The hnRNPs F and H2 bind to similar sequences to influence gene expression

Biochemical Journal

Volumn 393, Issue 1, 2006, Pages 361-371

  Alkan, Serkan A ^a,b   Martincic, Kathleen ^a   Milcarek, Christine ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Electrophoretic mobility shift assay (EMSA); Heterogeneous nuclear ribonucleoprotein (hnRNP); Polyadenylation; RNA interference (RNAi); UV cross linking

Indexed keywords

ASSAYS; FLUORESCENCE; GENES; MUTAGENESIS; MUTAGENS; RNA; ULTRAVIOLET RADIATION;

ELECTROPHORETIC MOBILITY-SHIFT ASSAY (EMSA); HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN (HNRNP); POLYADENYLATION; RNA INTERFERENCE (RNAI); UV-CROSS-LINKING;

PROTEINS;

CLEAVAGE STIMULATION FACTOR; GREEN FLUORESCENT PROTEIN; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; RNA POLYMERASE II; SMALL INTERFERING RNA;

ARTICLE; BINDING AFFINITY; CROSS LINKING; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION; NONHUMAN; POINT MUTATION; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN RNA BINDING; PROTEIN STRUCTURE; REPORTER GENE; RNA BINDING; SEQUENCE ANALYSIS;

BASE SEQUENCE; DOWN-REGULATION; GENE EXPRESSION REGULATION; GENES, REPORTER; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEIN GROUP F-H; HUMANS; MUTATION; OLIGORIBONUCLEOTIDES; PROTEIN BINDING; RNA INTERFERENCE;

SIMIAN VIRUS 40;

EID: 30044446861     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20050538     Document Type: Article

References (38)

1. Krecic, A. M. and Swanson, M. S. (1999) HnRNP complexes: composition, structure, and function. Curr. Opin. Cell Biol. 11, 363-371
2. Birney, E., Kumar, S. and Krainer, A. R. (1993) Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucleic Acids Res. 21, 5803-5816
3. Liu, H., Zhang, W., Reed, R. B., Liu, W. and Grabowski, P. J. (2002) Mutations in RRM4 uncouple the splicing repression and RNA-binding activities of polypyrimidine tract binding protein. RNA 8, 137-149
4. Shamoo, Y., Abdul-Manan, N. and Williams, K. R. (1995) Multiple RNA binding domains (RBDs) just don't add up. Nucleic Acids Res. 23, 725-728
5. Rasmussen, H. B., Vorum, H. H., Dejgaard, K., Liu, X., Gromov, P., Madsen, P., Gesser, B., Tommerup, N. and Celis, J. E. (1995) Heterogeneous nuclear ribonucleoproteins (hnRNP) H, H′, and F are members of a ubiquitously expressed subfamily of related but distinct proteins encoded by genes mapping to different chromosomes. J. Biol. Chem. 270, 28780-28789
6. Honore, B. (2000) The hnRNP 2H9 gene, which is involved in the splicing reaction, is a multiply spliced gene, Biochim. Biophys. Acta 1492, 108-119
7. Honore, B., Rasmussen, H. H., Vorum, H., Dejgaard, K., Liu, X. D., Gromov, P., Madsen, P., Gesser, B., Tommerup, N. and Celis, J. E. (1995) Heterogeneous nuclear ribonucleoprotein-H, ribonucleoprotein-H′, and ribonucleoprotein-F are members of a ubiquitously expressed subfamily of related but distinct proteins encoded by genes mapping to different chromosomes. J. Biol. Chem. 270, 28780-28789
8. Matunis, M. J., Xing, J. and Dreyfuss, G. (1994) The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization. Nucleic Acids Res. 22, 1059-1067
9. Grabowski, P. J. (2004) A molecular code for splicing silencing: configurations of guanosine-rich motifs. Biochem. Soc. Trans. 32, 924-927
10. Sironi, M., Menozzi, G., Riva, L., Cagliani, R., Comi, G. P., Bresolin, N., Giorda, R. and Pozzoli, U. (2004) Silencer elements as possible inhibitors of pseudoexon splicing. Nucleic Acids Res. 32, 1783-1791
11. Bagga, P. S., Ford, L. P., Chen, F. and Wilusz, J. (1995) The G-rich auxiliary downstream element has distinct sequence and position requirements and mediates efficient 3′ end pre-mRNA processing through a trans-acting factor. Nucleic Acids Res. 23, 1625-1631
12. Arhin, G. K., Boots, M., Bagga, P. S., Milcarek, C. and Wilusz, J. (2002) Downstream sequence elements with different affinities for the hnRNP H/H′ protein influence the processing efficiency of mammalian polyadenylation signals. Nucleic Acids Res. 30, 1842-1850
13. Veraldi, K. L., Arhin, G. K., Martincic, K., Chung-Ganster, L. H., Wilusz, J. and Milcarek, C. (2001) hnRNP F influences binding of a 64-kilodalton subunit of cleavage stimulation factor to mRNA precursors in mouse B cells. Mol. Cell. Biol. 21, 1228-1238
14. Chen, F., MacDonald, C. and Wilusz, J. (1995) Cleavage site determinants in the mammalian polyadenylation signal. Nucleic Acids Res. 23, 2614-2620
15. Bagga, P., Arhin, G. and Wilusz, J. (1998) DSEF-1 is a member of the hnRNP H family of RNA-binding proteins and stimulates pre-mRNA cleavage and polyadenylation in vitro. Nucleic Acids Res. 26, 5343-5350
16. Chou, M. Y., Rooke, N., Turck, C. W. and Black, D. L. (1999) hnRNP H is a component of a splicing enhancer complex that activates a c-src alternative exon in neuronal cells. Mol. Cell. Biol. 19, 69-77
17. Takagaki, Y., MacDonald, C. C., Shenk, T. and Manley, J. L. (1992) The human 64-kDa polyadenylation factor contains a ribonucleoprotein-type RNA binding domain and unusual auxiliary motifs. Proc. Natl. Acad. Sci. U.S.A. 89, 1403-1407
18. Veraldi, K., Edwalds-Gilbert, G., MacDonald, C., Wallace, A. and Milcarek, C. (2000) Isolation and characterization of polyadenylation complexes assembled in vitro. RNA 6, 768-777
19. Qian, Z. and Wilusz, J. (1991) An RNA binding protein specifically interacts with a functionally important domain of the downstream element of the SV40 late polyadenylation signal. Mol. Cell. Biol. 11, 5312-5320
20. Wilusz, J., Felig, D. I. and Shenk, T. (1988) The C proteins of heterogeneous nuclear ribonucleoprotein complexes interact with RNA sequences downstream of polyadenylation cleavage sites. Mol. Cell. Biol. 8, 4477-4483
21. Spear, M. A. (2000) Efficient DNA subcloning through selective restriction endonuclease digestion. BioTechniques 28, 660-662
22. Milligan, J. F., Groebe, D. R., Witherell, G. W. and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798
23. Baird, G. S., Zacharias, D. A. and Tsien, R. Y. (2000) Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral. Proc. Natl. Acad. Sci. U.S.A. 97, 11984-11989
24. 0 to S phase transition. Proc. Natl. Acad. Sci. U.S.A. 95, 11095-11100
25. Pfeffer, S. R., Stahl, S. J. and Chamberlin, M. J. (1977) Binding of Escherichia coli RNA polymerase to T7 DNA: displacement of holoenzyme from promoter complexes by heparin. J. Biol. Chem. 252, 5403-5407
26. Cooke, C., Hans, H. and Alwine, J. C. (1999) Utilization of splicing elements and polyadenylation signal elements in the coupling of polyadenylation and last-intron removal. Mol. Cell. Biol. 19, 4971-4979
27. Cooke, C. and Alwine, J. C. (2002) Characterization of specific protein-RNA complexes associated with the coupling of polyadenylation and last-intron removal. Mol. Cell. Biol. 22, 4579-4586
28. Caputi, M. and Zahler, A. M. (2002) SR proteins and hnRNP H regulate the splicing of the HIV-1 lev-specific exon 6D. EMBO J. 21, 845-855
29. Pagani, F., Buratti, E., Stuani, C. and Baralle, F. E. (2003) Missense, nonsense, and neutral mutations define juxtaposed regulatory elements of splicing in cystic fibrosis transmembrane regulator exon 9. J. Biol. Chem. 278, 26580-26588
30. Fogel, B. L. and McNally, M. T. (2000) A cellular protein, hnRNP H, binds to the negative regulator of splicing element from Rous sarcoma virus. J. Biol. Chem. 275, 32371-32378
31. Hastings, M. L., Wilson, C. M. and Munroe, S. H. (2001) A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA. RNA 7, 859-874
32. Jacquenet, S., Mereau, A., Bilodeau, P. S., Damier, L., Stoltzfus, C. M. and Branlant, C. (2001) A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of tat mRNA and binds protein hnRNP H. J. Biol. Chem. 276, 40464-40475
33. Chen, C. D., Kobayashi, R. and Helfman, D. M. (1999) Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing in the rat β-tropomyosin gene. Genes Dev. 13, 593-606
34. Romano, M., Marcucci, R., Buratti, E., Ayala, Y. M., Sebastio, G. and Baralle, F. E. (2002) Regulation of 3′ splice site selection in the 844ins68 polymorphism of the cystathionine β-synthase gene. J. Biol. Chem. 277, 43821-43829
35. Caputi, M. and Zahler, A. M. (2001) Determinalion of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H/H′/F/2H9 family. J. Biol. Chem. 276, 43850-43859
36. Canadillas, J. M. P. and Varani, G. (2003) Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein. EMBO J. 22, 2821-2830
37. Simpson, P. J., Monie, T. P., Szendroi, A., Davydova, N., Tyzack, J. K., Conte, M. R., Read, C. M., Cary, P. D., Svergun, D. I. and Konarev, P. V. (2004) Structure and RNA interactions of the N-terminal RRM domains of PTB. Structure 12, 1631-1643
38. Honore, B., Baandrup, U. and Vorum, H. (2004) Heterogeneous nuclear ribonucleoproteins F and H/H′ show differential expression in normal and selected cancer tissues. Exp. Cell Res. 294, 199-209