Functional selection of splicing enhancers that stimulate trans-splicing in vitro

RNA

Volumn 7, Issue 6, 2001, Pages 793-805

  Boukis, Lisa A ^a   Bruzik, James P ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Exon definition; Nematode; Splicing enhancer; Trans splicing

Indexed keywords

SMALL NUCLEAR RNA;

ARTICLE; BASE PAIRING; ENHANCER REGION; EXON; INTRON; NONHUMAN; PRIORITY JOURNAL; RNA SPLICING; SEQUENCE ANALYSIS; TRANS SPLICING;

ANIMALS; ASCARIS LUMBRICOIDES; BASE SEQUENCE; ENHANCER ELEMENTS (GENETICS); EXONS; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER;

EID: 0034968065     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838201010524     Document Type: Article

References (79)

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4. RNA processing and gene structure
5. Identification of a bidirectional splicing enhancer: Differential involvement of SR proteins in 5′ or 3′ splice site activation
6. Splicing glue: A role for SR proteins in trans-splicing?
7. Trans-splicing involves a novel form of small nuclear ribonucleoprotein particles
8. The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers
9. A two-step mechanism for 5′ and 3′ splice-site pairing
10. Suppression of mammalian 5′ splice-site defects by U1 small nuclear RNAs from a distance
11. An element in the 5′ common exon of the NCAM alternative splicing unit interacts with SR proteins and modulates 5′ splice site selection
12. Identification of a new class of exonic splicing enhancers by in vivo selection
13. The 35-kDa mammalian splicing factor SC35 mediates specific interactions between U1 and U2 small nuclear ribonucleoprotein particles at the 3′ splice site
14. Sorting out the complexity of SR protein functions
15. A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers
16. Trans-splicing of nematode pre-messenger RNA in vitro
17. U small nuclear ribonucleoprotein requirements for nematode cis- and trans-splicing in vitro
18. The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences
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20. Site-directed mutagenesis by overlap extension using the polymerase chain reaction
21. U1 snRNP targets an essential splicing factor, U2AF65, to the 3′ splice site by a network of interactions spanning the exon
22. A 32-nucleotide exon-splicing enhancer regulates usage of competing 5′ splice sites in a differential internal exon
23. Base pairing at the 5′ splice site with U1 small nuclear RNA promotes splicing of the upstream intron but may be dispensable for splicing of the downstream intron
24. A role for SRp54 during intron bridging of small introns with pyrimidine tracts upstream of the branch point
25. A U1 snRNA binding site improves the efficiency of in vitro pre-mRNA splicing
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27. RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation
28. The position of site-directed cleavage of RNA using RNase H and 2′-O-methyl oligonucleotides is dependent on the enzyme source
29. Splicing enhancement in the yeast rp51b intron
30. Exonic splicing enhancer motif recognized by human SC35 under splicing conditions
31. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins
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33. An intron enhancer containing a 5′ splice site sequence in the human calcitonin/calcitonin gene-related peptide gene
34. Characterization of human RNA splice signals by iterative functional selection of splice sites
35. An exon that prevents transport of a mature mRNA
36. A new twist in trypanosome RNA metabolism: Cis-splicing of pre-mRNA
37. Functional recognition of 5′ splice site by U4/U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly
38. Direct analysis of nematode cis- and trans-spliceosomes: A functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs
39. Inhibition of msl-2 splicing by Sex-lethal reveals interaction between U2AF35 and the 3′ splice site AG
40. Trans-splicing
41. Characterization and expression of a spliced leader RNA in the parasitic nematode Ascaris lumbricoides var. suum
42. PUF60: A novel U2AF65-related splicing activity
43. A minimal spliceosomal complex A recognizes the branch site and polypyrimidine tract
44. The organization of 3′ splice-site sequences in mammalian introns
45. A role for exon sequences and splice-site proximity in splice-site selection
46. Spliceosome assembly
47. The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome
48. Exon definition may facilitate splice site selection in RNAs with multiple exons
49. A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly
50. Developmental regulation of SR protein phosphorylation and activity
51. SR proteins are required for nematode trans-splicing in vitro
52. Evidence for a base-pairing interaction between U6 small nuclear RNA and 5′ splice site during the splicing reaction in yeast
53. Multiple distinct splicing enhancers in the protein-coding sequences of a constitutively spliced pre-mRNA
54. Selection and characterization of pre-mRNA splicing enhancers: Identification of novel SR protein-specific enhancer sequences
55. Uncoupling two functions of the U1 small nuclear ribonucleoprotein particle during in vitro splicing
56. Exonic splicing enhancers contribute to the use of both 3′ and 5′ splice site usage of rat beta-tropomyosin pre-mRNA
57. The spliceosomal U small nuclear RNAs of Ascaris lumbricoides
58. A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52
59. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins
60. Exon mutations that affect the choice of splice sites used in processing the SV40 late transcripts
61. Extremely stable transcripts may compensate for the elimination of the gene fert-1 from all Ascaris lumbricoides somatic cells
62. Sequence-specific RNA binding by an SR protein requires RS domain phosphorylation: Creation of an SRp40-specific splicing enhancer
63. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities
64. Determinants of SR protein specificity
65. Effect of 5′ splice site mutations on splicing of the preceding intron
66. The C. elegans trans-yin constitutive and spliced leader RNA is bound to Sm and has a trimethylguanosine cap
67. Selection of novel exon recognition elements from a pool of random sequences
68. A splicing enhancer exhibits both constitutive and regulated activities
69. Regulation of pre-mRNA splicing in metazoa
70. Alternative pre-mRNA splicing
71. Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing
72. U1-mediated exon definition interactions between AT-AC and GT-AG introns
73. Identification of a human protein that recognizes the 3′ splice site during the second step of pre-mRNA splicing
74. 35
75. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing
76. Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor
77. Functional properties of p54, a novel SR protein active in constitutive and alternative splicing
78. U1 small nuclear ribonucleoproteins are required early during spliceosome assembly
79. Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans