Regulation of alternative splicing within the supraspliceosome

Journal of Structural Biology

Volumn 177, Issue 1, 2012, Pages 152-159

  Sebbag Sznajder, Naama ^a   Raitskin, Oleg ^a   Angenitzki, Minna ^a   Sato, Taka Aki ^b   Sperling, Joseph ^c   Sperling, Ruth ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b UNIVERSITY OF TOKYO   (Japan)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Alternative splicing; Macromolecular assembly; Ribonucleoprotein; RNA splicing; SR proteins; Supraspliceosome

Indexed keywords

CERAMIDE; MESSENGER RNA; RIBONUCLEOPROTEIN; SERINE ARGININE RICH PROTEIN; SUPRASPLICEOSOME; SURVIVAL MOTOR NEURON PROTEIN; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; ARTICLE; GENE OVEREXPRESSION; HUMAN; HUMAN CELL; MOTONEURON; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; REGULATORY MECHANISM; UPREGULATION;

ALTERNATIVE SPLICING; CERAMIDES; EXONS; HELA CELLS; HETEROGENEOUS-NUCLEAR RIBONUCLEOPROTEINS; HUMANS; MICROSCOPY, ELECTRON; NUCLEAR PROTEINS; PHOSPHORYLATION; RIBONUCLEOPROTEINS; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; RNA-BINDING PROTEINS; SPLICEOSOMES; TRANS-ACTIVATORS; TRANSCRIPTOME; UP-REGULATION;

EUKARYOTA;

EID: 84855859152     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.11.005     Document Type: Article

References (51)

1. Azubel M., Wolf S.G., Sperling J., Sperling R. Three-dimensional structure of the native spliceosome by cryo-electron microscopy. Mol. Cell 2004, 15:833-839.
2. Azubel M., Habib N., Sperling J., Sperling R. Native spliceosomes assemble with pre-mRNA to form supraspliceosomes. J. Mol. Biol. 2006, 356:955-966.
3. Brett D., Pospisil H., Valcárcel J., Reich J., Bork P. Alternative splicing and genome complexity. Nat. Genet. 2002, 30:29-30.
4. Buratti E., Stuani C., De Prato G., Baralle F.E. SR protein-mediated inhibition of CFTR exon 9 inclusion: molecular characterization of the intronic splicing silencer. Nucleic Acids Res. 2007, 35:4359-4368.
5. Chalfant C.E., Ogretmen B., Galadari S., Kroesen B.J., Pettus B.J., Hannun Y.A. FAS activation induces dephosphorylation of SR proteins; dependence on the de novo generation of ceramide and activation of protein phosphatase 1. J. Biol. Chem. 2001, 276:44848-44855.
6. Chalfant C.E., Rathman K., Pinkerman R.L., Wood R.E., Obeid L.M., Ogretmen B., Hannun Y.A. De novo ceramide regulates the alternative splicing of caspase 9 and Bcl-x in A549 lung adenocarcinoma cells. Dependence on protein phosphatase-1. J. Biol. Chem. 2002, 277:12587-12595.
7. Cohen-Krausz S., Sperling R., Sperling J. Exploring the architecture of the intact supraspliceosome using electron microscopy. J. Mol. Biol. 2007, 368:319-327.
8. de Almeida S.F., Carmo-Fonseca M. The CTD role in cotranscriptional RNA processing and surveillance. FEBS Lett. 2008, 582:1971-1976.
9. Gallego M.E., Gattoni R., Stevenin J., Marie J., Expert-Bezancon A. The SR splicing factors ASF/SF2 and SC35 have antagonistic effects on intronic enhancer-dependent splicing of the beta-tropomyosin alternative exon 6A. EMBO J. 1997, 16:1772-1784.
10. Garcia-Blanco M.A., Baraniak A.P., Lasda E.L. Alternative splicing in disease and therapy. Nat. Biotechnol. 2004, 22:535-546.
11. Gerber A., O'Connell M.A., Keller W. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA 1997, 3:453-463.
12. Han J., Ding J.H., Byeon C.W., Kim J.H., Hertel K.J., Jeong S., Fu X.D. SR proteins induce alternative exon skipping through their activities on the flanking constitutive exons. Mol. Cell. Biol. 2011, 31:793-802.
13. Heinrich B., Zhang Z., Raitskin O., Hiller M., Benderska N., Hartmann A.M., Bracco L., Elliott D., Ben-Ari S., Soreq H., Sperling J., Sperling R., Stamm S. Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA. J. Biol. Chem. 2009, 284:14303-14315.
14. Ibrahim E.C., Schaal T.D., Hertel K.J., Reed R., Maniatis T. Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc. Natl. Acad. Sci. USA 2005, 102:5002-5007.
15. Jiang Z.H., Zhang W.J., Rao Y., Wu J.Y. Regulation of Ich-1 pre-mRNA alternative splicing and apoptosis by mammalian splicing factors. Proc. Natl. Acad. Sci. USA 1998, 95:9155-9160.
16. Kamhi E., Yahalom G., Kass G., Hacham Y., Sperling R., Sperling J. AUG sequences are required to sustain nonsense-codon-mediated suppression of splicing. Nucleic Acids Res. 2006, 34:3421-3433.
17. Khan F.A., Jaiswal A.K., Szer W. Cloning and sequence analysis of a human type A/B hnRNP protein. FEBS Lett. 1991, 290:159-161.
18. Kornblihtt A.R. Coupling transcription and alternative splicing. Adv. Exp. Med. Biol. 2007, 623:175-189.
19. Krainer A.R., Maniatis T., Ruskin B., Green M.R. Normal and mutant human β-globin pre-mRNAs are faithfully and efficiently spliced in vitro. Cell 1984, 36:993-1005.
20. Lai F., Chen C.-X., Carter K.C., Nishikura K. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases. Mol. Cell. Biol. 1997, 17:2413-2424.
21. Lau P.P., Zhu H.J., Nakamuta M., Chan L. Cloning of an Apobec-1-binding protein that also interacts with apolipoprotein B mRNA and evidence for its involvement in RNA editing. J. Biol. Chem. 1997, 272:1452-1455.
22. Lemaire R., Winne A., Sarkissian M., Lafyatis R. SF2 and SRp55 regulation of CD45 exon 4 skipping during T cell activation. Eur. J. Immunol. 1999, 29:823-837.
23. Li B., Wachtel C., Miriami E., Yahalom G., Friedlander G., Sharon G., Sperling R., Sperling J. Stop codons affect 5' splice site selection by surveillance of splicing. Proc. Natl. Acad. Sci. USA 2002, 99:5277-5282.
24. Lin S., Fu X.D. SR proteins and related factors in alternative splicing. Adv. Exp. Med. Biol. 2007, 623:107-122.
25. Long J.C., Caceres J.F. The SR protein family of splicing factors: master regulators of gene expression. Biochem. J. 2009, 417:15-27.
26. Lorson C.L., Hahnen E., Androphy E.J., Wirth B. A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proc. Natl. Acad. Sci. USA 1999, 96:6307-6311.
27. Markus M.A., Heinrich B., Raitskin O., Adams D.J., Mangs H., Goy C., Ladomery M., Sperling R., Stamm S., Morris B.J. WT1 interacts with the splicing protein RBM4 and regulates its ability to modulate alternative splicing in vivo. Exp. Cell Res. 2006, 312:3379-3388.
28. Medalia O., Heim M., Guckenberger R., Sperling R., Sperling J. Gold-tagged RNA-A probe for macromolecular assemblies. J. Struct. Biol. 1999, 127:113-119.
29. Medalia O., Typke D., Hegerl R., Angenitzki M., Sperling J., Sperling R. Cryoelectron microscopy and cryoelectron tomography of the nuclear pre-mRNA processing machine. J. Struct. Biol. 2002, 138:74-84.
30. Miriami E., Sperling J., Sperling R. Heat shock affects 5' splice site selection, cleavage and ligation of CAD pre-mRNA in hamster cells, but not its packaging in lnRNP particles. Nucleic Acids Res. 1994, 22:3084-3091.
31. Modrek B., Lee C. A genomic view of alternative splicing. Nat. Genet. 2002, 30:13-19.
32. Müller S., Wolpensinger B., Angenitzki M., Engel A., Sperling J., Sperling R. A supraspliceosome model for large nuclear ribonucleoprotein particles based on mass determinations by scanning transmission electron microscopy. J. Mol. Biol. 1998, 283:383-394.
33. Nadano D., Ishihara G., Aoki C., Yoshinaka T., Irie S., Sato T.A. Preparation and characterization of antibodies against human ribosomal proteins: heterogeneous expression of S11 and S30 in a panel of human cancer cell lines. Jpn. J. Cancer Res. 2000, 91:802-810.
34. Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 2008, 40:1413-1415.
35. Pandit S., Wang D., Fu X.D. Functional integration of transcriptional and RNA processing machineries. Curr. Opin. Cell Biol. 2008, 20:260-265.
36. Perales R., Bentley D. "Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell 2009, 36:178-191.
37. Raitskin O., Angenitzki M., Sperling J., Sperling R. Large nuclear RNP particles-the nuclear pre-mRNA processing machine. J. Struct. Biol. 2002, 140:123-130.
38. Raitskin O., Cho D.S., Sperling J., Nishikura K., Sperling R. RNA editing activity is associated with splicing factors in lnRNP particles: The nuclear pre-mRNA processing machinery. Proc. Natl. Acad. Sci. USA 2001, 98:6571-6576.
39. Screaton G.R., Caceres J.F., Mayeda A., Bell M.V., Plebanski M., Jackson D.G., Bell J.I., Krainer A.R. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J. 1995, 14:4336-4349.
40. Shepard P.J., Hertel K.J. The SR protein family. Genome Biol. 2009, 10:242.
41. Solis A.S., Peng R., Crawford J.B., Phillips J.A., Patton J.G. Growth hormone deficiency and splicing fidelity: two serine/arginine-rich proteins, ASF/SF2 and SC35, act antagonistically. J. Biol. Chem. 2008, 283:23619-23626.
42. Sommer B., Köhler M., Sprengel R., Seeburg P.H. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 1991, 67:11-19.
43. Sperling J., Azubel M., Sperling R. Structure and function of the pre-mRNA splicing machine. Structure 2008, 16:1605-1615.
44. Sperling R., Sperling J., Levine A.D., Spann P., Stark G.R., Kornberg R.D. Abundant nuclear ribonucleoprotein form of CAD RNA. Mol. Cell Biol. 1985, 5:569-575.
45. Sperling R., Koster A.J., Melamed-Bessudo C., Rubinstein A., Angenitzki M., Berkovitch-Yellin Z., Sperling J. Three-dimensional image reconstruction of large nuclear RNP (lnRNP) particles by automated electron tomography. J. Mol. Biol. 1997, 267:570-583.
46. Srebrow A., Kornblihtt A.R. The connection between splicing and cancer. J. Cell Sci. 2006, 119:2635-2641.
47. Sumanasekera C., Watt D.S., Stamm S. Substances that can change alternative splice-site selection. Biochem. Soc. Trans. 2008, 36:483-490.
48. ten Dam G.B., Zilch C.F., Wallace D., Wieringa B., Beverley P.C., Poels L.G., Screaton G.R. Regulation of alternative splicing of CD45 by antagonistic effects of SR protein splicing factors. J. Immunol. 2000, 164:5287-5295.
49. Wang G.S., Cooper T.A. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat. Rev. Genet. 2007, 8:749-761.
50. Wang Z., Burge C.B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 2008, 14:802-813.
51. Yitzhaki S., Miriami E., Sperling J., Sperling R. Phosphorylated Ser/Arg-rich proteins: limiting factors in the assembly of 200S large nuclear ribonucleoprotein particles. Proc. Natl. Acad. Sci. USA 1996, 93:8830-8835.