XB-ART-27603
Nucleic Acids Res
1988 Mar 25;165:2127-48.
Show Gene links
Show Anatomy links
Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA.
Jeppesen C
,
Stebbins-Boaz B
,
Gerbi SA
.
Abstract
Using a combination of RNA sequencing and construction of cDNA clones followed by DNA sequencing, we have determined the primary nucleotide sequence of U3 snRNA in Xenopus laevis and Xenopus borealis. This molecule has a length of 219 nucleotides. Alignment of the Xenopus sequences with U3 snRNA sequences from other organisms reveals three evolutionarily conserved blocks. We have probed the secondary structure of U3 snRNA in intact Xenopus laevis nuclei using single-strand specific chemical reagents; primer extension was used to map the positions of chemical modification. The three blocks of conserved sequences fall within single-stranded regions, and are therefore accessible for interaction with other molecules. Models of U3 snRNA function are discussed in light of these data.
PubMed ID: 3357768
PMC ID: PMC338204
Article link: Nucleic Acids Res
Grant support: [+]
References [+] :
Ares,
U2 RNA from yeast is unexpectedly large and contains homology to vertebrate U4, U5, and U6 small nuclear RNAs.
1986, Pubmed
Ares, U2 RNA from yeast is unexpectedly large and contains homology to vertebrate U4, U5, and U6 small nuclear RNAs. 1986, Pubmed
Bachellerie, Recognition signals for mouse pre-rRNA processing. A potential role for U3 nucleolar RNA. 1983, Pubmed
Bayev, The structure of the yeast ribosomal RNA genes. 3. Precise mapping of the 18 S and 25 S rRNA genes and structure of the adjacent regions. 1981, Pubmed
Berget, U1, U2, and U4/U6 small nuclear ribonucleoproteins are required for in vitro splicing but not polyadenylation. 1986, Pubmed
Bernstein, Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. 1983, Pubmed
Black, Pre-mRNA splicing in vitro requires intact U4/U6 small nuclear ribonucleoprotein. 1986, Pubmed
Black, U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. 1985, Pubmed
Busch, Methods for isolation of nuclei and nucleoli. 1977, Pubmed
Chabot, The 3' splice site of pre-messenger RNA is recognized by a small nuclear ribonucleoprotein. 1985, Pubmed
Ciesiolka, Identification of the site of cross-linking in 16S rRNA of an aromatic azide photoaffinity probe attached to the 5'-anticodon base of A site bound tRNA. 1985, Pubmed
Clark, Ribosomal RNA evolution by fragmentation of the 23S progenitor: maturation pathway parallels evolutionary emergence. 1982, Pubmed
Crouch, A model for the involvement of the small nucleolar RNA (U3) in processing eukaryotic ribosomal RNA. 1983, Pubmed
Ehresmann, Two-dimensional gel electrophoresis technique for determination of the cross-linked nucleotides in cleavable covalent RNA-RNA complexes. Application to Escherichia coli and Bacillus subtilis acetylvalyl-tRNA covalently linked to E. coli 16S and yeast 18S ribosomal RNA. 1984, Pubmed
England, 3'-terminal labelling of RNA with T4 RNA ligase. 1978, Pubmed
Epstein, Multiple states of U3 RNA in Novikoff hepatoma nucleoli. 1984, Pubmed
Furlong, The external transcribed spacer and preceding region of Xenopus borealis rDNA: comparison with the corresponding region of Xenopus laevis rDNA. 1983, Pubmed , Xenbase
Furlong, Patterns of major divergence between the internal transcribed spacers of ribosomal DNA in Xenopus borealis and Xenopus laevis, and of minimal divergence within ribosomal coding regions. 1983, Pubmed , Xenbase
Georgiev, The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisae. 1981, Pubmed , Xenbase
Green, Pre-mRNA splicing. 1986, Pubmed
Guerrier-Takada, The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. 1983, Pubmed
Hagenbüchle, Conservation of the primary structure at the 3' end of 18S rRNA from eucaryotic cells. 1978, Pubmed
Hall, Nucleotide sequence through the 18S-28S intergene region of a vertebrate ribosomal transcription unit. 1980, Pubmed , Xenbase
Hay, Fine structure of the nucleolus in normal and mutant Xenopus embryos. 1967, Pubmed , Xenbase
Hughes, The yeast homologue of U3 snRNA. 1987, Pubmed , Xenbase
Hügle, Ribocharin: a nuclear Mr 40,000 protein specific to precursor particles of the large ribosomal subunit. 1985, Pubmed , Xenbase
Inoue, Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. 1985, Pubmed
Jacq, Sequence homologies between eukaryotic 5.8S rRNA and the 5' end of prokaryotic 23S rRNa: evidences for a common evolutionary origin. 1981, Pubmed , Xenbase
Jensen, Synthesis of low molecular weight RNA components A, C and D by polymerase II in alpha-amanitin-resistant hamster cells. 1979, Pubmed
Jones, The role of the nucleolus in the formation of ribosomes. 1965, Pubmed
Kass, Primary processing of mammalian rRNA involves two adjacent cleavages and is not species specific. 1987, Pubmed
Krainer, Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. 1985, Pubmed
Krämer, The 5' terminus of the RNA moiety of U1 small nuclear ribonucleoprotein particles is required for the splicing of messenger RNA precursors. 1984, Pubmed
Labhart, Characterization of three sites of RNA 3' end formation in the Xenopus ribosomal gene spacer. 1986, Pubmed , Xenbase
Lapeyre, Nucleolin, the major nucleolar protein of growing eukaryotic cells: an unusual protein structure revealed by the nucleotide sequence. 1987, Pubmed
Lempereur, Conformation of yeast 18S rRNA. Direct chemical probing of the 5' domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible. 1985, Pubmed
Maden, Nucleotide sequence of an external transcribed spacer in Xenopus laevis rDNA: sequences flanking the 5' and 3' ends of 18S rRNA are non-complementary. 1982, Pubmed , Xenbase
Maniatis, The role of small nuclear ribonucleoprotein particles in pre-mRNA splicing. , Pubmed
Miller, Transcription of mouse rRNA genes by RNA polymerase I: in vitro and in vivo initiation and processing sites. 1981, Pubmed
Moazed, Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. 1986, Pubmed
Mount, The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro. 1983, Pubmed
Murphy, Transcription of a gene for human U1 small nuclear RNA. 1982, Pubmed , Xenbase
Nazar, A 5.8 S rRNA-like sequence in prokaryotic 23 S rRNA. 1980, Pubmed
Ofengand, Functional conservation near the 3' end of eukaryotic small subunit RNA: photochemical crosslinking of P site-bound acetylvalyl-tRNA to 18S RNA of yeast ribosomes. 1982, Pubmed
Ozaki, Sequence analysis of the transcribed and 5' non-transcribed regions of the ribosomal RNA gene in Dictyostelium discoideum. 1984, Pubmed , Xenbase
Padgett, Splicing of messenger RNA precursors. 1986, Pubmed
Parker, Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. 1987, Pubmed
Parker, Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA. 1987, Pubmed
Prestayko, Low molecular weight RNA associated with 28 s nucleolar RNA. 1970, Pubmed
Prince, Covalent crosslinking of tRNA1Val to 16S RNA at the ribosomal P site: identification of crosslinked residues. 1982, Pubmed
Qu, Improved methods for structure probing in large RNAs: a rapid 'heterologous' sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5' terminal domain of eukaryotic 28S rRNA. 1983, Pubmed
Reddy, Small nuclear RNAs and RNA processing. 1983, Pubmed
Reddy, Compilation of small RNA sequences. 1986, Pubmed
Roop, Structure and expression of a chicken gene coding for U1 RNA. 1981, Pubmed
Rubtsov, The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae. 1980, Pubmed
Sanger, DNA sequencing with chain-terminating inhibitors. 1977, Pubmed
Schaufele, Compensatory mutations suggest that base-pairing with a small nuclear RNA is required to form the 3' end of H3 messenger RNA. , Pubmed , Xenbase
Schmidt-Zachmann, A constitutive nucleolar protein identified as a member of the nucleoplasmin family. 1987, Pubmed , Xenbase
Sharp, Splicing of messenger RNA precursors. 1987, Pubmed
Skryabin, Structure and function of the nontranscribed spacer regions of yeast rDNA. 1984, Pubmed , Xenbase
Stroke, Genes and pseudogenes for rat U3A and U3B small nuclear RNA. 1985, Pubmed , Xenbase
Subrahmanyam, Nucleotide sequence of the region between the 18S rRNA sequence and the 28S rRNA sequence of rat ribosomal DNA. 1982, Pubmed , Xenbase
Suh, Isolation and characterization of a human U3 small nucleolar RNA gene. 1986, Pubmed , Xenbase
Tague, Processing of the large rRNA precursor: two proposed categories of RNA-RNA interactions in eukaryotes. 1984, Pubmed
Veldman, The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript. 1981, Pubmed
Wise, Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a dispersed multigene family. 1980, Pubmed
Woese, Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. 1983, Pubmed
Youvan, Reverse transcriptase pauses at N2-methylguanine during in vitro transcription of Escherichia coli 16S ribosomal RNA. 1979, Pubmed
Zhuang, A compensatory base change in U1 snRNA suppresses a 5' splice site mutation. 1986, Pubmed
Zieve, Small RNA species of the HeLa cell: metabolism and subcellular localization. 1976, Pubmed