Autoregulation of Fox protein expression to produce dominant negative splicing factors

RNA

Volumn 16, Issue 2, 2010, Pages 405-416

  Damianov, Andrey ^a   Black, Douglas L ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

A2BP1; Alternative splicing; Autoregulation; Fox; HRNBP3; RBM9

Indexed keywords

COMPLEMENTARY DNA; ISOPROTEIN; PROTEIN FOX1; PROTEIN FOX2; PROTEIN FOX3; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; AUTOREGULATION; CARBOXY TERMINAL SEQUENCE; CELL STRAIN HEK293; CONTROLLED STUDY; EXON; FEMALE; HUMAN; HUMAN CELL; MALE; MOUSE; NEUROBLASTOMA CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN RNA BINDING;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CELL LINE; DNA PRIMERS; FEMALE; GENE EXPRESSION; HOMEOSTASIS; HUMANS; MALE; MICE; MOLECULAR SEQUENCE DATA; RNA-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

MAMMALIA;

EID: 75149194407     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1838210     Document Type: Article

References (54)

1. Auweter SD, Fasan R, Reymond L, Underwood JG, Black DL, Pitsch S, Allain FH. 2006. Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J 25: 163-173.
2. Baraniak AP, Chen JR, Garcia-Blanco MA. 2006. Fox-2 mediates epithelial cell-specific fibroblast growth factor receptor 2 exon choice. Mol Cell Biol 26: 1209-1222.
3. Bhalla K, Phillips HA, Crawford J, McKenzie OL, Mulley JC, Eyre H, Gardner AE, Kremmidiotis G, Callen DF. 2004. The de novo chromosome 16 translocations of two patients with abnormal phenotypes (mental retardation and epilepsy) disrupt the A2BP1 gene. J Hum Genet 49: 308-311.
4. Black DL. 1992. Activation of c-src neuron-specific splicing by an unusual RNA element in vivo and in vitro. Cell 69: 795-807.
5. Boutz PL, Chawla G, Stoilov P, Black DL. 2007a. MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development. Genes & Dev 21: 71-84.
6. Boutz PL, Stoilov P, Li Q, Lin CH, Chawla G, Ostrow K, Shiue L, Ares M Jr, Black DL. 2007b. A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes & Dev 21: 1636-1652.
7. Deguillien M, Huang SC, Moriniere M, Dreumont N, Benz EJ Jr, Baklouti F. 2001. Multiple cis elements regulate an alternative splicing event at 4.1R pre-mRNA during erythroid differentiation. Blood 98: 3809-3816.
8. Del Gatto F, Plet A, Gesnel MC, Fort C, Breathnach R. 1997. Multiple interdependent sequence elements control splicing of a fibroblast growth factor receptor 2 alternative exon. Mol Cell Biol 17: 5106-5116.
9. Dredge BK, Stefani G, Engelhard CC, Darnell RB. 2005. Nova autoregulation reveals dual functions in neuronal splicing. EMBO J 24: 1608-1620.
10. Grabowski PJ. 2005. Splicing-active nuclear extracts from rat brain. Methods 37: 323-330.
11. Hase ME, Yalamanchili P, Visa N. 2006. The Drosophila heterogeneous nuclear ribonucleoprotein M protein, HRP59, regulates alternative splicing and controls the production of its own mRNA. J Biol Chem 281: 39135-39141.
12. Hedjran F, Yeakley JM, Huh GS, Hynes RO, Rosenfeld MG. 1997. Control of alternative pre-mRNA splicing by distributed pentameric repeats. Proc Natl Acad Sci 94: 12343-12347.
13. Hodgkin J, Zellan JD, Albertson DG. 1994. Identification of a candidate primary sex determination locus, fox-1, on the X chromosome of Caenorhabditis elegans. Development 120: 3681-3689.
14. Huh GS, Hynes RO. 1994. Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element. Genes & Dev 8: 1561-1574.
15. Huynh DP, Del Bigio MR, Ho DH, Pulst SM. 1999. Expression of ataxin-2 in brains from normal individuals and patients with Alzheimer's disease and spinocerebellar ataxia 2. Ann Neurol 45: 232-241.
16. Jin Y, Suzuki H, Maegawa S, Endo H, Sugano S, Hashimoto K, Yasuda K, Inoue K. 2003. A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J 22: 905-912.
17. Jumaa H, Nielsen PJ. 1997. The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation. EMBO J 16: 5077-5085.
18. Kawamoto S. 1996. Neuron-specific alternative splicing of nonmuscle myosin II heavy chain-B pre-mRNA requires a cis-acting intron sequence. J Biol Chem 271: 17613-17616.
19. Kiehl TR, Shibata H, Vo T, Huynh DP, Pulst SM. 2001. Identification and expression of a mouse ortholog of A2BP1. Mamm Genome 12: 595-601.
20. Kim KK, Adelstein RS, Kawamoto S. 2009. Identification of neuronal nuclei (NeuN) as Fox-3, a new member of the Fox-1 gene family of splicing factors. J Biol Chem 284: 31052-31061.
21. Kubo Y. 1991. Comparison of initial stages of muscle differentiation in rat and mouse myoblastic and mouse mesodermal stem cell lines. J Physiol 442: 743-759.
22. Kumar S, Lopez AJ. 2005. Negative feedback regulation among SR splicing factors encoded by Rbp1 and Rbp1-like in Drosophila. EMBO J 24: 2646-2655.
23. Lareau LF, Inada M, Green RE, Wengrod JC, Brenner SE. 2007. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446: 926-929.
24. Lee JA, Tang ZZ, Black DL. 2009. An inducible change in Fox-1/A2BP1 splicing modulates the alternative splicing of downstream neuronal target exons. Genes & Dev 23: 2284-2293.
25. Lieberman AP, Friedlich DL, Harmison G, Howell BW, Jordan CL, Breedlove SM, Fischbeck KH. 2001. Androgens regulate the mammalian homologues of invertebrate sex determination genes tra-2 and fox-1. Biochem Biophys Res Commun 282: 499-506.
26. Lim LP, Sharp PA. 1998. Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats. Mol Cell Biol 18: 3900-3906.
27. Lim J, Hao T, Shaw C, Patel AJ, Szabo G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, et al. 2006. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 125: 801-814.
28. Makeyev EV, Maniatis T. 2008. Multilevel regulation of gene expression by microRNAs. Science 319: 1789-1790.
29. Martin CL, Duvall JA, Ilkin Y, Simon JS, Arreaza MG, Wilkes K, Alvarez-Retuerto A, Whichello A, Powell CM, Rao K, et al. 2007. Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am J Med Genet B Neuropsychiatr Genet 144B: 869-876.
30. Mauger DM, Lin C, Garcia-Blanco MA. 2008. hnRNP H and hnRNP F complex with Fox2 to silence fibroblast growth factor receptor 2 exon IIIc. Mol Cell Biol 28: 5403-5419.
31. McKee AE, Minet E, Stern C, Riahi S, Stiles CD, Silver PA. 2005. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC Dev Biol 5: 14. doi: 10.1186/1471-213X-5-14.
32. Modafferi EF, Black DL. 1997. A complex intronic splicing enhancer from the c-src pre-mRNA activates inclusion of a heterologous exon. Mol Cell Biol 17: 6537-6545.
33. Nakahata S, Kawamoto S. 2005. Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities. Nucleic Acids Res 33: 2078-2089.
34. Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M Jr. 2007. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes & Dev 21: 708-718.
35. Nicoll M, Akerib CC, Meyer BJ. 1997. X-chromosome-counting mechanisms that determine nematode sex. Nature 388: 200-204.
36. Ponthier JL, Schluepen C, Chen W, Lersch RA, Gee SL, Hou VC, Lo AJ, Short SA, Chasis JA, Winkelmann JC, et al. 2006. Fox-2 splicing factor binds to a conserved intron motif to promote inclusion of protein 4.1R alternative exon 16. J Biol Chem 281: 12468-12474.
37. Rossbach O, Hung LH, Schreiner S, Grishina I, Heiner M, Hui J, Bindereif A. 2009. Auto- and cross-regulation of the hnRNP L proteins by alternative splicing. Mol Cell Biol 29: 1442-1451.
38. Saltzman AL, Kim YK, Pan Q, Fagnani MM, Maquat LE, Blencowe BJ. 2008. Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol 28: 4320-4330.
39. Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, et al. 2007. Strong association of de novo copy number mutations with autism. Science 316: 445-449.
40. Servadio A, Koshy B, Armstrong D, Antalffy B, Orr HT, Zoghbi HY. 1995. Expression analysis of the ataxin-1 protein in tissues from normal and spinocerebellar ataxia type 1 individuals. Nat Genet 10: 94-98.
41. Shibata H, Huynh DP, Pulst SM. 2000. A novel protein with RNA-binding motifs interacts with ataxin-2. HumMol Genet 9: 1303-1313.
42. Sorek R, Ast G. 2003. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res 13: 1631-1637.
43. Spellman R, Llorian M, Smith CW. 2007. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol Cell 27: 420-434.
44. Stoilov P, Daoud R, Nayler O, Stamm S. 2004. Human tra2-beta1 autoregulates its protein concentration by influencing alternative splicing of its pre-mRNA. Hum Mol Genet 13: 509-524.
45. Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, Wang H, Williams A, Kulp D, Blume JE, Haussler D, et al. 2006. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol 2: e4. doi: 10.1371/journal.pcbi. 0020004.
46. Sureau A, Gattoni R, Dooghe Y, Stevenin J, Soret J. 2001. SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs. EMBO J 20: 1785-1796.
47. Tang ZZ, Zheng S, Nikolic J, Black DL. 2009. Developmental control of CaV1.2 L-type calcium channel splicing by Fox proteins. Mol Cell Biol 29: 4757-4765.
48. Tsai CC, Kao HY, Mitzutani A, Banayo E, Rajan H, McKeown M, Evans RM. 2004. Ataxin 1, a SCA1 neurodegenerative disorder protein, is functionally linked to the silencing mediator of retinoid and thyroid hormone receptors. Proc Natl Acad Sci 101: 4047-4052.
49. Underwood JG, Boutz PL, Dougherty JD, Stoilov P, Black DL. 2005. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol Cell Biol 25: 10005-10016.
50. Wollerton MC, Gooding C, Wagner EJ, Garcia-Blanco MA, Smith CW. 2004. Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol Cell 13: 91-100.
51. Yang G, Huang SC, Wu JY, Benz EJ Jr. 2008. Regulated Fox-2 isoform expression mediates protein 4.1R splicing during erythroid differentiation. Blood 111: 392-401.
52. Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB. 2005. Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci 102: 2850-2855.
53. YeoGW, CoufalNG, Liang TY, PengGE, Fu XD,Gage FH. 2009. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16: 130-137.
54. Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer AR, Zhang MQ. 2008. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes & Dev 22: 2550-2563.