Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal

RNA

Volumn 6, Issue 6, 2000, Pages 901-911

  Singh, Ravinder ^a   Banerjee, Hiren ^a   Green, Michael R ^b  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Pre mRNA splicing; Ribonucleoprotein consensus motif; RNA recognition motif; RNA binding proteins; Sex determination

Indexed keywords

ETHYLNITROSOUREA; HYDRAZINE; HYDROXYL GROUP; MESSENGER RNA PRECURSOR; PHOSPHATE; PYRIMIDINE DERIVATIVE; RIBONUCLEOPROTEIN; RNA BINDING PROTEIN; SPLICING FACTOR U2AF; UNCLASSIFIED DRUG; URACIL;

ARTICLE; CONTROLLED STUDY; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN RNA BINDING; REPRESSOR GENE; RNA SEQUENCE; RNA SPLICING; SEX DETERMINATION;

AMINO ACID MOTIFS; ANIMALS; BASE COMPOSITION; CONSENSUS SEQUENCE; DNA FOOTPRINTING; DNA-BINDING PROTEINS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; MODELS, MOLECULAR; MUTAGENESIS; NUCLEAR PROTEINS; POLYPYRIMIDINE TRACT-BINDING PROTEIN; PYRIMIDINES; RIBONUCLEOPROTEINS; RNA PRECURSORS; RNA SPLICING; RNA-BINDING PROTEINS; SUBSTRATE SPECIFICITY;

EID: 0034098296     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200000376     Document Type: Article

References (65)

1. Adams MD, Rudner DZ, Rio DC. 1996. Biochemistry and regulation of pre-mRNA splicing. Curr Opin Cell Biol 8:331-339.
2. Albrecht EB, Salz HK. 1993. The Drosophila sex determination gene snf is utilized for the establishment of the female-specific splicing pattern of Sex-lethal. Genetics 134:801-807.
3. Bashaw GJ, Baker BS. 1997. The regulation of the Drosophila msl-2 gene reveals a function for Sex-lethal in translational control. Cell 89:789-798.
4. Been MD, Cech TR. 1987. Selection of circularization sites in a group I IVS RNA requires multiple alignments of an internal template-like sequence. Cell 50:951-961.
5. Bell LR, Maine EM, Schedl P, Cline TW. 1988. Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins. Cell 55: 1037-1046.
6. Burd CG, Dreyfuss G. 1994. Conserved structures and diversity of functions of RNA-binding proteins. Science 265:615-621.
7. Burge CB, Tuschl T, Sharp PA. 1999. Splicing of precursors to mRNAs by the spliceosomes. In: Gesteland RF, Cech TR, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 525-560.
8. Chang KA, Kuroda Ml. 1998. Modulation of MSL1 abundance in female Drosophila contributes to the sex specificity of dosage compensation. Genetics 150:699-709.
9. Cline TW, Meyer BJ. 1996. Vive la difference: Males vs. females in flies vs. worms. Annu Rev Genet 30:637-702.
10. Conway L, Wickens M. 1989. Modification interference analysis of reactions using RN A substrates. Methods Enzymol 180:369-379.
11. Deo RC, Bonanno JB, Sonenberg N, Burley SK. 1999. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98: 835-845.
12. Ding J, Hayashi MK, Zhang Y, Manche L, Krainer AR, Xu RM. 1999. Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes & Dev 13:1102-1115.
13. Ehresmann C, Baudin F, Mougel M, Romby P, Ebel J-P, Ehresmann B. 1987. Probing the structure of RNAs in solution. Nucleic Acids Res 15:9109-9127.
14. Ellington AD, Szostak JW. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822.
15. Fleckner J, Zhang M, Valcarcel J, Green MR. 1997. U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes & Dev 11:1864-1872.
16. Gebauer F, Merendino L, Hentze MW, Valcarcel J. 1998. The Drosophila splicing regulator sex-lethal directly inhibits translation of male-specific-lethal 2 mRNA. RNA 4:142-150.
17. Gish G, Eckstein F. 1988. DNA and RNA sequence determination based on phosphorothioate chemistry. Science 240:1520-1522.
18. Gozani O, Potashkin J, Reed R. 1998. A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol Cell Biol 18:4752-4760.
19. Granadino B, Campuzano S, Sanchez L. 1990. The Drosophila melanogaster fl(2)d gene is needed for the female-specific splicing of Sex-lethal RNA. EMBO J 9:2597-2602.
20. Granadino B, Penalva LOF, Green MR, Valcarcel J, Sanchez L. 1997. Distinct mechanisms of splicing regulation in vivo by the Drosophila protein Sex-lethal. Proc Natl Acad Sci USA 94:7343-7348.
21. Granadino B, San Juan A, Santamaria P, Sanchez L. 1992. Evidence of a dual function in fl(2)d, a gene needed for Sex-lethal expression in Drosophila melanogaster. Genetics 130:597-612.
22. Green MR. 1991. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu Rev Cell Biol 7:559-599.
23. Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y, Muto Y, Yokoyama S. 1999. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398:579-585.
24. ts (virilizer) identifies a new gene involved in sex determination of Drosophila. Roux Arch Dev Biol 200:240-248.
25. Horabin JI, Schedl P. 1993. Sex-lethal autoregulation requires multiple cis-acting elements upstream and downstream of the male exon and appears to depend largely on controlling the use of the male exon 5′ splice site. Mol Cell Biol 13:7734-7746.
26. Inoue K, Hoshijima K, Sakamoto H, Shimura Y. 1990. Binding of the Drosophila sex-lethal gene product to the alternative splice site of transformer primary transcript. Nature 344:461-463.
27. Ishikawa F, Matunis MJ, Dreyfuss G, Cech TR. 1993. Nuclear proteins that bind the pre-mRNA 3′ splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n. Mol Cell Biol 13:4301-4310.
28. Kanaar R, Lee AL, Rudner DZ, Wemmer DE, Rio DC. 1995. Interaction of the sex-lethal RNA binding domains with RNA. EMBO J 14:4530-4539.
29. Kanaar R, Roche SE, Beall EL, Green MR, Rio DC. 1993. The conserved pre-mRNA splicing factor U2AF from Drosophila: Requirement for viability. Science 262:569-573.
30. Kelley RL, Solovyeva I, Lyman LM, Richman R, Solovyev V, Kuroda MI. 1995. Expression of msl-2 causes assembly of dosage compensation regulators on the X chromosomes and female lethality in Drosophila. Cell 81:867-877.
31. Kelley RL, Wang J, Bell L, Kuroda MI. 1997. Sex lethal controls dosage compensation in Drosophila by a non-splicing mechanism. Nature 387:195-199.
32. Lee AL, Volkman BF, Robertson SA, Rudner DZ, Barbash DA, Cline TW, Kanaar R, Rio DC, Wemmer DE. 1997. Chemical shift mapping of the RNA-binding interface of the multiple-RBD protein sex-lethal. Biochemistry 36:14306-14317.
33. Mattaj IW. 1993. RNA recognition: A family matter? Cell 73:837-840.
34. McKeown M. 1992. Alternative mRNA splicing. Annu Rev Cell Biol 8:133-155.
35. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783-8798.
36. Moazed D, Noller HF. 1986. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47:985-994.
37. Nadal-Ginard B, Smith CW, Patton JG, Breitbart RE. 1991. Alternative splicing is an efficient mechanism for the generation of protein diversity: Contractile protein genes as a model system. Adv Enzyme Regul 31:261-286.
38. Nagai K. 1996. RNA-protein complexes. Curr Opin Struct Biol 6: 53-61.
39. Oliver B, Perrimon N, Mahowald AP. 1988. Genetic evidence that the sans fille locus is involved in Drosophila sex determination. Genetics 120:159-171.
40. O'Neil MT, Belote JM. 1992. Interspecific comparison of the transformer gene of Drosophila reveals an unusually high degree of evolutionary divergence. Genetics 131:113-128.
41. Oubridge C, Ito N, Evans PR, Teo CH, Nagai K. 1994. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372:432-438.
42. Potashkin J, Naik K, Wentz-Hunter K. 1993. U2AF homolog required for splicing in vivo. Science 262:573-575.
43. Price SR, Evans PR, Nagai K. 1998. Crystal structure of the spliceosomal U2B″-U2A′ protein complex bound to a fragment of U2 small nuclear RNA. Nature 394:645-650.
44. Puglisi JD, Williamson JR. 1999. RNA interactions with small ligands and small peptides. In: Gesteland RF, Cech TR, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 403-425.
45. Robertson DL, Joyce GF. 1990. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467-468.
46. Ruskin B, Zamore PD, Green MR. 1988. A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell 52: 207-219.
47. Rymond BC, Rosbash M. 1988. A chemical modification/interference study of yeast pre-mRNA spliceosome assembly and splicing. Genes & Dev 2:428-439.
48. Saenger W. 1994. Defining terms for nucleic acids. In: Cantor CR, ed. Principles of nucleic acid structure. New York: Springer-Verlag Inc. pp 21-23.
49. Sakamoto H, Inoue K, Higuchi I, Ono Y, Shimura Y. 1992. Control of Drosophila Sex-lethal pre-mRNA splicing by its own female-specific product. Nucleic Acids Res 20:5533-5540.
50. Sakashita E, Sakamoto H. 1994. Characterization of RNA binding specificity of the Drosophila sex-lethal protein by in vitro ligand selection. Nucleic Acids Res 22:4082-4086.
51. Samuels ME, Bopp D, Colvin RA, Roscigno RF, Garcia-Blanco MA, Schedl P. 1994. RNA binding by Sxl proteins in vitro and in vivo. Mol Cell Biol 14:4975-4990.
52. Singh R, Valcarcel J, Green MR. 1995. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 268:1173-1176.
53. Sosnowski BA, Belote JM, McKeown M. 1989. Sex-specific alternative splicing of RNA from the transformer gene results from sequence-dependent splice site blockage. Cell 53:449-459.
54. Sosnowski BA, Davis DD, Boggs RT, Madigan SJ, McKeown M. 1994. Multiple portions of a small region of the Drosophila transformer gene are required for efficient in vivo sex-specific regulated RNA splicing and in vitro sex-lethal binding. Dev Biol 161: 302-312.
55. Steinmann-Zwicky M. 1988. Sex determination in Drosophila: The X-chromosomal gene liz is required for Sxl activity. EMBO J 7:3889-3898.
56. Steitz TA. 1999. RNA recognition by proteins. In: Gesteland RF, Cech TR, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 427-450.
57. Tuerk C, Gold L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510.
58. Valcarcel J, Gaur RK, Singh R, Green MR. 1996. Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273:1706-1709.
59. Valcarcel J, Singh R, Zamore PD, Green MR. 1993. The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA. Nature 362:171-175.
60. Vlassov VV, Giege R, Ebel JP. 1980. The tertiary structure of yeast tRNAPhe in solution studied by phosphodiester bond modification with ethylnitrosourea. FEBS Lett 120:12-16.
61. Wang J, Bell LR. 1994. The Sex-lethal amino terminus mediates cooperative interactions in RNA binding and is essential for splicing regulation. Genes & Dev 8:2072-2085.
62. Yanowitz JL, Deshpande G, Calhoun G, Schedl PD. 1999. An N-terminal truncation uncouples the sex-transforming and dosage compensation functions of sex-lethal. Mol Cell Biol 19:3018-3028.
63. Zamore PD, Green MR. 1989. Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc Natl Acad Sci USA 86:9243-9247.
64. Zhou SB, Yang YF, Scott MJ, Pannuti A, Fehr KC, Eisen A, Koonin EV, Fouts DL, Wrightsman R, Manning JE, Lucchesi JC. 1995. Male-specific lethal 2, a dosage compensation gene of Drosophila, undergoes sex-specific regulation and encodes a protein with a RING finger and a metallothionein-like cysteine cluster. EMBO J 14:2884-2895.
65. Zorio DA, Blumenthal T. 1999. U2AF35 is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Caenorhabditis elegans. RNA 5:487-494.