Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Wang, Pingzhang ^a,b,c   Yu, Peng ^a   Gao, Peng ^a   Shi, Taiping ^a,b,c   Ma, Dalong ^a,b,c  

^a CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

^b PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

^c PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME; COMPLEMENTARY DNA; TNFRSF1A PROTEIN, HUMAN; TUMOR NECROSIS FACTOR RECEPTOR 1;

ARTICLE; EXON; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; INTRON; NUCLEOTIDE SEQUENCE; POLYADENYLATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; CHEMISTRY; DNA MICROARRAY; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; HUMAN GENOME; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; BASE SEQUENCE; CLONING, MOLECULAR; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, HUMAN; GENOMICS; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYADENYLATION; RECEPTORS, TUMOR NECROSIS FACTOR, TYPE I; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE DELETION; TRANSCRIPTION, GENETIC;

EID: 71049126222     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-518     Document Type: Article

References (74)

1. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456(7221):470-476. 2593745, 18978772.
2. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40(12):1413-1415.
3. Matlin AJ, Clark F, Smith CW. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005, 6(5):386-398.
4. Modrek B, Lee C. A genomic view of alternative splicing. Nat Genet 2002, 30(1):13-19.
5. Roberts GC, Smith CW. Alternative splicing: combinatorial output from the genome. Curr Opin Chem Biol 2002, 6(3):375-383.
6. Pauws E, van Kampen AH, Graaf SA, de Vijlder JJ, Ris-Stalpers C. Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res 2001, 29(8):1690-1694. 31324, 11292841.
7. Zhao J, Hyman L, Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999, 63(2):405-445. 98971, 10357856.
8. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res 2000, 10(7):1001-1010. 310884, 10899149.
9. Hu J, Lutz CS, Wilusz J, Tian B. Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. Rna 2005, 11(10):1485-1493. 1370832, 16131587.
10. Cheng Y, Miura RM, Tian B. Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 2006, 22(19):2320-2325.
11. Tian B, Hu J, Zhang H, Lutz CS. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005, 33(1):201-212. 546146, 15647503.
12. Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol 2004, 5(10):R74. 545594, 15461793.
13. 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.
14. Venables JP. Aberrant and alternative splicing in cancer. Cancer Res 2004, 64(21):7647-7654.
15. Faustino NA, Cooper TA. Pre-mRNA splicing and human disease. Genes Dev 2003, 17(4):419-437.
16. Philips AV, Cooper TA. RNA processing and human disease. Cell Mol Life Sci 2000, 57(2):235-249.
17. Tian B, Pan Z, Lee JY. Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res 2007, 17(2):156-165. 1781347, 17210931.
18. Edwalds-Gilbert G, Veraldi KL, Milcarek C. Alternative poly(A) site selection in complex transcription units: means to an end?. Nucleic Acids Res 1997, 25(13):2547-2561. 146782, 9185563.
19. Yan J, Marr TG. Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res 2005, 15(3):369-375. 551563, 15741508.
20. Thomas CP, Andrews JI, Liu KZ. Intronic polyadenylation signal sequences and alternate splicing generate human soluble Flt1 variants and regulate the abundance of soluble Flt1 in the placenta. Faseb J 2007, 21(14):3885-3895.
21. Peterson ML, Bingham GL, Cowan C. Multiple features contribute to the use of the immunoglobulin M secretion-specific poly(A) signal but are not required for developmental regulation. Mol Cell Biol 2006, 26(18):6762-6771. 1592873, 16943419.
22. Boldin MP, Goncharov TM, Goltsev YV, Wallach D. Involvement of MACH, a novel MORT1/FADD-interacting protease, in Fas/APO-1- and TNF receptor-induced cell death. Cell 1996, 85(6):803-815.
23. Iwami KI, Matsuguchi T, Masuda A, Kikuchi T, Musikacharoen T, Yoshikai Y. Cutting edge: naturally occurring soluble form of mouse Toll-like receptor 4 inhibits lipopolysaccharide signaling. J Immunol 2000, 165(12):6682-6686.
24. Tabuchi M, Tanaka N, Nishida-Kitayama J, Ohno H, Kishi F. Alternative splicing regulates the subcellular localization of divalent metal transporter 1 isoforms. Mol Biol Cell 2002, 13(12):4371-4387. 138640, 12475959.
25. Wang H, Wang P, Sun X, Luo Y, Wang X, Ma D, Wu J. Cloning and characterization of a novel caspase-10 isoform that activates NF-kappa B activity. Biochim Biophys Acta 2007, 1770(11):1528-1537.
26. Zervos AS, Faccio L, Gatto JP, Kyriakis JM, Brent R. Mxi2, a mitogen-activated protein kinase that recognizes and phosphorylates Max protein. Proc Natl Acad Sci USA 1995, 92(23):10531-10534. 40645, 7479834.
27. Sanz-Moreno V, Casar B, Crespo P. p38alpha isoform Mxi2 binds to extracellular signal-regulated kinase 1 and 2 mitogen-activated protein kinase and regulates its nuclear activity by sustaining its phosphorylation levels. Mol Cell Biol 2003, 23(9):3079-3090. 153192, 12697810.
28. Winchester JS, Rouchka EC, Rowland NS, Rice NA. In Silico characterization of phosphorylase kinase: evidence for an alternate intronic polyadenylation site in PHKG1. Mol Genet Metab 2007, 92(3):234-242. 2706538, 17692548.
29. Pan Z, Zhang H, Hague LK, Lee JY, Lutz CS, Tian B. An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. Gene 2006, 366(2):325-334.
30. Zhang H, Hu J, Recce M, Tian B. PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res 2005, (33 Database):D116-120. 540009, 15608159.
31. Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 2007, (35 Database):D165-168. 1899096, 17202160.
32. Lee JY, Park JY, Tian B. Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags, and Trace. Methods Mol Biol 2008, 419:23-37.
33. Ji H, Zhou Q, Wen F, Xia H, Lu X, Li Y. AsMamDB: an alternative splice database of mammals. Nucleic Acids Res 2001, 29(1):260-263. 29817, 11125106.
34. Hsu FR, Chang HY, Lin YL, Tsai YT, Peng HL, Chen YT, Cheng CY, Shih MY, Liu CH, Chen CF. AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs. Bioinformation 2005, 1(1):16-18. 1891626, 17597845.
35. Sakharkar MK, Perumal BS, Lim YP, Chern LP, Yu Y, Kangueane P. Alternatively spliced human genes by exon skipping--a database (ASHESdb). In Silico Biol 2005, 5(3):221-225.
36. Castrignano T, Rizzi R, Talamo IG, De Meo PD, Anselmo A, Bonizzoni P, Pesole G. ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. Nucleic Acids Res 2006, 34:W440-443. 1538898, 16845044.
37. Galperin MY. The Molecular Biology Database Collection: 2008 update. Nucleic Acids Res 2008, 36:D2-4. 2238887, 18025043.
38. Iseli C, Stevenson BJ, de Souza SJ, Samaia HB, Camargo AA, Buetow KH, Strausberg RL, Simpson AJ, Bucher P, Jongeneel CV. Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res 2002, 12(7):1068-1074. 186619, 12097343.
39. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316(5830):1484-1488.
40. Wang P, Shi T, Ma D. Cloning of a novel human caspase-9 splice variant containing only the CARD domain. Life Sci 2006, 79(10):934-940.
41. Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 2006, (34 Database):D46-55. 1347394, 16381912.
42. Lee C, Atanelov L, Modrek B, Xing Y. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 2003, 31(1):101-105. 165476, 12519958.
43. Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res 2007, (35 Database):D93-98. 1669709, 17108355.
44. Koscielny G, Texier VL, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 2009, 93(3):213-220.
45. Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, Gautheret D, Thanaraj TA. AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics 2006, 7:169. 1435940, 16556303.
46. Muro EM, Herrington R, Janmohamed S, Frelin C, Andrade-Navarro MA, Iscove NN. Identification of gene 3' ends by automated EST cluster analysis. Proc Natl Acad Sci USA 2008, 105(51):20286-20290. 2629301, 19095794.
47. Aggarwal BB. Signalling pathways of the TNF superfamily: a double-edged sword. Nat Rev Immunol 2003, 3(9):745-756.
48. Lavrik I, Golks A, Krammer PH. Death receptor signaling. J Cell Sci 2005, 118(Pt 2):265-267.
49. Micheau O, Tschopp J. Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes. Cell 2003, 114(2):181-190.
50. Locksley RM, Killeen N, Lenardo MJ. The TNF and TNF receptor superfamilies: integrating mammalian biology. Cell 2001, 104(4):487-501.
51. Nophar Y, Kemper O, Brakebusch C, Englemann H, Zwang R, Aderka D, Holtmann H, Wallach D. Soluble forms of tumor necrosis factor receptors (TNF-Rs). The cDNA for the type I TNF-R, cloned using amino acid sequence data of its soluble form, encodes both the cell surface and a soluble form of the receptor. Embo J 1990, 9(10):3269-3278. 552060, 1698610.
52. Porteu F, Nathan C. Shedding of tumor necrosis factor receptors by activated human neutrophils. J Exp Med 1990, 172(2):599-607. 2188336, 2165128.
53. Waetzig GH, Rosenstiel P, Arlt A, Till A, Brautigam K, Schafer H, Rose-John S, Seegert D, Schreiber S. Soluble tumor necrosis factor (TNF) receptor-1 induces apoptosis via reverse TNF signaling and autocrine transforming growth factor-beta1. Faseb J 2005, 19(1):91-93.
54. Serwin AB, Mysliwiec H, Hukalowicz K, Porebski P, Borawska M, Chodynicka B. Soluble tumor necrosis factor-alpha receptor type 1 during selenium supplementation in psoriasis patients. Nutrition 2003, 19(10):847-850.
55. Taniguchi A, Fukushima M, Nakai Y, Ohgushi M, Kuroe A, Ohya M, Seino Y. Soluble tumor necrosis factor receptor 1 is strongly and independently associated with serum homocysteine in nonobese Japanese type 2 diabetic patients. Diabetes Care 2006, 29(4):949-950.
56. Ogura H, Tsukumo Y, Sugimoto H, Igarashi M, Nagai K, Kataoka T. Ectodomain shedding of TNF receptor 1 induced by protein synthesis inhibitors regulates TNF-alpha-mediated activation of NF-kappaB and caspase-8. Exp Cell Res 2008, 314(6):1406-1414.
57. Schlondorff J, Blobel CP. Metalloprotease-disintegrins: modular proteins capable of promoting cell-cell interactions and triggering signals by protein-ectodomain shedding. J Cell Sci 1999, 112(Pt 21):3603-3617.
58. Mohan MJ, Seaton T, Mitchell J, Howe A, Blackburn K, Burkhart W, Moyer M, Patel I, Waitt GM, Becherer JD. The tumor necrosis factor-alpha converting enzyme (TACE): a unique metalloproteinase with highly defined substrate selectivity. Biochemistry 2002, 41(30):9462-9469.
59. Beaudoing E, Gautheret D. Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res 2001, 11(9):1520-1526. 311108, 11544195.
60. Zhang H, Lee JY, Tian B. Biased alternative polyadenylation in human tissues. Genome Biol 2005, 6(12):R100. 1414089, 16356263.
61. Lopez F, Granjeaud S, Ara T, Ghattas B, Gautheret D. The disparate nature of "intergenic" polyadenylation sites. Rna 2006, 12(10):1794-1801. 1581981, 16931874.
62. Legendre M, Gautheret D. Sequence determinants in human polyadenylation site selection. BMC Genomics 2003, 4(1):7. 151664, 12600277.
63. Nam DK, Lee S, Zhou G, Cao X, Wang C, Clark T, Chen J, Rowley JD, Wang SM. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci USA 2002, 99(9):6152-6156. 122918, 11972056.
64. West S, Gromak N, Norbury CJ, Proudfoot NJ. Adenylation and exosome-mediated degradation of cotranscriptionally cleaved pre-messenger RNA in human cells. Mol Cell 2006, 21(3):437-443.
65. LaCava J, Houseley J, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 2005, 121(5):713-724.
66. Houseley J, LaCava J, Tollervey D. RNA-quality control by the exosome. Nat Rev Mol Cell Biol 2006, 7(7):529-539.
67. McGlincy NJ, Smith CW. Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?. Trends Biochem Sci 2008, 33(8):385-393.
68. Muhlemann O, Eberle AB, Stalder L, Zamudio Orozco R. Recognition and elimination of nonsense mRNA. Biochim Biophys Acta 2008, 1779(9):538-549.
69. Stalder L, Muhlemann O. The meaning of nonsense. Trends Cell Biol 2008, 18(7):315-321.
70. Gilat R, Shweiki D. A novel function for alternative polyadenylation as a rescue pathway from NMD surveillance. Biochem Biophys Res Commun 2007, 353(2):487-492.
71. Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet 2006, 15(Spec No 1):R17-29.
72. He S, Liu C, Skogerbo G, Zhao H, Wang J, Liu T, Bai B, Zhao Y, Chen R. NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 2008, (36 Database):D170-172. 2238973, 18000000.
73. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ. The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31(1):51-54. 165576, 12519945.
74. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2008, (36 Database):D773-779. 2238835, 18086701.