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Cuadrado A, Bernal J, Muñoz A. Identification of the mammalian homolog of the splicing regulator Suppressor-of-white-apricot as a thyroid hormone regulated gene. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1999; 71:332-40. [PMID: 10521587 DOI: 10.1016/s0169-328x(99)00212-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mammalian brain development is controlled by thyroid hormone through the regulation of target genes. In this study, we describe for the first time that a splicing regulator gene is under thyroid hormone control in the rat brain during the critical period of neuronal differentiation. By differential display, we have identified the mammalian homolog of the Drosophila splicing regulator Suppressor-of-white-apricot (SWAP) as a thyroid hormone-regulated gene in an immortal line of rat neuroblasts, E18 cells. Using Northern blotting and in situ hybridization, we found that expression of SWAP is under thyroid control in the developing rat brain. SWAP gene expression is highest during the first 10 days of life (P0-P10), preferentially in cerebral cortex, cerebellum, subventricular epithelium, piriform cortex, hippocampus, amygdala, and caudate putamen. At later stages (P15-P30) SWAP expression decreases, being detectable only in the cerebellum, hippocampus, and layers II/III of cerebral and piriform cortexes. We found that hypothyroidism causes an abnormal high level of SWAP RNA expression at P5-P15 throughout the brain except the cerebellum. Significantly, thyroid hormone treatment in vivo of hypothyroid animals led to a normalization of SWAP RNA expression. Furthermore, similar hormone treatment caused a decrease in SWAP expression in control rats. By modulating the expression of SWAP and perhaps other splicing regulators thyroid hormone may exert wide regulatory effects on multiple genes. The regulation of SWAP gene defines a novel mechanism of action of thyroid hormone which can be important for its effects in the developing brain.
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Affiliation(s)
- A Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier 4, 28029, Madrid, Spain
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Ségault V, Will CL, Polycarpou-Schwarz M, Mattaj IW, Branlant C, Lührmann R. Conserved loop I of U5 small nuclear RNA is dispensable for both catalytic steps of pre-mRNA splicing in HeLa nuclear extracts. Mol Cell Biol 1999; 19:2782-90. [PMID: 10082544 PMCID: PMC84071 DOI: 10.1128/mcb.19.4.2782] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The function of conserved regions of the metazoan U5 snRNA was investigated by reconstituting U5 small nuclear ribonucleoprotein particles (snRNPs) from purified snRNP proteins and HeLa or Xenopus U5 snRNA mutants and testing their ability to restore splicing to U5-depleted nuclear extracts. Substitution of conserved nucleotides comprising internal loop 2 or deletion of internal loop 1 had no significant effect on the ability of reconstituted U5 snRNPs to complement splicing. However, deletion of internal loop 2 abolished U5 activity in splicing and spliceosome formation. Surprisingly, substitution of the invariant loop 1 nucleotides with a GAGA tetraloop had no effect on U5 activity. Furthermore, U5 snRNPs reconstituted from an RNA formed by annealing the 5' and 3' halves of the U5 snRNA, which lacked all loop 1 nucleotides, complemented both steps of splicing. Thus, in contrast to yeast, loop 1 of the human U5 snRNA is dispensable for both steps of splicing in HeLa nuclear extracts. This suggests that its function can be compensated for in vitro by other spliceosomal components: for example, by proteins associated with the U5 snRNP. Consistent with this idea, immunoprecipitation studies indicated that several functionally important U5 proteins associate stably with U5 snRNPs containing a GAGA loop 1 substitution.
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Affiliation(s)
- V Ségault
- UMR CNRS 7567 Maturation des ARN et Enzymologie Moleculaire Université H. Poincaré, 54506 Vandoeuvre-Les-Nancy Cédex, France
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Liu ZR, Sargueil B, Smith CW. 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. Mol Cell Biol 1998; 18:6910-20. [PMID: 9819379 PMCID: PMC109274 DOI: 10.1128/mcb.18.12.6910] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Assembly of spliceosomes involves a number of sequential steps in which small nuclear ribonucleoprotein particles (snRNPs) and some non-snRNP proteins recognize the splice site sequences and undergo various conformational rearrangements. A number of important intermolecular RNA-RNA duplexes are formed transiently during the process of splice site recognition. Various steps in the assembly pathway are dependent upon ATP hydrolysis, either for protein phosphorylation or for the activity of helicases, which may modulate the RNA structures. Major efforts have been made to identify proteins that interact with specific regions of the pre-mRNA during the stages of spliceosome assembly and catalysis by site-specific UV cross-linking. However, UV cross-linking is often inefficient for the detection of proteins that interact with base-paired RNA. Here we have used the complementary approach of methylene blue-mediated photo-cross-linking to detect specifically proteins that interact with the duplexes formed between pre-mRNA and small nuclear RNA (snRNA). We have detected a novel cross-link between a 65-kDa protein (p65) and the 5' splice site. A range of data suggest that p65 cross-links to the transient duplex formed by U1 snRNA and the 5' splice site. Moreover, although p65 cross-linking requires only a 5' splice site within the pre-mRNA, it also requires ATP hydrolysis, suggesting that its detection reflects a very early ATP-dependent event during splicing.
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Affiliation(s)
- Z R Liu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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Abstract
The purpose of this review is to highlight the unique and common features of splice site selection in plants compared with the better understood yeast and vertebrate systems. A key question in plant splicing is the role of AU sequences and how and at what stage they are involved in spliceosome assembly. Clearly, intronic U- or AU-rich and exonic GC- and AG-rich elements can influence splice site selection and splicing efficiency and are likely to bind proteins. It is becoming clear that splicing of a particular intron depends on a fine balance in the "strength" of the multiple intron signals involved in splice site selection. Individual introns contain varying strengths of signals and what is critical to splicing of one intron may be of less importance to the splicing of another. Thus, small changes to signals may severely disrupt splicing or have little or no effect depending on the overall sequence context of a specific intron/exon organization.
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Affiliation(s)
- J. W. S. Brown
- Department of Cell and Molecular Genetics, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom; e-mail: ;
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Kuldau GA, Raju NB, Glass NL. Repeat-induced point mutations in Pad-1, a putative RNA splicing factor from Neurospora crassa, confer dominant lethal effects on ascus development. Fungal Genet Biol 1998; 23:169-80. [PMID: 9578630 DOI: 10.1006/fgbi.1998.1034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe the characterization of a gene, Pad-1, from Neurospora crassa which displays sequence characteristics of the RS class of hnRNA-binding proteins (hnRNP) and mRNA splicing factors. This is the first report of the isolation of a putative hnRNP gene from N. crassa. PAD-1 showed 30% identity and 57% similarity to a protein, HCC1, which was isolated using autoantibodies from patients suffering from hepatocellular carcinoma. Both HCC1 and PAD-1 show amino acid sequence similarities to the human splicing factor, U2AF65. Mutations induced in Pad-1 by repeat-induced point (RIP) mutation show dominant effects on ascus and ascospore formation, a novel phenotypic class of RIP mutants. A mutant isolated from the Pad-1 RIP cross displayed a severe vegetative growth defect and dominant effects on ascus development, indicating that Pad-1 is essential for both asexual and sexual development.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- Fungal Proteins
- Genes, Dominant
- Genes, Fungal
- Humans
- Molecular Sequence Data
- Mutagenesis
- Neurospora crassa/genetics
- Neurospora crassa/growth & development
- Neurospora crassa/physiology
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Point Mutation/genetics
- RNA Splicing/genetics
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Nuclear/genetics
- RNA, Nuclear/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/genetics
- Ribonucleoproteins, Small Nuclear
- Sequence Alignment
- Splicing Factor U2AF
- Spores, Fungal/physiology
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Affiliation(s)
- G A Kuldau
- Botany Department and Biotechnology Laboratory, University of British Columbia, Vancouver, Canada
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Arenas JE, Abelson JN. Prp43: An RNA helicase-like factor involved in spliceosome disassembly. Proc Natl Acad Sci U S A 1997; 94:11798-802. [PMID: 9342317 PMCID: PMC23592 DOI: 10.1073/pnas.94.22.11798] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Saccharomyces cerevisiae genes PRP2, PRP16, and PRP22 encode pre-mRNA splicing factors that belong to the highly conserved "DEAH" family of putative RNA helicases. We previously identified two additional members of this family, JA1 and JA2. To investigate its biological function, we cloned the JA1 gene and generated alleles carrying mutations identical to those found in highly conserved regions of other members of the DEAH family. A ja1 allele carrying a mutation identical to that in the temperature-sensitive (ts) prp22-1 gene conferred ts phenotype when integrated into the genome of a wild-type strain by gene replacement. Northern analysis of RNA obtained from the ts strain shifted to a nonpermissive temperature revealed accumulation of unspliced pre-mRNAs and excised intron lariats. Furthermore, analysis of splicing complexes showed that intron lariats accumulated in spliceosomes. The results presented indicate that JA1 encodes a pre-mRNA processing factor (Prp) involved in disassembly of spliceosomes after the release of mature mRNA. We have therefore renamed this gene PRP43.
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Affiliation(s)
- J E Arenas
- Division of Biology, 147-75, California Institute of Technology, Pasadena, CA 91125, USA.
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Sontheimer EJ, Sun S, Piccirilli JA. Metal ion catalysis during splicing of premessenger RNA. Nature 1997; 388:801-5. [PMID: 9285595 DOI: 10.1038/42068] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The removal of intervening sequences from premessenger RNA is essential for the expression of most eukaryotic genes. The spliceosome ribonucleoprotein complex catalyses intron removal by two sequential phosphotransesterification reactions, but the catalytic mechanisms are unknown. It has been proposed that two divalent metal ions may mediate catalysis of both reaction steps, activating the 2'- or 3'-hydroxyl groups for nucleophilic attack and stabilizing the 3'-oxyanion leaving groups by direct coordination. Here we show that in splicing reactions with a precursor RNA containing a 3'-sulphur substitution at the 5' splice site, interaction between metal ion and leaving group is essential for catalysis of the first reaction step. This establishes that the spliceosome is a metalloenzyme and demonstrates a direct parallel with the catalytic strategy used by the self-splicing group I intron from Tetrahymena. In contrast, 3'-sulphur substitution at the 3' splice site provides no evidence for a metal ion-leaving group interaction in the second reaction step, suggesting that the two steps of splicing proceed by different catalytic mechanisms and therefore in distinct active sites.
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Affiliation(s)
- E J Sontheimer
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, The University of Chicago, Illinois 60637, USA
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Abstract
Intron excision is an essential step in eukaryotic gene expression, but the molecular mechanisms by which the spliceosome accurately identifies splice sites in nuclear precursors to messenger RNAs (pre-mRNAs) are not well understood. A bimolecular assay for the second step of splicing has now revealed that exon ligation by the human spliceosome does not require covalent attachment of a 3' splice site to the branch site. Furthermore, accurate definition of the 3' splice site in this system is independent of either a covalently attached polypyrimidine tract or specific 3' exon sequences. Rather, in this system 3' splice site selection apparently occurs with a 5' --> 3' directionality.
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Affiliation(s)
- K Anderson
- W. M. Keck Institute for Cellular Visualization, Department of Biochemistry, Brandeis University, Waltham, MA 02254, USA
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Min H, Turck CW, Nikolic JM, Black DL. A new regulatory protein, KSRP, mediates exon inclusion through an intronic splicing enhancer. Genes Dev 1997; 11:1023-36. [PMID: 9136930 DOI: 10.1101/gad.11.8.1023] [Citation(s) in RCA: 254] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have purified and cloned a new splicing factor, KSRP. KSRP is a component of a multiprotein complex that binds specifically to an intronic splicing enhancer element downstream of the neuron-specific c-src N1 exon. This 75-kD protein induces the assembly of five other proteins, including the heterogeneous nuclear ribonucleoprotein F, onto the splicing enhancer. The sequence of the KSRP cDNA indicates that the protein contains four K homology RNA-binding domains and an unusual carboxy-terminal domain. KSRP is similar to two proteins, FUSE-binding protein and P-element somatic inhibitor. KSRP is expressed in both neural and non-neural cell lines, although it is present at higher levels in neural cells. Antibodies specific for KSRP inhibit the splicing of the N1 exon in vitro. Moreover, this inhibition of N1 splicing can be rescued by the addition of purified KSRP. KSRP is likely to regulate splicing from a number of intronic splicing enhancer sequences.
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Affiliation(s)
- H Min
- Molecular Biology Institute, University of California at Los Angeles, 90095-1662, USA
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MacMillan AM, McCaw PS, Crispino JD, Sharp PA. SC35-mediated reconstitution of splicing in U2AF-depleted nuclear extract. Proc Natl Acad Sci U S A 1997; 94:133-6. [PMID: 8990173 PMCID: PMC19256 DOI: 10.1073/pnas.94.1.133] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Assembly of the mammalian spliceosome is known to proceed in an ordered fashion through several discrete complexes, but the mechanism of this assembly process may not be universal. In an early step, pre-mRNAs are committed to the splicing pathway through association with U1 small nuclear ribonucleoprotein (snRNP) and non-snRNP splicing factors, including U2AF and members of the SR protein family. As a means of studying the steps of spliceosome assembly, we have prepared HeLa nuclear extracts specifically depleted of the splicing factor U2AF. Surprisingly, the SR protein SC35 can functionally substitute for U2AF65 in the reconstitution of pre-mRNA splicing in U2AF-depleted extracts. This reconstitution is substrate-specific and is reminiscent of the SC35-mediated reconstitution of splicing in extracts depleted of U1 snRNP. However, SC35 reconstitution of splicing in U2AF-depleted extracts is dependent on the presence of functional U1 snRNP. These observations suggest that there are at least three distinguishable mechanisms for the binding of U2 snRNP to the pre-mRNA, including U2AF-dependent and -independent pathways.
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Affiliation(s)
- A M MacMillan
- Center for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge 02139-4307, USA
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