative splicing in disease and therapy Nat Biotechnol 2004, 22:535-546 10.1038/nbt964 15122293
8. Skotheim RI Nees M Alternative splicing in cancer: Noise, functional, or systematic? Int J Biochem Cell Biol 2007, 39:1432-1449 10.1016/ j.biocel.2007.02.016 17416541
9. Xie T Rowen L Aguado B Ahearn ME Madan A Qin S Campbell RD Hood L Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse Genome Res 2003, 13:2621-2636 403804 14656967 10.1101/gr.1736803
10. Milner CM Campbell RD Genetic organization of the human MHC class III region Front Biosci 2001, 6:D914-926 10.2741/Milner 11487476
11. Gruen JR Weissman SM Human MHC class III and IV genes and disease associations Front Biosci 2001, 6:D960-972 10.2741/Gruen 11487469
12. Mallya M Campbell RD Aguado B Transcriptional analysis of a novel cluster of LY-6 family members in the human and mouse major histocompatibility complex: Five genes with many splice forms Genomics 2002, 80:113-123 10.1006/geno.2002.6794 12079290
13. Mallya M Campbell RD Aguado B Characterization of the five novel Ly-6 superfamily members encoded in the MHC, and detection of cells expressing their potential ligands Protein Sci 2006, 15:2244-2256 2242401 17008713 10.1110/ps.062242606
14. Stroncek DF Caruccio L Bettinotti M CD177: A member of the Ly-6 gene superfamily involved with neutrophil proliferation and polycythemia vera J Transl Med 2004, 2:8 411062 15050027 10.1186/1479-5876-2-8
15. Conti E Izaurralde E Nonsense-mediated mRNA decay: Molecular insights and mechanistic variations across species Curr Opin Cell Biol 2005, 17:316-325 10.1016/j.ceb.2005.04.005 15901503
16. Lejeune F Maquat LE Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells Curr Opin Cell Biol 2005, 17:309-315 10.1016/j.ceb.2005.03.002 15901502
17. Sakabe NJ de Souza SJ Sequence features responsible for intron retention in human BMC Genomics 2007, 8:59 1831480 17324281 10.1186/1471-2164-8-59
18. Galante PA Sakabe NJ Kirschbaum-Slager N de Souza SJ Detection and evaluation of intron retention events in the human transcriptome Rna 2004, 10:757-765 1370565 15100430 10.1261/rna.5123504
19. Akiva P Toporik A Edelheit S Peretz Y Diber A Shemesh R Novik A Sorek R Transcription-mediated gene fusion in the human genome Genome Res 2006, 16:30-36 1356126 16344562 10.1101/gr.4137606
20. Parra G Reymond A Dabbouseh N Dermitzakis ET Castelo R Thomson TM Antonarakis SE Guigo R Tandem chimerism as a means to increase protein complexity in the human genome Genome Res 2006, 16:37-44 1356127 16344564 10.1101/gr.4145906
21. The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by ENCODE pilot project Nature 2007, 447:799-816 2212820 17571346 10.1038/nature05874
22. Kowalski JC Belfort M Stapleton MA Holpert M Dansereau JT Pietrokovski S Baxter SM Derbyshire V Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: Coincidence of computational and molecular findings Nucleic Acids Res 1999, 27:2115-2125 148431 10219084 10.1093/ nar/27.10.2115
23. Pradet-Balade B Medema JP Lopez-Fraga M Lozano JC Kolfschoten GM Picard A Martinez AC Garcia-Sanz JA Hahne M An endogenous hybrid mRNA encodes TWE-PRIL, a functional cell surface TWEAK-APRIL fusion protein Embo J 2002, 21:5711-5720 131062 12411489 10.1093/emboj/cdf565
24. Hernandez-Sanchez C Bartulos O Valenciano AI Mansilla A de Pablo F The regulated expression of chimeric tyrosine hydroxylase-insulin transcripts during early development Nucleic Acids Res 2006, 34:3455-3464 1524912 16840532 10.1093/nar/gkl436
25. Livak KJ Schmittgen TD Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method Methods 2001, 25:402-408 10.1006/meth.2001.1262 11846609
26. Chen CD Kobayashi R Helfman DM Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene Genes Dev 1999, 13:593-606 316507 10072387 10.1101/gad.13.5.593
27. Expert-Bezancon A Sureau A Durosay P Salesse R Groeneveld H Lecaer JP Marie J hnRNP A1 and the SR proteins ASF/SF2 and SC35 have antagonistic functions in splicing of beta-tropomyosin exon 6B J Biol Chem 2004, 279:38249-38259 10.1074/jbc.M405377200 15208309
28. Wang HF Feng L Niu DK Relationship between mRNA stability and intron presence Biochem Biophys Res Commun 2007, 354:203-208 10.1016/ j.bbrc.2006.12.184 17207776
29. Albertella MR Jones H Thomson W Olavesen MG Neville M Campbell RD Localisation of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit, and DNA sequence analysis of the class III region DNA Seq 1996, 7:9-12 10.3109/10425179609015638 9063629
30. Garcia A Senis YA Antrobus R Hughes CE Dwek RA Watson SP Zitzmann N A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: Involvement of G6f, a novel platelet Grb2-binding membrane adapter Proteomics 2006, 6:5332-5343 1869047 16941570 10.1002/pmic.200600299
31. Macaulay IC Tijssen MR Thijssen-Timmer DC Gusnanto A Steward M Burns P Langford CF Ellis PD Dudbridge F Zwaginga JJ Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins Blood 2007, 109:3260-3269 10.1182/blood-2006-07-036269 17192395
32. De Vet EC Aguado B Campbell RD Adaptor signalling proteins Grb2 and Grb7 are recruited by human G6f, a novel member of the immunoglobulin superfamily encoded in the MHC Biochem J 2003, 375:207-213 1223670 12852788 10.1042/BJ20030293
33. Lareau LF Green RE Bhatnagar RS Brenner SE The evolving roles of alternative splicing Curr Opin Struct Biol 2004, 14:273-282 10.1016/ j.sbi.2004.05.002 15193306
34. Yan MD Hong CC Lai GM Cheng AL Lin YW Chuang ES Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas Hum Mol Genet 2005, 14:I1465-1474 10.1093/hmg/ddi156
35. Nakaya HI Amaral PP Louro R Lopes A Fachel AA Moreira YB El-Jundi TA da Silva AM Reis EM Verjovski-Almeida S Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription Genome Biol 2007, 8:R43 1868932 17386095 10.1186/gb-2007-8-3-r43