Quantification of alternatively spliced FGFR2 RNAs using the RNA invasive cleavage assay

RNA

Volumn 9, Issue 12, 2003, Pages 1552-1561

  Wagner, Eric J ^a,d   Curtis, Michelle L ^b   Robson, Nicole D ^a   Baraniak, Andrew P ^a   Eis, Peggy S ^b,c   Garcia Blanco, Mariano A ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b Third Wave Technologies Inc   (United States)

^c UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^d UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Alternative splicing; FGFR2; Gene expression; Invader RNA assay; Invasive cleavage; RNA quantification

Indexed keywords

FIBROBLAST GROWTH FACTOR RECEPTOR 2; IMMUNOGLOBULIN; RECEPTOR SUBTYPE; RNA;

ACCURACY; ALTERNATIVE RNA SPLICING; ANIMAL CELL; ARTICLE; BIOASSAY; CANCER CELL; CELL LYSATE; CONTROLLED STUDY; EXON; GENE EXPRESSION; GENE SILENCING; NONHUMAN; PRIORITY JOURNAL; PROSTATE CARCINOMA; PROTEIN DOMAIN; PROTEIN EXPRESSION; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA CLEAVAGE; RNA PURIFICATION; RNA STRUCTURE; TISSUE CULTURE;

ALTERNATIVE SPLICING; BASE SEQUENCE; DNA PRIMERS; HUMANS; HYDROLYSIS; MOLECULAR SEQUENCE DATA; RECEPTOR PROTEIN-TYROSINE KINASES; RECEPTOR, FIBROBLAST GROWTH FACTOR, TYPE 2; RECEPTORS, FIBROBLAST GROWTH FACTOR; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA;

ANIMALIA;

EID: 0345305414     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5840803     Document Type: Article

References (24)

1. Black, D.L. 2000. Protein diversity from alternative splicing: A challenge for bioinformatics and post-genome biology. Cell. 103: 367-370.
2. Carstens, R.P., Eaton, J.V., Krigman, H.R., Walther, P.J., and Garcia-Blanco, M.A. 1997. Alternative splicing of fibroblast growth factor receptor 2 (FGF-R2) in human prostate cancer. Oncogene 15: 3059-3065.
3. Carstens, R.P., McKeehan, W.L., and Garcia-Blanco, M.A. 1998. An intronic sequence element mediates both activation and repression of rat fibroblast growth factor receptor 2-pre-mRNA splicing. Mol. Cell. Biol. 18: 2205-2217.
4. Carstens, R.P., Wagner, E.J., and Garcia-Blanco, M.A. 2000. An intronic splicing silencer causes skipping of the IIIb exon of fibroblast growth factor receptor 2 through involvement of polypyrimidine tract binding protein. Mol. Cell. Biol. 20: 7388-7400.
5. Cartegni, L. and Krainer, A.R. 2002. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat. Genet. 30: 377-384.
6. Cartegni, L., Chew, S.L., and Krainer, A.R. 2002. Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nat. Rev. Genet. 3: 285-298.
7. de Arruda, M., Lyamichev, V.I., Eis, P.S., Iszczyszyn, W., Kwiatkowski, R.W., Law, S.M., Olson, M.C., and Rasmussen, E.B. 2002. Invader technology for DNA and RNA analysis: Principles and applications. Expert Rev. Mol. Diagn. 2: 487-496.
8. De Moerlooze, L., Spencer-Dene, B., Revest, J., Hajihosseini, M., Rosewell, I., and Dickson, C. 2000. An important role for the IIIb isoform of fibroblast growth factor receptor 2 (FGFR2) in mesenchymal-epithelial signalling during mouse organogenesis. Development 127: 483-492.
9. Del Gatto, F., Plet, A., Gesnel, M.C., Fort, C., and Breathnach, R. 1997. Multiple interdependent sequence elements control splicing of a fibroblast growth factor receptor 2 alternative exon. Mol. Cell. Biol. 17: 5106-5116.
10. Eis, P.S., Olson, M.C., Takova, T., Curtis, M.L., Olson, S.M., Vener, T.I., Ip, H.S., Vedvik, K.L., Bartholomay, C.T., Allawi, H.T., et al. 2001. An invasive cleavage assay for direct quantitation of specific RNAs. Nat. Biotechnol. 19: 673-676.
11. Ghosh, S.S., Eis, P.S.; Blumeyer, K., Fearon, K., and Millar, D.P. 1994. Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer. Nucleic Acids Res. 22: 3155-3159.
12. Hall, J.G., Eis, P.S., Law, S.M., Reynaldo, L.P., Prudent, J.R., Marshall, D.J., Allawi, H.T., Mast, A.L., Dahlberg, J.E., Kwiatkowski, R.W., et al. 2000. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl. Acad. Sci. 97: 8272-8277.
13. Harju, S. and Peterson, K.R. 2001. Sensitive ribonuclease protection assay employing glycogen as a carrier and a single inactivation/precipitation step. Biotechniques 30: 1199-1203.
14. Jones, R.B., Wang, F., Luo, Y., Yu, C., Jin, C., Suzuki, T., Kan, M., and McKeehan, W.L. 2001. The nonsense-mediated decay pathway and mutually exclusive expression of alternatively spliced FGFR2IIIb and -IIIc mRNAs. J. Biol. Chem. 276: 4158-4167.
15. Kaiser, M.W., Lyamicheva, N., Ma, W., Miller, C., Neri, B., Fors, L., and Lyamichev, V.I. 1999. A comparison of eubacterial and archaeal structure-specific 5′-exonucleases. J. Biol. Chem. 274: 21387-21394.
16. Lyamichev, V., Mast, A.L., Hall, J.G., Prudent, J.R., Kaiser, M.W., Takova, T., Kwiatkowski, R.W., Sander, T.J., de Arruda, M., Arco; D.A., et al. 1999. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17: 292-296.
17. Lyamichev, V.I., Kaiser, M.W., Lyamicheva, N.E., Vologodskii, A.V., Hall, J.G., Ma, W.P., Allawi, H.T., and Neri, B.P. 2000. Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry 39: 9523-9532.
18. Ma, W.P., Kaiser, M.W., Lyamicheva, N., Schaefer, J.J., Allawi, H.T., Takova, T., Neri, B.P., and Lyamichev, V.I. 2000. RNA template-dependent 5′ nuclease activity of Thermus aquaticus and Thermus thermophilus DNA polymerases. J. Biol. Chem. 275: 24693-24700.
19. Miki, T., Fleming, T.P., Bottaro, D.P., Rubin, J.S., Ron, D., and Aaronson, S.A. 1991. Expression cDNA cloning of the KGF receptor by creation of a transforming autocrine loop. Science 251: 72-75.
20. Modrek, B. and Lee, C. 2002. A genomic view of alternative splicing. Nat. Genet. 30: 13-19.
21. Savkur, R.S., Philips, A.V., and Cooper, T.A. 2001. Aberrant regulation of insulin receptor alternative splicing is associated with insulin resistance in myotonic dystrophy. Nat. Genet. 29: 40-47.
22. Wagner, E.J. and Garcia-Blanco, M.A. 2001. Polypyrimidine tract binding protein antagonizes exon definition. Mol. Cell. Biol. 21: 3281-3288.
23. -. 2002. RNAi-mediated PTB depletion leads to enhanced exon definition. Mol. Cell. 10: 943-949.
24. Yan G., Fukabori, Y., McBride, G., Nikolaropolous, S., and McKeehan, W.L. 1993. Exon switching and activation of stromal and embryonic fibroblast growth factor (FGF)-FGF receptor genes in prostate epithelial cells accompany stromal independence and malignancy. Mol. Cell. Biol. 13: 4513-4522.