Bioinformatic analyses of mammalian 5′-UTR sequence properties of mRNAs predicts alternative translation initiation sites

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Wegrzyn, Jill L ^a,c   Drudge, Thomas M ^b   Valafar, Faramarz ^a,b   Hook, Vivian ^c,d  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b San Diego State University   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATIC ANALYSIS; BIOLOGICAL FUNCTIONS; CLASSIFICATION AND IDENTIFICATIONS; CLASSIFICATION TREES; NUCLEOTIDE SEQUENCES; PROTEIN TRANSLATION; SECONDARY STRUCTURES; TRANSLATION INITIATION SITE;

DECISION TREES; FORECASTING; IDENTIFICATION (CONTROL SYSTEMS); MAMMALS; NEURAL NETWORKS; NUCLEOTIDES; PROTEINS;

BIOINFORMATICS;

CYTOSINE; GUANINE; MESSENGER RNA;

5' UNTRANSLATED REGION; ACCURACY; ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOINFORMATICS; CLASSIFICATION ALGORITHM; CONSENSUS SEQUENCE; CONTROLLED STUDY; DECISION TREE; GENOME ANALYSIS; HUMAN; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PREDICTION; PROTEIN SECONDARY STRUCTURE; RAT; RNA SEQUENCE; RNA TRANSLATION; START CODON; TRANSLATION INITIATION; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; GENETICS; METHODOLOGY; RNA SPLICING; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

MAMMALIA;

5' UNTRANSLATED REGIONS; ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; MODELS, GENETIC; RNA SPLICE SITES; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION INITIATION SITE;

EID: 44449100617     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-232     Document Type: Article

References (53)

1. Stephanie CB Touriel Sophie Bonnal Sylvie Audiger Herve Prats Anna-Catherine Prats Stephan Vagner Generation of Protein Isoform Diversity by Alternative Initiation of Translation at non-AUG Codons Biology of the Cell 2003, 95:169-178. 10.1016/S0248-4900(03)00033-9 12867081
2. Peabody DS Translation Initiation at non-AUG triplets in Mammalian Cells Journal of Biological Chemistry 1989, 264:5031-5035. 2538469
3. Lock P Ralph S Stanley E Boulet I Ramsay R Dunn AR Two isoforms of murine hck, generated by utilization of alternative translational initiation codons, exhibit different patterns of subcellular localization Mol Cell Biol 1991, 11(9):4363-70. 1875927 361298
4. Bruening W Pelletier J A non-AUG translational initiation event generates novel WT1 isoforms Journal of Biological Chemistry 1996, 271(15):. 8621495
5. Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K Dewar K Doyle M FitzHugh W Funke R Gage D Harris K Heaford A Howland J Kann L Lehoczky J LeVine R McEwan P McKernan K Meldrim J Mesirov JP Miranda C Morris W Naylor J Raymond C Rosetti M Santos R Sheridan A Sougnez C Stange-Thomann N Stojanovic N Subramanian A Wyman D Rogers J Sulston J Ainscough R Beck S Bentley D Burton J Clee C Carter N Coulson A Deadman R Deloukas P Dunham A Dunham I Durbin R French L Grafham D Gregory S Hubbard T Humphray S Hunt A Jones M Lloyd C McMurray A Matthews L Mercer S Milne S Mullikin JC Mungall A Plumb R Ross M Shownkeen R Sims S Waterston RH Wilson RK Hillier LW McPherson JD Marra MA Mardis ER Fulton LA Chinwalla AT Pepin KH Gish WR Chissoe SL Wendl MC Delehaunty KD Miner TL Delehaunty A Kramer JB Cook LL Fulton RS Johnson DL Minx PJ Clifton SW Hawkins T Branscomb E Predki P Richardson P Wenning S Slezak T Doggett N Cheng JF Olsen A Lucas S Elkin C Uberbacher E et al. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome Nature 2001, 409:860-921. 10.1038/35057062 11237011
6. Pruitt KDTT Maglott DR NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts, and proteins Nucleic Acids Research 2005, 33(1):D501-D504. 539979 15608248
7. Taira M Iizasa T Shimada H Kudoh J Shimizu N Tatibana M A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon Journal of Biological Chemistry 1990, 265(27):.
8. Bernards A de la Monte SM The ltk receptor tyrosine kinase is expressed in pre-B lymphocytes and cerebral neurons and uses a non-AUG translational initiator The EMBO Journal 1990, 9(7):. 551953 2357970
9. Hann SR Dixit M Sears RC Sealy L The alternatively initiated c-Myc proteins differentially regulate transcription through a noncanonical DNA-binding site Genes & Development 1994, 8(20):. 7958908
10. Grana X Claudio PP De Luca A Sang N Giordano A PISSLRE, a human novel CDC2-related protein kinase Oncogene 1994, 9(7):2097-103. 8208557
11. Palmiter RD Cole TB Findley SD ZnT-2, a mammalian protein that confers resistance to zinc by facilitating vesicular sequestration The EMBO Journal 1996, 15(8):. 450094 8617223
12. Stewart AF Richard CW 3rd Suzow J Stephan D Weremowicz S Morton CC Adra CN Cloning of human RTEF-1, a transcriptional enhancer factor-1-related gene preferentially expressed in skeletal muscle: Evidence for an ancient multigene family Genomics 1996, 37(1):. 8921372
13. Imataka H Olsen HS Sonenberg N A new translational regulator with homology to eukaryotic translation initiation factor 4G The EMBO Journal 1997, 16(4):. 1169682 9049310
14. Dodds DC Omeis IA Cushman SJ Helms JA Perin MS Neuronal pentraxin receptor, a novel putative integral membrane pentraxin that interacts with neuronal pentraxin 1 and 2 and taipoxin-associated calcium-binding protein 49 Journal of Biological Chemistry 1997, 272(34):. 9261167
15. Takayama S Krajewski S Krajewska M Kitada S Zapata JM Kochel K Knee D Scudiero D Tudor G Miller GJ Miyashita T Yamada M Reed JC Expression and location of Hsp70/Hsc-binding anti-apoptotic protein BAG-1 and its variants in normal tissues and tumor cell lines Cancer Res 1998, 58(14):3116-31. 9679980
16. Yang X Chernenko G Hao Y Ding Z Pater MM Pater A Tang SC Human BAG-1/ RAP46 protein is generated as four isoforms by alternative translation initiation and overexpressed in cancer cells Oncogene 1998, 17(8):981-9. 9747877 9747877 10.1038/sj.onc.1202032
17. Bertilsson G Heidrich J Svensson K Asman M Jendeberg L Sydow-Backman M Ohlsson R Postlind H Blomquist P Berkenstam A Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction Proc Natl Acad Sci U S A 1998, 95(21):12208-13. 9770465 22810 10.1073/ pnas.95.21.12208
18. Arnaud E Touriol C Boutonnet C Gensac MC Vagner S Prats H Prats AC A new 34-kilodalton isoform of human fibroblast growth factor 2 is cap dependently synthesized by using a non-AUG start codon and behaves as a survival factor Molecular and Cellular Biology 1999, 19(1):.
19. Dolstra H Fredrix H Maas F Coulie PG Brasseur F Mensink E Adema GJ de Witte TM Figdor CG Wiel-van Kemenade van de E A human minor histocompatibility antigen specific for B cell acute lymphoblastic leukemia Journal of Experimental Medicine 1999, 189(2):. 2192993 9892612
20. Shaughnessy JD Jr Largaespada DA Tian E Fletcher CF Cho BC Vyas P Jenkins NA Copeland NG Mrvi1, a common MRV integration site in BXH2 myeloid leukemias, encodes a protein with homology to a lymphoid-restricted membrane protein Jaw1 Oncogene 1999, 18(12):. 10321731
21. Jiang SW Wu K Eberhardt NL Human placental TEF-5 transactivates the human chorionic somatomammotropin gene enhancer Molecular endocrinology 1999, 13(6):. 10379887
22. Thebault S Gachon F Lemasson I Devaux C Mesnard JM Molecular cloning of a novel human I-mfa domain-containing protein that differently regulates human T-cell leukemia virus type I and HIV-1 expression Journal of Biological Chemistry 2000, 275(7):. 10671520
23. Burgess DL Gefrides LA Foreman PJ Noebels JL A cluster of three novel Ca2+ channel gamma subunit genes on chromosome 19q13.4: Evolution and expression profile of the gamma subunit gene family Genomics 2001, 71(3):. 11170751
24. Flomerfelt FA Kim MG Schwartz RH Spatial, a gene expressed in thymic stromal cells, depends on three-dimensional thymus organization for its expression Genes Immun 2000, 1(6):391-401. 11196687 10.1038/ sj.gene.6363695
25. Williams RT Manji SS Parker NJ Hancock MS Van Stekelenburg L Eid JP Senior PV Kazenwadel JS Shandala T Saint R Smith PJ Dziadek MA Identification and characterization of the STIM (stromal interaction molecule) gene family: Coding for a novel class of transmembrane proteins The Biochemical Journal 2001, 357:. 1221997 11463338
26. Peretti M Villard J Barras E Zufferey M Reith W Expression of the three human major histocompatibility complex class II isotypes exhibits a differential dependence on the transcription factor RFXAP Mol Cell Biol 2001, 21(17):. 87290 11486010
27. Uhlmann-Schiffler H Rossler OG Stahl H The mRNA of DEAD box protein p72 is alternatively translated into an 82-kDa RNA helicase The Journal of Biological Chemistry 2002, 277(2):. 11675387
28. Short JD Pfarr CM Translational regulation of the JunD messenger RNA J Biol Chem 2002, 277(36):. 12105216
29. Sapetschnig A Koch F Rischitor G Mennenga T Suske G Complexity of translationally controlled transcription factor Sp3 isoform expression J Biol Chem 2004, 279(40):.
30. Shiokawa D Shika Y Saito K Yamazaki K Tanuma S Physical and biochemical properties of mammalian DNase X proteins: Non-AUG translation initiation of porcine and bovine mRNAs for DNase X The Biochemical Journal 2005, 392:. 1316290 16107205
31. Kozak M An Analysis of Vertebrate mRNA Sequences: Intimations of Translational Control Journal of Cell Biology 1991, 115(4):887-903. 10.1083/jcb.115.4.887 1955461 2289952
32. Crooks GE Hon G Chandonia JM Brenner SE Web Logo: A sequence logo generator Genome Research 2004, 14:. 419797 15173120
33. Carmela FG Mignone Sabino Liuni Graziano Pesole Untranslated Regions on mRNAs Genome Biology 2002, 3(3):4.1-4.10.
34. Stefanie MD Kos George Reid Frank Gannon Upstream Open Reading Frames Regulate the Translation of the Multiple mRNA Variants of the Estrogen Receptor a Journal of Biological Chemistry 2002, 227(40):37131-37138.
35. Kozak M Pushing the limits of the scanning mechanism for initiation of translation Gene 2002, 299:1-34. 10.1016/S0378-1119(02)01056-9 12459250
36. Boyd L Thummel C Selection of CUG and AUG initiator codons for Drosophila E74A translation depends on downstream sequences Proceedings of the National Academy of Sciences of the United States of America 1993, 90(19):9164-9167. 10.1073/pnas.90.19.9164 8415672 47522
37. O'Donnell S Janssen G The Initiation Codon Affects Ribosome Binding and Translational Efficiency in Escherichia coli of cI mRNA with or without the 5′ Untranslated Leader J Bacteriol 2001, 183(4):1277-1283. 10.1128/JB.183.4.1277-1283.2001 11157940 95001
38. Morris D Geballe A Upstream Open Reading Frames as Regulators of mRNA Translation Molecular and Cellular Biology 2000, 20:8635-8642. 10.1128/ MCB.20.23.8635-8642.2000
39. Jackson RJ Alternative Mechanisms of Initiating Translation of Mammalian mRNAs Biochem Soc Trans 2005, 33(Pt 6):1231-41. 16246087
40. Kozak M Constraints on reinitiation of translation in mammals Nucleic Acids Research 2001, 29(24):5226-5232. 10.1093/nar/29.24.5226 11812856 97554
41. Hatzigeorgiou A Translation initiation start prediction in human cDNAs with high accuracy Bioinformatics 2002, 18:343-350. 10.1093/ bioinformatics/18.2.343 11847092
42. Zeng F Yap R Using Feature Generation and Feature Selection for Accurate Prediction of Translation Initiation Sites Genome Informatics 2002, 13:192-200. 14571388
43. Benson DA Karsch-Mizrachi I Lipman DJ Ostell J Wheller DL GenBank Nucleic Acids Research 2006, 34:D16-20. 10.1093/nar/gkj157 16381837 1347519
44. Carmela FG Mignone Sabino Liuni Graziano Pesole UTRdb and UTRsite: A collection of sequences and regulatory emotifs of the untranslated regions of eukaryotic mRNAs Nucleic Acids Research 2005, 33(Database):D141-D146. 539975 15608165
45. Zhang J Long M Li L Translational effects of differential codon usage among intragenic domains of new genes in Drosophilia Biochimica et Biophysica Acta 2005, 1728:135-142. 15833448
46. Qin H Wu WB Comeron J Kreitman M Li W Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes Genetics 2004, 160:2245-2260. 10.1534/genetics.104.030866
47. Gustafsson C Govindarajan S Minshull J Codon Bias and heterologous protein expression Trends in Biotechnology 2004, 22:346-353. 10.1016/ j.tibtech.2004.04.006 15245907
48. Peden J CodonW: A Codon Usage Analysis Program 1997. http://www.bio.net/ bionet/mm/bionews/1997-July/003992.html
49. Fuglsang A Estimating the "Effective Number of Codons": The Wright Way of Determining Codon Homozygosity Leads to Superior Estimates Genetics 2006, 172:1301-1307. 10.1534/genetics.105.049643 16299393 1456227
50. Zuker AM Mathews B Turner C Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide http://www.bioinfo.rpi.edu/~zukerm/seqanal/
51. Dimitrov RA Zuker M Prediction of hybridization and melting for double-stranded nucleic acids Biophysical Journal 2005, 87:215-226. 10.1529/biophysj.103.020743
52. Witten I Frank E Data Mining: Practical machine learning tools and techniques Morgan Kaufmann, San Francisco 2 2005.
53. Bajic V Tang S Han H Brusic V Hatzigeorgiou A Artificial Neural Networks Based Systems for Recognition of Genomic Signals and Regions: A Review J Informatica 2002, 26:389-400.