Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts

RNA

Volumn 16, Issue 9, 2010, Pages 1760-1768

  Han, Siew Ping ^a   Kassahn, Karin S ^a   Skarshewski, Adam ^a   Ragan, Mark A ^a   Rothnagel, Joseph A ^a   Smith, Ross ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Alternative splicing; Evolution; hnRNP A B

Indexed keywords

HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN B; MESSENGER RNA; NUCLEIC ACID; UNCLASSIFIED DRUG; REGULATORY RNA SEQUENCE; RNA SPLICING;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; EXON; GENE SEQUENCE; GENETIC TRANSCRIPTION; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; RNA PROCESSING; RNA TRANSLATION; ANIMAL; GENETICS; HELA CELL LINE; METABOLISM; MOLECULAR EVOLUTION; MOUSE; RAT; REGULATORY RNA SEQUENCE; RNA SPLICING;

ALTERNATIVE SPLICING; ANIMALS; EVOLUTION, MOLECULAR; HELA CELLS; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEIN GROUP A-B; HUMANS; MICE; RATS; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RNA SPLICE SITES; RNA, MESSENGER;

EID: 77956036658     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2142810     Document Type: Article

References (52)

1. Ainger K, Avossa D, Diana AS, Barry C, Barbarese E, Carson JH. 1997. Transport and localization elements in myelin basic protein mRNA. J Cell Biol 138: 1077-1087. (Pubitemid 27386457)
2. Akindahunsi AA, Bandiera A, Manzini G. 2005. Vertebrate 2xRBD hnRNP proteins: A comparative analysis of genome, mRNA and protein sequences. Comput Biol Chem 29: 13-23. (Pubitemid 40146363)
3. Alekseyenko AV, Kim N, Lee CJ. 2007. Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA 13: 661-670. (Pubitemid 46641524)
4. Ast G. 2004. How did alternative splicing evolve? Nat Rev Genet 5: 773-782.
5. Bowes JB, Snyder KA, Segerdell E, Jarabek CJ, Azam K, Zorn AM, Vize PD. 2010. Xenbase: Gene expression and improved integration. Nucleic Acids Res. 38: D607-D612.
6. Buvoli M, Cobianchi F, Bestagno MG, Mangiarotti A, Bassi MT, Biamonti G, Riva S. 1990. Alternative splicing in the human gene for the core protein-A1 generates another hnRNP protein. EMBO J 9: 1229-1235.
7. Chabot B, Blanchette M, Lapierre I, LaBranche H. 1997. An intron element modulating 5′ splice site selection in the hnRNP A1 pre-mRNA interacts with hnRNP A1. Mol Cell Biol 17: 1776-1786. (Pubitemid 27133262)
8. Dreyfuss G, Matunis MJ, Pinolroma S, Burd CG. 1993. hnRNP proteins and the biogenesis of messenger-RNA. Annu Rev Biochem 62: 289-321.
9. Dreyfuss G, Kim VN, Kataoka N. 2002. Messenger-RNA-binding proteins and the messages they carry. Nat Rev Mol Cell Biol 3: 195-205.
10. Fairbrother WG, Yeh RF, Sharp PA, Burge CB. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007-1013.
11. Gao Y, Tatavarty V, Korza G, Levin MK, Carson JH. 2008. Multiplexed dendritic targeting of α-calcium calmodulin-dependent protein kinase II, neurogranin, and activity-regulated cytoskeleton-associated protein RNAs by the A2 pathway. Mol Biol Cell 19: 2311-2327.
12. Han SP, Friend LR, Carson JH, Korza G, Barbarese E, Maggipinto M, Hatfield JT, Rothnagel JA, Smith R. 2010. Differential subcellular distributions and trafficking functions of hnRNP A2/B1 spliceoforms. Traffic 11: 886-898.
13. Hatfield JT, Rothnagel JA, Smith R. 2002. Characterization of the mouse hnRNP A2/B1/B0 gene and identification of processed pseudogenes. Gene 295: 33-42. (Pubitemid 35283814)
14. He YW, Smith R. 2009. Nuclear functions of heterogeneous nuclear ribonucleoproteins A/B. Cell Mol Life Sci 66: 1239-1256.
15. He YW, Brown MA, Rothnagel JA, Saunders NA, Smith R. 2005. Roles of heterogeneous nuclear ribonucleoproteins A and B in cell proliferation. J Cell Sci 118: 3173-3183. (Pubitemid 41149920)
16. Hertel KJ. 2008. Combinatorial control of exon recognition. J Biol Chem 283: 1211-1215.
17. Hoek KS, Kidd GJ, Carson JH, Smith R. 1998. hnRNP A2 selectively binds the cytoplasmic transport sequence of myelin basic protein mRNA. Biochemistry 37: 7021-7029. (Pubitemid 28228140)
18. Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, et al. 2009. Ensembl 2009. Nucleic Acids Res 37: D690-D697.
19. Hutchison S, LeBel C, Blanchette M, Chabot B. 2002. Distinct sets of adjacent heterogeneous nuclear ribonucleoprotein (hnRNP) A1/A2 binding sites control 5′ splice site selection in the hnRNP A1 mRNA precursor. J Biol Chem 277: 29745-29752.
20. Kamma H, Horiguchi H, Wan LL, Matsui M, Fujiwara M, Fujimoto M, Yazawa T, Dreyfuss G. 1999. Molecular characterization of the hnRNP A2/B1 proteins: Tissue-specific expression and novel isoforms. Exp Cell Res 246: 399-411. (Pubitemid 29394003)
21. Kamma H, Satoh H, Matusi M, Wu WW, Fujiwara M, Horiguchi H. 2001. Characterization of hnRNP A2 and B1 using monoclonal antibodies: Intracellular distribution and metabolism through cell cycle. Immunol Lett 76: 49-54. (Pubitemid 32166911)
22. Kim E, Goren A, Ast G. 2008. Alternative splicing: Current perspectives. Bioessays 30: 38-47.
23. Koren E, Lev-Maor G, Ast G. 2007. The emergence of alternative 3′ and 5′ splice site Exons from constitutive exons. PLoS Comput Biol 3: 895-908. (Pubitemid 46827935)
24. Kozak M. 1991. Structural features in eukaryotic messenger-RNAs that modulate the initiation of translation. J Biol Chem 266: 19867-19870. (Pubitemid 21908396)
25. Krecic AM, Swanson MS. 1999. hnRNP complexes: Composition, structure, and function. Curr Opin Cell Biol 11: 363-371.
26. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and clustal X version 2.0. Bioinformatics 23: 2947-2948.
27. Lev-Maor G, Goren A, Sela N, Kim E, Keren H, Doron-Faigenboim A, Leibman-Barak S, Pupko T, Ast G. 2007. The 'alternative' choice of constitutive exons throughout evolution. PLoS Genet 3: 2221-2234.
28. Ma ASW, Moran-Jones K, Shan J, Munro TP, Snee MJ, Hoek KS, Smith R. 2002. Heterogeneous nuclear ribonucleoprotein A3, a novel RNA trafficking response element-binding protein. J Biol Chem 277: 18010-18020. (Pubitemid 34967613)
29. Maggipinto M, Rabiner C, Kidd GJ, Hawkins AJ, Smith R, Barbarese E. 2004. Increased expression of the MBP mRNA binding protein HnRNP A2 during oligodendrocyte differentiation. J Neurosci Res 75: 614-623. (Pubitemid 38280701)
30. Maglott D, Ostell J, Pruitt KD, Tatusova T. 2005. Entrez Gene: Gene-centered information at NCBI. Nucleic Acids Res 33: D54-D58. (Pubitemid 40207830)
31. Maris C, Dominguez C, Allain FHT. 2005. The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J 272: 2118-2131. (Pubitemid 40655326)
32. Matsui M, Horiguchi H, Kamma H, Fujiwara M, Ohtsubo R, Ogata T. 2000. Testis- and developmental stage-specific expression of hnRNP A2/B1 splicing isoforms, B0a/b. Biochim Biophys Acta 1493: 33-40.
33. Mayeda A, Munroe SH, Caceres JF, Krainer AR. 1994. Function of conserved domains of hnRNP A1 and other hnRNP A/B proteins. EMBO J 13: 5483-5495. (Pubitemid 24351827)
34. Modrek B, Lee CJ. 2003. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet 34: 177-180. (Pubitemid 36666928)
35. Moran-Jones K, Wayman L, Kennedy DD, Reddel RR, Sara S, Snee MJ, Smith R. 2005. hnRNP A2, a potential ssDNA/RNA molecular adapter at the telomere. Nucleic Acids Res 33: 486-496. (Pubitemid 40360978)
36. Munro TP, Magee RJ, Kidd GJ, Carson JH, Barbarese E, Smith LM, Smith R. 1999. Mutational analysis of a heterogeneous nuclear ribonucleoprotein A2 response element for RNA trafficking. J Biol Chem 274: 34389-34395. (Pubitemid 129511783)
37. 0. RNA 1: 171-182.
38. Needleman S, Wunsch CD. 1970. A general method applicable to search for similarities in amino acid sequence of 2 proteins. J Mol Biol 48: 443-453.
39. Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ. 2005. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet 21: 73-77. (Pubitemid 40127349)
40. Roca X, Sachidanandam R, Krainer AR. 2005. Determinants of the inherent strength of human 5′ splice sites. RNA 11: 683-698. (Pubitemid 40594335)
41. Shan JG, Munro TP, Barbarese E, Carson JH, Smith R. 2003. A molecular mechanism for mRNA trafficking in neuronal dendrites. J Neurosci 23: 8859-8866. (Pubitemid 37210898)
42. Shapiro MB, Senapathy P. 1987. RNA splice junctions of different classes of eukaryotes - sequence statistics and functional implications in gene-expression. Nucleic Acids Res 15: 7155-7174.
43. Smith R. 2004. Moving molecules: mRNA trafficking in mammalian oligodendrocytes and neurons. Neuroscientist 10: 495-500. (Pubitemid 39546392)
44. Sorek R. 2007. The birth of new exons: Mechanisms and evolutionary consequences. RNA 13: 1603-1608. (Pubitemid 47481668)
45. Sueoka E, Sueoka N, Iwanaga K, Sato A, Suga K, Hayashi S, Nagasawa K, Nakachi K. 2005. Detection of plasma hnRNP B1 mRNA, a new cancer biomarker, in lung cancer patients by quantitative real-time polymerase chain reaction. Lung Cancer 48: 77-83. (Pubitemid 40381002)
46. Tanaka E, Fukuda H, Nakashima K, Tsuchiya N, Seimiya H, Nakagama H. 2007. HnRNP A3 binds to and protects mammalian telomeric repeats in vitro. Biochem Biophys Res Commun 358: 608-614. (Pubitemid 46755748)
47. Venables JP, Koh CS, Froehlich U, Lapointe E, Couture S, Inkel L, Bramard A, Paquet ER, Watier V, Durand M, et al. 2008. Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol Cell Biol 28: 6033-6043.
48. Wang ZF, Burge CB. 2008. Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. RNA 14: 802-813.
49. Wang XQ, Rothnagel JA. 2004. 5′-Untranslated regions with multiple upstream AUG codons can support low-level translation via leaky scanning and reinitiation. Nucleic Acids Res 32: 1382-1391.
50. Wu SL, Sato M, Endo C, Sakurada A, Dong BM, Aikawa H, Chen Y, Okada Y, Matsumura Y, Sueoka E, et al. 2003. hnRNP B1 protein may be a possible prognostic factor in squamous cell carcinoma of the lung. Lung Cancer 41: 179-186. (Pubitemid 36842781)
51. Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394. (Pubitemid 38901668)
52. Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB. 2005. Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci 102: 2850-2855. (Pubitemid 40299880)