Home LiteratureArticle Details
PMID: 9254712 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Antisense oligonucleotide binding to U5 snRNP induces a conformational change that exposes the conserved loop of U5 snRNA.

Nucleic acids research ·Vol. 25 ·No. 17 ·1997-09-01 ·Pages 3508-13

Ast G, Weiner AM

Abstract

Conformational rearrangements of the spliceosomal small nuclear RNAs (U snRNAs) are essential for proper assembly of the active site prior to the first catalytic step of splicing. We have previously shown that conformational changes caused by binding of an antisense 2'-O-methyl RNA oligonucleotide (BU5Ae) to U5 snRNA nt 68-88 disrupted the U4/U5/U6 complex and induced formation of the U1/U4/U5 and U2/U6 complexes. Here we show that the conformational change induced by BU5Ae exposes the invariant loop of U5 that binds the 5'exon and also reorganizes internal loop 1 (IL1) and the top of stem 2. Interestingly, we have also previously found that the U1/U4/U5 complex induced by BU5Ae brings the invariant loop of U5 into close proximity with the 5'-end of U1. Taken together, these data suggest that U1 and U5 may both contribute to the ability of the U1/U4/U5 complex to bind the 5' splice site.

MeSH Terms
Base Composition Base Sequence Binding Sites Cross-Linking Reagents Cytosine/chemistry Ficusin HeLa Cells Humans Molecular Sequence Data Nucleic Acid Conformation Oligonucleotides, Antisense/metabolism RNA Splicing Ribonucleoprotein, U5 Small Nuclear/chemistry,metabolism Spliceosomes/chemistry Uridine/chemistry
Chemicals
Cross-Linking Reagents Oligonucleotides, Antisense Ribonucleoprotein, U5 Small Nuclear Cytosine Ficusin Uridine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Ast G
Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520-8114, USA.
Weiner A M
References (62)
62 references, click to expand
  1. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei.
    Nucleic Acids Res. 1983 Mar 11;11(5):1475-89 PMID: 6828386
  2. U4/U5/U6 snRNP recognizes the 5' splice site in the absence of U2 snRNP.
    Genes Dev. 1994 Aug 15;8(16):1962-73 PMID: 7958870
  3. Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry.
    Annu Rev Biochem. 1985;54:1151-93 PMID: 2411210
  4. A compensatory base change in U1 snRNA suppresses a 5' splice site mutation.
    Cell. 1986 Sep 12;46(6):827-35 PMID: 3757028
  5. Electrophoresis of ribonucleoproteins reveals an ordered assembly pathway of yeast splicing complexes.
    Nature. 1986 Nov 27-Dec 3;324(6095):341-5 PMID: 3537805
  6. Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA.
    Cell. 1987 Apr 24;49(2):229-39 PMID: 3552247
  7. An essential yeast snRNA with a U5-like domain is required for splicing in vivo.
    Cell. 1987 Jun 5;49(5):613-24 PMID: 3555841
  8. Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes.
    Cell. 1987 Jun 19;49(6):763-74 PMID: 2953438
  9. Spliceosome assembly in yeast.
    Genes Dev. 1987 Nov;1(9):1014-27 PMID: 2962902
  10. Association of U2, U4, U5, and U6 small nuclear ribonucleoproteins in a spliceosome-type complex in absence of precursor RNA.
    Proc Natl Acad Sci U S A. 1988 Aug;85(15):5459-62 PMID: 2969592
  11. Mutations in yeast U5 snRNA alter the specificity of 5' splice-site cleavage.
    Cell. 1991 Apr 5;65(1):115-23 PMID: 2013092
  12. Antisense probes containing 2-aminoadenosine allow efficient depletion of U5 snRNP from HeLa splicing extracts.
    Nucleic Acids Res. 1991 Jun 25;19(12):3193-8 PMID: 1648201
  13. Genetic depletion indicates a late role for U5 snRNP during in vitro spliceosome assembly.
    Nucleic Acids Res. 1991 Jul 25;19(14):3857-60 PMID: 1830649
  14. Immunoaffinity purification of a [U4/U6.U5] tri-snRNP from human cells.
    Genes Dev. 1991 Aug;5(8):1439-52 PMID: 1831175
  15. Base pairing between U2 and U6 snRNAs is necessary for splicing of a mammalian pre-mRNA.
    Nature. 1991 Aug 29;352(6338):818-21 PMID: 1831878
  16. Genetic evidence for base pairing between U2 and U6 snRNA in mammalian mRNA splicing.
    Nature. 1991 Aug 29;352(6338):821-4 PMID: 1831879
  17. U4 small nuclear RNA dissociates from a yeast spliceosome and does not participate in the subsequent splicing reaction.
    Mol Cell Biol. 1991 Nov;11(11):5571-7 PMID: 1833635
  18. The yeast PRP8 protein interacts directly with pre-mRNA.
    Nucleic Acids Res. 1991 Oct 25;19(20):5483-9 PMID: 1945827
  19. Association of U6 snRNA with the 5'-splice site region of pre-mRNA in the spliceosome.
    Genes Dev. 1992 Feb;6(2):244-54 PMID: 1310665
  20. U5 snRNA interacts with exon sequences at 5' and 3' splice sites.
    Cell. 1992 Feb 21;68(4):743-54 PMID: 1739979
  21. Dynamic association of proteins with the pre-mRNA branch region.
    Genes Dev. 1994 Dec 15;8(24):3008-20 PMID: 8001820
  22. Evidence for a Prp24 binding site in U6 snRNA and in a putative intermediate in the annealing of U6 and U4 snRNAs.
    EMBO J. 1995 Feb 15;14(4):820-32 PMID: 7882985
  23. Dynamic RNA-RNA interactions in the spliceosome.
    Annu Rev Genet. 1994;28:1-26 PMID: 7534458
  24. A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing.
    Genes Dev. 1995 Apr 1;9(7):843-54 PMID: 7705661
  25. A novel role for a U5 snRNP protein in 3' splice site selection.
    Genes Dev. 1995 Apr 1;9(7):855-68 PMID: 7535718
  26. Rearrangement of snRNA structure during assembly and function of the spliceosome.
    Prog Nucleic Acid Res Mol Biol. 1995;50:131-59 PMID: 7754032
  27. Extensive interactions of PRP8 protein with the 5' and 3' splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA.
    EMBO J. 1995 Jun 1;14(11):2602-12 PMID: 7781612
  28. In vitro reconstitution of mammalian U2 and U5 snRNPs active in splicing: Sm proteins are functionally interchangeable and are essential for the formation of functional U2 and U5 snRNPs.
    EMBO J. 1995 Aug 15;14(16):4010-21 PMID: 7664740
  29. snRNA interactions at 5' and 3' splice sites monitored by photoactivated crosslinking in yeast spliceosomes.
    RNA. 1995 Nov;1(9):968-80 PMID: 8548661
  30. The canonical GU dinucleotide at the 5' splice site is recognized by p220 of the U5 snRNP within the spliceosome.
    RNA. 1996 Mar;2(3):213-25 PMID: 8608445
  31. A U1/U4/U5 snRNP complex induced by a 2'-O-methyl-oligoribonucleotide complementary to U5 snRNA.
    Science. 1996 May 10;272(5263):881-4 PMID: 8629024
  32. The invariant U5 snRNA loop 1 sequence is dispensable for the first catalytic step of pre-mRNA splicing in yeast.
    Cell. 1996 Aug 23;86(4):679-89 PMID: 8752221
  33. A spontaneous duplication in U6 spliceosomal RNA uncouples the early and late functions of the ACAGA element in vivo.
    RNA. 1996 Sep;2(9):879-94 PMID: 8809015
  34. A novel U1/U5 interaction indicates proximity between U1 and U5 snRNAs during an early step of mRNA splicing.
    RNA. 1997 Apr;3(4):371-81 PMID: 9085844
  35. A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5' cleavage site.
    EMBO J. 1988 Aug;7(8):2533-8 PMID: 3056718
  36. 5' splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirements.
    Genes Dev. 1988 Oct;2(10):1258-67 PMID: 3060402
  37. Spliceosomal snRNAs.
    Annu Rev Genet. 1988;22:387-419 PMID: 2977088
  38. U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6.
    Mol Cell Biol. 1989 Aug;9(8):3350-9 PMID: 2552294
  39. Evidence from complementation assays in vitro that U5 snRNP is required for both steps of mRNA splicing.
    EMBO J. 1989 Oct;8(10):3105-12 PMID: 2531074
  40. A compensatory base change in human U2 snRNA can suppress a branch site mutation.
    Genes Dev. 1989 Oct;3(10):1545-52 PMID: 2612904
  41. Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing.
    Genes Dev. 1989 Oct;3(10):1553-61 PMID: 2558966
  42. A mammalian protein of 220 kDa binds pre-mRNAs in the spliceosome: a potential homologue of the yeast PRP8 protein.
    Proc Natl Acad Sci U S A. 1990 Apr;87(8):3082-6 PMID: 2139226
  43. Evidence for base-pairing between mammalian U2 and U6 small nuclear ribonucleoprotein particles.
    Genes Dev. 1990 Dec;4(12A):2146-56 PMID: 2176635
  44. Protein-RNA interactions in 20S U5 snRNPs.
    Biochim Biophys Acta. 1991 Jan 17;1088(1):139-43 PMID: 1703442
  45. Probing DNA structure with psoralen in vitro.
    Methods Enzymol. 1992;212:242-62 PMID: 1325599
  46. Protein components specifically associated with prespliceosome and spliceosome complexes.
    Genes Dev. 1992 Oct;6(10):1986-2000 PMID: 1398075
  47. Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing.
    Science. 1992 Sep 25;257(5078):1918-25 PMID: 1411506
  48. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome.
    Cell. 1992 Nov 27;71(5):803-17 PMID: 1423631
  49. Evidence for a base-pairing interaction between U6 small nuclear RNA and 5' splice site during the splicing reaction in yeast.
    Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11269-73 PMID: 1333604
  50. A functional association between the 5' and 3' splice site is established in the earliest prespliceosome complex (E) in mammals.
    Genes Dev. 1993 Jun;7(6):1008-20 PMID: 8504926
  51. Site-specific cross-linking of mammalian U5 snRNP to the 5' splice site before the first step of pre-mRNA splicing.
    Genes Dev. 1992 Dec;6(12B):2542-53 PMID: 1340469
  52. Disruption of base pairing between the 5' splice site and the 5' end of U1 snRNA is required for spliceosome assembly.
    Cell. 1993 Dec 3;75(5):863-73 PMID: 8252623
  53. Specific interactions between proteins implicated in splice site selection and regulated alternative splicing.
    Cell. 1993 Dec 17;75(6):1061-70 PMID: 8261509
  54. Mutations in the conserved loop of human U5 snRNA generate use of novel cryptic 5' splice sites in vivo.
    EMBO J. 1993 Dec 15;12(13):5181-9 PMID: 8262061
  55. Mutations in U6 snRNA that alter splice site specificity: implications for the active site.
    Science. 1993 Dec 24;262(5142):1982-8 PMID: 8266093
  56. The U5 and U6 small nuclear RNAs as active site components of the spliceosome.
    Science. 1993 Dec 24;262(5142):1989-96 PMID: 8266094
  57. Involvement of U6 snRNA in 5' splice site selection.
    Science. 1993 Dec 24;262(5142):2035-9 PMID: 8266100
  58. Architecture of the U5 small nuclear RNA.
    Mol Cell Biol. 1994 Mar;14(3):2180-90 PMID: 8114748
  59. Protein-protein interactions and 5'-splice-site recognition in mammalian mRNA precursors.
    Nature. 1994 Mar 10;368(6467):119-24 PMID: 8139654
  60. Pre-mRNA splicing.
    Curr Opin Genet Dev. 1994 Apr;4(2):298-304 PMID: 8032208
  61. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition.
    Genes Dev. 1994 Apr 1;8(7):843-54 PMID: 7926772
  62. U1, U2 and U5 small nuclear RNAs are found in plants cells. Complete nucleotide sequence of the U5 RNA family from pea nuclei.
    Nucleic Acids Res. 1983 Dec 20;11(24):8583-94 PMID: 6200829
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/25.17.3508
Published
1997-09-01
Pages
3508-13
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146904
Subset
IM
Grants
NIGMS NIH HHS · GM31073 · United States
External Links
PubMed source DOI: 10.1093/nar/25.17.3508 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2