Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Hernández Torres, Francisco ^a,b   Rastrojo, Alberto ^a   Aguado, Begoña ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b UNIVERSITY OF JAÉN   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CASEIN KINASE II; CELL PROTEIN; PROTEIN CSNK2B; PROTEIN CSNK2B LY6G5B; PROTEIN LY6G5B; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELLULAR DISTRIBUTION; CHIMERA; CONTROLLED STUDY; CSNK2B GENE; CSNK2B LY6G5B GENE; ENZYME SPECIFICITY; EXON SKIPPING; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE OVEREXPRESSION; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; INTRON; LY6G5B GENE; MAMMAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DEFECT; PROTEIN LOCALIZATION; PROTEIN PROCESSING; TISSUE SECTION;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, LY; CASEIN KINASE II; CATTLE; HUMANS; INTRONS; MAMMALS; MICE; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEIN ISOFORMS; RATS; SEQUENCE ALIGNMENT; SWINE;

MAMMALIA;

EID: 84875197291     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-199     Document Type: Article

References (50)

1. Villate O, Rastrojo A, Lopez-Diez R, Hernandez-Torres F, Aguado B. Differential splicing, disease and drug targets. Infect Disord Drug Targets 2008, 8(4):241-251. 10.2174/187152608786734188, 19075799.
2. Irimia M, Blencowe BJ. Alternative splicing: decoding an expansive regulatory layer. Curr Opin Cell Biol 2012, 24(3):323-332. 10.1016/j.ceb.2012.03.005, 22465326.
3. Kalsotra A, Cooper TA. Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet 2011, 12(10):715-729. 10.1038/nrg3052, 3321218, 21921927.
4. Chow LT, Gelinas RE, Broker TR, Roberts RJ. An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA. Cell 1977, 12(1):1-8. 10.1016/0092-8674(77)90180-5, 902310.
5. Gelinas RE, Roberts RJ. One predominant 5'-undecanucleotide in adenovirus 2 late messenger RNAs. Cell 1977, 11(3):533-544. 10.1016/0092-8674(77)90071-X, 884734.
6. Berget SM, Moore C, Sharp PA. Spliced segments at the 5' terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA 1977, 74(8):3171-3175. 10.1073/pnas.74.8.3171, 431482, 269380.
7. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF. Schroth GP 2008, Burge CB: Alternative isoform regulation in human tissue transcriptomes. Nature.
8. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD. Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 2003, 302(5653):2141-2144. 10.1126/science.1090100, 14684825.
9. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921. 10.1038/35057062, 11237011.
10. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA. The sequence of the human genome. Science 2001, 291(5507):1304-1351. 10.1126/science.1058040, 11181995.
11. 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(12):2621-2636. 10.1101/gr.1736803, 403804, 14656967.
12. The MHC sequencing consortium Complete sequence and gene map of a human major histocompatibility complex. Nature 1999, 401(6756):921-923. 10.1038/44853, 10553908, The MHC sequencing consortium.
13. 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(1):113-123. 10.1006/geno.2002.6794, 12079290.
14. 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(10):2244-2256. 10.1110/ps.062242606, 2242401, 17008713.
15. 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(1):8. 10.1186/1479-5876-2-8, 411062, 15050027.
16. Calvanese V, Mallya M, Campbell RD, Aguado B. Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism. BMC Mol Biol 2008, 9:81. 10.1186/1471-2199-9-81, 2562388, 18817541.
17. Kim E, Magen A, Ast G. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 2007, 35(1):125-131. 10.1093/nar/gkm529, 1802581, 17158149.
18. Lejeune F, Maquat LE. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr Opin Cell Biol 2005, 17(3):309-315. 10.1016/j.ceb.2005.03.002, 15901502.
19. Conti E, Izaurralde E. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol 2005, 17(3):316-325. 10.1016/j.ceb.2005.04.005, 15901503.
20. Jakobi R, Voss H, Pyerin W. Human phosvitin/casein kinase type II. Molecular cloning and sequencing of full-length cDNA encoding subunit beta. Eur J Biochem 1989, 183(1):227-233. 10.1111/j.1432-1033.1989.tb14917.x, 2666134.
21. Rodriguez FA, Contreras C, Bolanos-Garcia V, Allende JE. Protein kinase CK2 as an ectokinase: the role of the regulatory CK2beta subunit. Proc Natl Acad Sci USA 2008, 105(15):5693-5698. 10.1073/pnas.0802065105, 2311332, 18391191.
22. 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(1):37-44. 1356127, 16344564.
23. 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(1):30-36. 1356126, 16344562.
24. Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics 2011, 4:11. 10.1186/1755-8794-4-11, 3041646, 21261984.
25. Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 2007, 17(6):746-759. 10.1101/gr.5660607, 1891335, 17567994.
26. Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R. Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts. Genome Res 2012, 22(7):1231-1242. 10.1101/gr.130062.111, 3396365, 22588898.
27. Bolanos-Garcia VM, Fernandez-Recio J, Allende JE, Blundell TL. Identifying interaction motifs in CK2beta-a ubiquitous kinase regulatory subunit. Trends Biochem Sci 2006, 31(12):654-661. 10.1016/j.tibs.2006.10.005, 17084631.
28. Kumar-Sinha C, Kalyana-Sundaram S, Chinnaiyan AM. SLC45A3-ELK4 chimera in prostate cancer: spotlight on cis-splicing. Cancer discovery 2012, 2(7):582-585. 10.1158/2159-8290.CD-12-0212, 22787087.
29. Zhang Y, Gong M, Yuan H, Park HG, Frierson HF, Li H. Chimeric transcript generated by cis-splicing of adjacent genes regulates prostate cancer cell proliferation. Cancer discovery 2012, 2(7):598-607. 10.1158/2159-8290.CD-12-0042, 22719019.
30. Ackerman P, Glover CV, Osheroff N. Stimulation of casein kinase II by epidermal growth factor: relationship between the physiological activity of the kinase and the phosphorylation state of its beta subunit. Proc Natl Acad Sci USA 1990, 87(2):821-825. 10.1073/pnas.87.2.821, 53358, 2300566.
31. Rodriguez F, Allende CC, Allende JE. Protein kinase casein kinase 2 holoenzyme produced ectopically in human cells can be exported to the external side of the cellular membrane. Proc Natl Acad Sci USA 2005, 102(13):4718-4723. 10.1073/pnas.0501074102, 555726, 15774585.
32. Adams MD, Soares MB, Kerlavage AR, Fields C, Venter JC. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat Genet 1993, 4(4):373-380. 10.1038/ng0893-373, 8401585.
33. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C. The transcriptional landscape of the mammalian genome. Science 2005, 309(5740):1559-1563.
34. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H. Functional annotation of a full-length mouse cDNA collection. Nature 2001, 409(6821):685-690. 10.1038/35055500, 11217851.
35. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol 2012, 30(1):99-104.
36. Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods 2008, 5(7):629-635. 10.1038/nmeth.1216, 2713501, 18500348.
37. Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segal E. Genomics: ENCODE explained. Nature 2012, 489(7414):52-55. 10.1038/489052a, 22955614.
38. Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011, 39(Database issue):D146-D151. 3013714, 21112873.
39. Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet 2006, 15(Spec No 1):R17-R29.
40. Holt CE, Bullock SL. Subcellular mRNA localization in animal cells and why it matters. Science 2009, 326(5957):1212-1216. 10.1126/science.1176488, 19965463.
41. Martin KC, Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell 2009, 136(4):719-730. 10.1016/j.cell.2009.01.044, 2819924, 19239891.
42. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009, 10:421. 10.1186/1471-2105-10-421, 2803857, 20003500.
43. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
44. Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 2010, 38(Web Server issue):W695-W699. 2896090, 20439314.
45. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K. The Pfam protein families database. Nucleic Acids Res 2010, 38(Database issue):D211-D222. 2808889, 19920124.
46. Bucher P, Karplus K, Moeri N, Hofmann K. A flexible motif search technique based on generalized profiles. Comput Chem 1996, 20(1):3-23. 10.1016/S0097-8485(96)80003-9, 8867839.
47. Scordis P, Flower DR, Attwood TK. FingerPRINTScan: intelligent searching of the PRINTS motif database. Bioinformatics 1999, 15(10):799-806. 10.1093/bioinformatics/15.10.799, 10705433.
48. Eddy SR. Profile hidden Markov models. Bioinformatics 1998, 14(9):755-763. 10.1093/bioinformatics/14.9.755, 9918945.
49. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
50. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 1988, 16(22):10881-10890. 10.1093/nar/16.22.10881, 338945, 2849754.