Characterization of U4 and U6 interactions with the 5′ splice site using a S. cerevisiae in vitro trans-splicing system

Genes and Development

Volumn 15, Issue 15, 2001, Pages 1957-1970

  Johnson, T L ^a   Abelson, J ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

RNA cross linking; Saccharomyces cerevisiae; Trans splicing

Indexed keywords

ADENOSINE TRIPHOSPHATE; MAGNESIUM ION; MESSENGER RNA PRECURSOR; OLIGONUCLEOTIDE; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RNA;

ARTICLE; BASE PAIRING; BINDING SITE; CROSS LINKING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; RNA SPLICING; SACCHAROMYCES CEREVISIAE; SPLICEOSOME; TRANS SPLICING;

5' UNTRANSLATED REGIONS; ACTINS; ADENOSINE TRIPHOSPHATE; BASE SEQUENCE; BINDING SITES; CROSS-LINKING REAGENTS; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEOPROTEIN, U4-U6 SMALL NUCLEAR; RNA PRECURSORS; RNA SPLICING; RNA, FUNGAL; RNA, MESSENGER; RNA, SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE; SUBSTRATE SPECIFICITY;

SACCHAROMYCES CEREVISIAE;

EID: 0035423681     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.895601     Document Type: Article

References (77)

1. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein
2. A convenient synthesis of s-cyanoethyl-protected 4-thiouridine and its incorporation into oligoribonucleotides
3. Targeted snRNP depletion reveals an additional role for mammalian U1 snRNP in spliceosome assembly
4. Pre-mRNA splicing in vitro requires intact U4/U6 small nuclear ribonucleoprotein
5. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals
6. An element in human U6 RNA destabilizes the U4/U6 spliceosomal RNA complex
7. Splicing of precursors to mRNAs by the spliceosome
8. Spliceosome assembly in yeast
9. Allele-specific genetic interactions between Prp8 and RNA active site residues suggest a function for Prp8 at the catalytic core of the spliceosome
10. A U6 snRNA:pre-mRNA interaction can be rate-limiting for U1 independent splicing
11. Complementation by SR proteins of pre-mRNA splicing reactions depleted of U1 snRNP
12. Cis-acting elements distinct from the 5′ splice site promote U1-independent pre-mRNA splicing
13. Functional association of U2 snRNP with the ATP-independent spliceosomal complex E
14. Genetic evidence for base pairing between U2 and U6 snRNA in mammalian mRNA splicing
15. Yeast U1 snRNP-pre-mRNA complex formation without U1 snRNA-pre-mRNA base pairing
16. Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing
17. A stem/loop in U6 snRNA defines a conformational switch required for pre-mRNA splicing
18. Splicing pathways of SV40 mRNAs in X. laevis oocytes differ in their requirements for snRNPs
19. Dynamic exchanges of RNA interactions leading to catalytic core formation in the U12-dependent spliceosome
20. In vitro trans-splicing in Saccharomyces cerevisiae
21. The 5′ splice site consensus RNA oligonucleotide induces assembly of U2/U4/U5/U6 small nuclear ribonucleoprotein complexes
22. Evidence for base-pairing between mammalian U2 and U6 small nuclear ribonucleoprotein particles
23. Stages in the second reaction of pre-mRNA splicing: The final step is ATP independent
24. Involvement of U6 snRNA in 5′ splice site selection
25. Site-specific crosslinks of yeast U6 snRNA to the pre-mRNA near the 5′ splice site
26. The first ATPase domain of the yeast 246-kDa protein is required for in vivo unwinding of the U4/U6 duplex
27. U4/U5/U6 snRNP recognizes the 5′ splice site in the absence of U2 SnRNP
28. A short 5′ splice site RNA oligo can participate in both steps of splicing in mammalian extracts
29. Disruption of base pairing between the 5′ splice site and the 5′ end of U1 snRNA is required for spliceosome assembly
30. Presplicing complex formation requires two proteins and U2 snRNP
31. S. cerevisiae U1 RNA is large and has limited primary sequence homology to metazoan U1 snRNA
32. Suppressors of a cold-sensitive mutation in yeast U4 RNA define five domains in the splicing factor Prp8 that influence spliceosome activation
33. Splicing factor Prp8 governs U4/U6 RNA unwinding during activation of the spliceosome
34. The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro
35. Mutations in U6 that alter splice site specificity: Implications for the active site
36. A spontaneous duplication in U6 spliceosomal RNA uncouples the early and late functions of the ACAGA element in vivo
37. Requirements for the U2 snRNP addition to yeast pre-mRNA
38. Yeast mRNA splicing in vitro
39. Detection of a novel ATP-dependent cross-linked protein at the 5′ splice site-U1 small nuclear RNA duplex by methylene blue-mediated photo-cross-linking
40. A novel base pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome
41. Multiple roles for U6 snRNA in the splicing pathway
42. Functional recognition of the 5′ splice site by U4/U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly
43. An ATP-independent complex commits pre-mRNA to the mammalian spliceosome assembly pathway
44. A catalogue of splice junction sequences
45. snRNA interactions at the 5′ and 3′ splice sites monitored by photoactivated cross-linking in yeast spliceosomes
46. Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA
47. ATP can be dispensable for prespliceosome formation in yeast
48. Assemblage of the prespliceosome complex with separated fractions isolated from HeLa cells
49. A minimal spliceosomal complex A recognizes the branch site and polypyrimidine tract
50. RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2
51. An early hierarchic role of U1 small nuclear ribonucleoprotein in spliceosome assembly
52. Evidence for a base-pairing interaction between U6 small nuclear RNA and 5′ splice site during the splicing reaction in yeast
53. Association of U6 snRNA with the 5′-splice site region of pre-mRNA in the spliceosome
54. Uncoupling two functions of the U1 small nuclear ribonucleoprotein particle during in vitro splicing
55. A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5′ cleavage site
56. 5′ splice site selection in yeast: Genetic alterations in base-pairing with U1 reveal additional requirements
57. The U5 and U6 small nuclear RNAs as active site components of the spliceosome
58. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p
59. Purification of the yeast U4/U6.U5 small nuclear ribonucleoprotein particle and identification of its proteins
60. A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family
61. SR proteins can compensate for the loss of U1 snRNP functions in vitro
62. Modulation of a 5′ splice site choice in pre-messenger RNA by two distinct steps
63. A tertiary interaction detected in human U2-U6 snRNA complex assembled in vitro resembles a genetically proven interaction in yeast
64. Functional contacts with a range of splicing proteins suggest a central role for Brr2p in the dynamic control of the order of events in spliceosomes of Saccharomyces cerevisiae
65. Alternative splicing of SV40 early pre-mRNA in vitro
66. Characterization of U6 snRNA-protein interactions
67. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome
68. Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing
69. Protein functions in pre-mRNA splicing
70. Splicing function of mammalian U6 small nuclear RNA: Conserved positions in central domain and helix I are essential during the first and second step of pre-mRNA splicing
71. Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing
72. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing
73. U4 small nuclear RNA dissociates from the yeast spliceosome and does not participate in the subsequent splicing reaction
74. Functional reconstitution of U6 snRNA in nematode cis- and transsplicing: U6 can serve as both a branch acceptor and a 5′ exon
75. Identification of eight proteins that cross-link to pre-mRNA in the yeast commitment complex
76. A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation
77. A compensatory base change in human U2 snRNA can suppress a branch site mutation