SR Protein-mediated Inhibition of CFTR Exon 9 Inclusion: Molecular Characterization of the Intronic Splicing Silencer

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2007 Jun 20

PMID 17576688

Citations 35

Authors

Emanuele Buratti

Cristiana Stuani

Greta De Prato

Francisco E Baralle

Affiliations

Soon will be listed here.

Abstract

The intronic splicing silencer (ISS) of CFTR exon 9 promotes exclusion of this exon from the mature mRNA. This negative influence has important consequences with regards to human pathologic events, as lack of exon 9 correlates well with the occurrence of monosymptomatic and full forms of CF disease. We have previously shown that the ISS element interacts with members of the SR protein family. In this work, we now provide the identification of SF2/ASF and SRp40 as the specific SR proteins binding to this element and map their precise binding sites in IVS9. We have also performed a functional analysis of the ISS element using a variety of unrelated SR-binding sequences and different splicing systems. Our results suggest that SR proteins mediate CFTR exon 9 exclusion by providing a 'decoy' sequence in the vicinity of its suboptimal donor site. The results of this study give an insight on intron 'exonization' mechanisms and provide useful indications for the development of novel therapeutic strategies aimed at the recovery of exon inclusion.

Citing Articles

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Disruption of splicing-regulatory elements using CRISPR/Cas9 to rescue spinal muscular atrophy in human iPSCs and mice.

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Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing.

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Activation of Cryptic 3' Splice-Sites by SRSF2 Contributes to Cassette Exon Skipping.

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References

Sanford J, Ellis J, Caceres J . Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem Soc Trans. 2005; 33(Pt 3):443-6. DOI: 10.1042/BST0330443. View

Matlin A, Clark F, Smith C . Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol. 2005; 6(5):386-98. DOI: 10.1038/nrm1645. View

Li X, Manley J . Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell. 2005; 122(3):365-78. DOI: 10.1016/j.cell.2005.06.008. View

Garcia-Blanco M . Making antisense of splicing. Curr Opin Mol Ther. 2005; 7(5):476-82. View

Wilton S, Fletcher S . RNA splicing manipulation: strategies to modify gene expression for a variety of therapeutic outcomes. Curr Gene Ther. 2005; 5(5):467-83. DOI: 10.2174/156652305774329249. View

Mercado P, Ayala Y, Romano M, Buratti E, Baralle F . Depletion of TDP 43 overrides the need for exonic and intronic splicing enhancers in the human apoA-II gene. Nucleic Acids Res. 2005; 33(18):6000-10. PMC: 1270946. DOI: 10.1093/nar/gki897. View

Buratti E, Brindisi A, Giombi M, Tisminetzky S, Ayala Y, Baralle F . TDP-43 binds heterogeneous nuclear ribonucleoprotein A/B through its C-terminal tail: an important region for the inhibition of cystic fibrosis transmembrane conductance regulator exon 9 splicing. J Biol Chem. 2005; 280(45):37572-84. DOI: 10.1074/jbc.M505557200. View

Li X, Wang J, Manley J . Loss of splicing factor ASF/SF2 induces G2 cell cycle arrest and apoptosis, but inhibits internucleosomal DNA fragmentation. Genes Dev. 2005; 19(22):2705-14. PMC: 1283963. DOI: 10.1101/gad.1359305. View

Blaustein M, Pelisch F, Tanos T, Munoz M, Wengier D, Quadrana L . Concerted regulation of nuclear and cytoplasmic activities of SR proteins by AKT. Nat Struct Mol Biol. 2005; 12(12):1037-44. DOI: 10.1038/nsmb1020. View

10.

Li X, Manley J . New talents for an old acquaintance: the SR protein splicing factor ASF/SF2 functions in the maintenance of genome stability. Cell Cycle. 2005; 4(12):1706-8. DOI: 10.4161/cc.4.12.2210. View

11.

Ayala Y, Pagani F, Baralle F . TDP43 depletion rescues aberrant CFTR exon 9 skipping. FEBS Lett. 2006; 580(5):1339-44. DOI: 10.1016/j.febslet.2006.01.052. View

12.

Dye M, Gromak N, Proudfoot N . Exon tethering in transcription by RNA polymerase II. Mol Cell. 2006; 21(6):849-59. DOI: 10.1016/j.molcel.2006.01.032. View

13.

Buratti E, Baralle M, Baralle F . Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Res. 2006; 34(12):3494-510. PMC: 1524908. DOI: 10.1093/nar/gkl498. View

14.

Ram O, Ast G . SR proteins: a foot on the exon before the transition from intron to exon definition. Trends Genet. 2006; 23(1):5-7. DOI: 10.1016/j.tig.2006.10.002. View

15.

Aznarez I, Chan E, Zielenski J, Blencowe B, Tsui L . Characterization of disease-associated mutations affecting an exonic splicing enhancer and two cryptic splice sites in exon 13 of the cystic fibrosis transmembrane conductance regulator gene. Hum Mol Genet. 2003; 12(16):2031-40. DOI: 10.1093/hmg/ddg215. View

16.

Groman J, Hefferon T, Casals T, Bassas L, Estivill X, des Georges M . Variation in a repeat sequence determines whether a common variant of the cystic fibrosis transmembrane conductance regulator gene is pathogenic or benign. Am J Hum Genet. 2003; 74(1):176-9. PMC: 1181905. DOI: 10.1086/381001. View

17.

Buratti E, Muro A, Giombi M, Gherbassi D, Iaconcig A, Baralle F . RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon. Mol Cell Biol. 2004; 24(3):1387-400. PMC: 321440. DOI: 10.1128/MCB.24.3.1387-1400.2004. View

18.

Shin C, Feng Y, Manley J . Dephosphorylated SRp38 acts as a splicing repressor in response to heat shock. Nature. 2004; 427(6974):553-8. DOI: 10.1038/nature02288. View

19.

Shen H, Kan J, Green M . Arginine-serine-rich domains bound at splicing enhancers contact the branchpoint to promote prespliceosome assembly. Mol Cell. 2004; 13(3):367-76. DOI: 10.1016/s1097-2765(04)00025-5. View

20.

Nilsen T . Too hot to splice. Nat Struct Mol Biol. 2004; 11(3):208-9. DOI: 10.1038/nsmb0304-208. View