RNA metabolism and ubiquitin/ubiquitin-like modifications collide

Briefings in Functional Genomics

Volumn 12, Issue 1, 2013, Pages 66-71

  Pelisch, Federico ^a   Risso, Guillermo ^a   Srebrow, Anabella ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

Alternative splicing; Post translational modifications; SR proteins; SUMO conjugation

Indexed keywords

MESSENGER RNA; SUMO PROTEIN; UBIQUITIN; UBIQUITIN PROTEIN LIGASE E3;

ARTICLE; BIOGENESIS; EXTRACELLULAR MATRIX; GENE EXPRESSION; HUMAN; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN RNA BINDING; RNA EDITING; RNA METABOLISM; RNA PROCESSING; RNA SPLICING; RNA TRANSCRIPTION; RNA TRANSLATION; SPLICEOSOME; TRANSLATION INITIATION;

ALTERNATIVE SPLICING; ANIMALS; HUMANS; MODELS, BIOLOGICAL; PROTEIN PROCESSING, POST-TRANSLATIONAL; RNA; UBIQUITIN;

EUKARYOTA;

EID: 84872805835     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/els053     Document Type: Article

References (51)

1. Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature 2010;463:457-63.
2. Walsh CT, Garneau-Tsodikova S, Gatto GJ, Jr. Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed Engl 2005;44:7342-72.
3. Han J, Xiong J, Wang D, et al. Pre-mRNA splicing: where and when in the nucleus. Trends Cell Biol 2011;21:336-43.
4. Biamonti G, Bonomi S, Gallo S, et al. Making alternative splicing decisions during epithelial-to-mesenchymal transition (EMT). Cell Mol Life Sci 2012;69:2515-26.
5. Grabowski P. Alternative splicing takes shape during neuronal development. Curr Opin Genet Dev 2011;21:388-94.
6. Kalsotra A, Cooper TA. Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet 2011;12:715-29.
7. Llorian M, Smith CW. Decoding muscle alternative splicing. Curr Opin GenetDev 2011;21:380-7.
8. Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009;136: 701-18.
9. Busch A, Hertel KJ. Evolution of SR protein and hnRNP splicing regulatory factors. Wiley Interdiscip Rev RNA 2012;3: 1-12.
10. Long JC, Caceres JF. The SR protein family of splicing factors: master regulators of gene expression. Biochem J 2009;417:15-27.
11. Hunter T. The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol Cell 2007;28:730-8.
12. Finley D. Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem 2009;78: 477-513.
13. Geiss-Friedlander R, Melchior F. Concepts in sumoylation: a decade on. Nat Rev Mol Cell Biol 2007;8:947-56.
14. Bernassola F, Karin M, Ciechanover A, et al. The HECT family of E3 ubiquitin ligases: multiple players in cancer development. Cancer Cell 2008;14:10-21.
15. Deshaies RJ, Joazeiro CA. RING domain E3 ubiquitin ligases. Annu Rev Biochem 2009;78:399-434.
16. Kahyo T, Nishida T, Yasuda H. Involvement of PIAS1 in the sumoylation of tumor suppressor p53. Mol Cell 2001;8: 713-8.
17. Weger S, Hammer E, Heilbronn R. Topors acts as a SUMO-1 E3 ligase for p53 in vitro and in vivo. FEBS Lett 2005;579:5007-12.
18. Kagey MH, Melhuish TA, Wotton D. The polycomb protein Pc2 is a SUMO E3. Cell 2003;113:127-37.
19. Pichler A, Knipscheer P, Saitoh H, et al. The RanBP2 SUMO E3 ligase is neither HECT- nor RING-type. Nat Struct Mol Biol 2004;11:984-91.
20. Pichler A, Gast A, Seeler JS, et al. The nucleoporin RanBP2 has SUMO1 E3 ligase activity. Cell 2002;108:109-20.
21. Hammer E, Heilbronn R, Weger S. The E3 ligase Topors induces the accumulation of polysumoylated forms of DNA topoisomerase I in vitro and in vivo. FEBS Lett 2007;581: 5418-24.
22. Yunus AA, Lima CD. Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA. Mol Cell 2009;35:669-82.
23. Blaustein M, Pelisch F, Srebrow A. Signals, pathways and splicing regulation. Int J Biochem Cell Biol 2007;39:2031-48.
24. Blaustein M, Pelisch F, Coso OA, et al. Mammary epithelial-mesenchymal interaction regulates fibronectinalternative splicing via phosphatidylinositol 3-kinase. J Biol Chem 2004;279:21029-37.
25. Blaustein M, Pelisch F, Tanos T, et al. Concerted regulation of nuclear and cytoplasmic activities of SR proteins by AKT. Nat StructMol Biol 2005;12:1037-44.
26. Patel NA, Kaneko S, Apostolatos HS, et al. Molecular and genetic studies imply Akt-mediated signaling promotes protein kinase CbetaII alternative splicing via phosphorylation of serine/arginine-rich splicing factor SRp40. J Biol Chem 2005;280:14302-9.
27. Shultz JC, Goehe RW, Wijesinghe DS, et al. Alternative splicing of caspase 9 is modulated by the phosphoinositide 3-kinase/Akt pathway via phosphorylation of SRp30a. Cancer Res 2010;70:9185-96.
28. White ES, Sagana RL, Booth AJ, et al. Control of fibroblast fibronectin expression and alternative splicing via the PI3K/ Akt/mTOR pathway. Exp Cell Res 2010;316:2644-53.
29. Zhou Z, Qiu J, Liu W, et al. The Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus. Mol Cell 2012; 47:422-33.
30. Graveley BR. Coordinated control of splicing and translation. Nat StructMol Biol 2005;12:1022-3.
31. Blaustein M, Quadrana L, Risso G, et al. SF2/ASF regulates proteomic diversity by affecting the balance between translation initiation mechanisms. J Cell Biochem 2009;107: 826-33.
32. Wagner SA, Beli P, Weinert BT, et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics 2011;10: M111 013284.
33. Xu G, Paige JS, Jaffrey SR. Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling. Nat Biotechnol 2010;28:868-73.
34. Li T, Evdokimov E, Shen RF, et al. Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins: a proteomic analysis. Proc Natl Acad Sci USA 2004;101:8551-6.
35. Vassileva MT, Matunis MJ. SUMO modification of heterogeneous nuclear ribonucleoproteins. Mol Cell Biol 2004;24: 3623-32.
36. Blomster HA, Hietakangas V, Wu J, et al. Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol Cell Proteomics 2009;8:1382-90.
37. Golebiowski F, Matic I, Tatham MH, et al. System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2009;2:ra24.
38. Vertegaal AC, Ogg SC, Jaffray E, et al. A proteomic study of SUMO-2 target proteins. J Biol Chem 2004;279:33791-8.
39. Song EJ, Werner SL, Neubauer J, et al. The Prp19 complex and the Usp4Sart3 deubiquitinating enzyme control reversible ubiquitination at the spliceosome. Genes Dev 2010;24: 1434-47.
40. Desterro JM, Keegan LP, Jaffray E, et al. SUMO-1 modification alters ADAR1 editing activity. Mol BiolCell 2005;16: 5115-26.
41. Vethantham V, Rao N, Manley JL. Sumoylation modulates the assembly and activity of the pre-mRNA 3' processing complex. Mol Cell Biol 2007;27:8848-58.
42. Vethantham V, Rao N, Manley JL. Sumoylation regulates multiple aspects of mammalian poly(A) polymerase function. Genes Dev 2008;22:499-511.
43. Pelisch F, Khauv D, Risso G, et al. Involvement of hnRNP A1 in the matrix metalloprotease-3-dependent regulation of Rac1 pre-mRNA splicing. J Cell Biochem 2012;113: 2319-29.
44. Pelisch F, Gerez J, Druker J, et al. The serine/arginine-rich protein SF2/ASF regulates protein sumoylation. Proc Natl Acad Sci USA 2010;107:16119-24.
45. Rappsilber J, Ryder U, Lamond AI, et al. Large-scale proteomic analysis of the human spliceosome. Genome Res 2002; 12:1231-45.
46. Chiodi I, Corioni M, Giordano M, et al. RNA recognition motif 2 directs the recruitment of SF2/ASF to nuclear stress bodies. Nucleic Acids Res 2004;32:4127-36.
47. Denegri M, Chiodi I, Corioni M, et al. Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors. Mol Biol Cell 2001;12:3502-14.
48. Metz A, Soret J, Vourc'h C, et al. A key role for stressinduced satellite III transcripts in the relocalization of splicing factors into nuclear stress granules. J Cell Sci 2004;117: 4551-8.
49. Loomis RJ, Naoe Y, Parker JB, et al. Chromatin binding of SRp20 and ASF/SF2 and dissociation from mitotic chromosomes is modulated by histone H3 serine 10 phosphorylation. Mol Cell 2009;33:450-61.
50. Michlewski G, Sanford JR, Caceres JF. The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol Cell 2008;30: 179-89.
51. Sanford JR, Gray NK, Beckmann K, et al. A novel role for shuttling SR proteins in mRNA translation. Genes Dev 2004;18:755-68.