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PubMed1998

Crystal structure of the spliceosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA.

We have determined the crystal structure at 2.4 A resolution of a ternary complex between the spliceosomal U2B"/U2A' protein complex and hairpin-loop IV of U2 small nuclear RNA. Unlike its close homologue the U1A protein, U2B" binds to its cognate RNA only in the presence of U2A', which contains leucine-rich repeats in its sequence. The concave surface of a parallel beta-sheet within the leucine-rich-repeat region of U2A' interacts with the ribonucleoprotein domain of U2B" on the surface opposite its RNA-binding surface. The basic carboxy-terminal region of U2A' interacts with the RNA stem. The crystal structure reveals how protein-protein interaction regulates RNA-binding specificity, and how replacing only a few key residues allows the U2B" and U1A proteins to discriminate between their cognate RNA hairpins by forming alternative networks of interactions.

Amino Acid Sequence↗
PubMed1989

Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth.

The single-copy gene snu4, which encodes the small nuclear RNA (snRNA) U4, has been cloned and sequenced. Schizosaccharomyces pombe U4 is 128 nucleotides in length, similar in size to vertebrate U4 and shows substantial primary and secondary structure homology. The gene lacks sequences closely resembling vertebrate snRNA transcription signals, but has a TATA box at -33 to -30; TATA sequences flanked by several additional conserved nucleotides are found in the same position in the 5' regions of other snRNA genes from Schiz. pombe. The cloned snu4 gene was disrupted by transposon mutagenesis and used to replace one chromosomal copy of snu4 in a diploid strain. On sporulation snu4- haploid strains could not be recovered, demonstrating that U4 is required, at least for spore germination. Haploid snu4- strains are viable if they also carry snu4+ on a replicating plasmid but are unable to loose the plasmid under non-selective growth, demonstrating a continuous requirement for U4 for viability.

Animals↗
PubMed1987

The highly conserved U small nuclear RNA 3'-end formation signal is quite tolerant to mutation.

Formation of the 3' end of U1 and U2 small nuclear RNA (snRNA) precursors is directed by a conserved sequence called the 3' box located 9 to 28 nucleotides downstream of all metazoan U1 to U4 snRNA genes sequenced so far. Deletion of part or all of the 3' box from human U1 and U2 genes drastically reduces 3'-end formation. To define the essential nucleotides within this box that direct 3'-end formation, we constructed a set of point mutations in the conserved residues of the human U1 3' box. The ability of the various mutations to direct 3'-end formation was tested by microinjection into Xenopus oocytes and transfection into HeLa cells. We found that the point mutations had diverse effects on 3'-end formation, ranging from no effect at all to severe inhibition; however, no single or double point mutation we tested completely eliminated 3'-end formation. We also showed that a rat U3 3' flank can effectively substitute for the human U1 3' flank, indicating that the 3' boxes of the different U snRNA genes are functionally equivalent.

Base Sequence↗
PubMedDate not supplied

[The loss of dinucleotides CpG from DNA. IV. Methylation and divergence of genes and pseudogenes of small nuclear RNA].

The frequency of neighboring base pairs in nucleotide sequences of over 80 genes and pseudogenes of low molecular weight RNAs U1-U8, 4.5S and 7S in different eukaryotes was determined. The probable frequency of CpG----TpG + CpA substitutions, caused as a result of the deamination of 5-methylcytosine residues in DNA, was determined. It was found that the genes of small RNAs do not reveal a single level of CpG methylation for all the species studied. In most cases CpG in the genes of U1, 4.5S and 7S RNA are methylated, whereas in the genes of U2-U6-RNA these sites must have never been subjected to methylation. Nearly all the investigated pseudogenes of different small RNAs are strongly methylated due to a considerable lack of CpG. It was established that CpG----TpG + CpA transitions may amount to as much third of all the mutations accumulated in the genes of the same RNAs in different species. Such transitions in pseudogenes may account for 40% of all the nucleotide substitutions. This disproportionately high level of mutations in CpG dinucleotides (3-5-fold higher than in other DNA dupletes) must be the direct result of the methylation of these sites. Consequently, CpG methylation causes a dramatic acceleration of the divergence rate of DNA sequences. It has been concluded that protection of most vital genes against methylation is one of the essential conditions for sustaining the high level of stability of the macromolecular structure and for the reliability of macromolecular functioning in a cell.

Animals↗
PubMed1982

Mouse DNA sequences complementary to small nuclear RNA U1.

A mouse genomic library was screened for sequences complementary to U1 nuclear RNA. Out of the eight clones tested, none contained more than one copy of U1. Six of them were identical and one of those (clone 0U1-XIII) was further analyzed. This latter clone contained no other gene for discrete species of small size RNA in the 8 Kb EcoRI fragment encoding U1. A 248 bp Bg1II fragment from 0U1-XIII encompassing the full length of U1 as well as flanking regions on both sides has been subcloned and sequenced in M13 phage. Although the coding region was 96.5% homologous to rat U1a RNA, there is no direct evidence that this clone is a true gene. 3' and 5' flanking sequences of this as well as other published clones have been searched for homologies and the results of this search are discussed.

Animals↗
PubMed1994

m3G cap hypermethylation of U1 small nuclear ribonucleoprotein (snRNP) in vitro: evidence that the U1 small nuclear RNA-(guanosine-N2)-methyltransferase is a non-snRNP cytoplasmic protein that requires a binding site on the Sm core domain.

The RNA components of small nuclear ribonucleoproteins (U snRNPs) possess a characteristic 5'-terminal trimethylguanosine cap structure (m3G cap). This cap is an important component of the nuclear localization signal of U snRNPs. It arises by hypermethylation of a cotranscriptionally added m7G cap. Here we describe an in vitro assay for the hypermethylation, which employs U snRNP particles reconstituted in vitro from purified components and subsequent analysis by m3G cap-specific immunoprecipitation. Complementation studies in vitro revealed that both cytosol and S-adenosylmethionine are required for the hypermethylation of an m7G-capped U1 snRNP reconstituted in vitro, indicating that the U1 snRNA-(guanosine-N2)-methyltransferase is a trans-active non-snRNP protein. Chemical modification revealed one cytoplasmic component required for hypermethylation and one located on the snRNP: these components have different patterns of sensitivity to modification by N-ethylmaleimide and iodoacetic acid (IAA). In the presence of cytosol and S-adenosylmethionine, an intact Sm core domain is a necessary and sufficient substrate for cap hypermethylation. These data, together with our observation that isolated native U1 snRNPs but not naked U1 RNA inhibit the trimethylation of in vitro-reconstituted U1 snRNP, indicate that the Sm core binds the methyltransferase specifically. Moreover, isolated native U2 snRNP also inhibits trimethylation of U1 snRNP, suggesting that other Sm-class U snRNPs might share the same methyltransferase. IAA modification of m7G-capped U1 snRNPs inhibited hypermethylation when they were microinjected into Xenopus oocytes and consequently also inhibited nuclear import. In contrast, modification with IAA of m3G-capped U1 snRNPs reconstituted in vitro did not interfere with their nuclear transport in oocytes. These data suggest that m3G cap formation and nuclear transport of U1 snRNPs are mediated by distinct factors, which require distinct binding sites on the Sm core of U1 snRNP.

Animals↗
PubMed1986

Occurrence of novel small RNAs with concomitant inhibition of host cellular U small nuclear RNA synthesis in Vero cells infected with herpes simplex virus type 1.

In eukaryotic cells, small nuclear and small cytoplasmic RNAs (sn- or scRNAs) are associated with distinct proteins, forming ribonucleoproteins (snRNPs or scRNPs). In the present study we analysed the protein composition as well as the small RNA pattern in non-infected and herpes simplex virus type 1 (HSV)-infected Vero cells. We found that concomitantly with the shut-off of host cell mRNA synthesis, synthesis of U-snRNAs was stopped. Due to their stability, however, U-snRNAs were still present in cells 36 h after HSV infection. Besides these RNAs, two novel small RNAs which we termed HVR1 and HVR2 were detected in infected cells. On the basis of their relative mobilities in urea gels, the apparent chain lengths of these newly synthesized RNAs were determined to be 255 and 154 nucleotides respectively. The small RNA-binding proteins Sm, RNP, Ro and La were found to increase up to 15-fold after HSV infection. The data presented suggest that new, virus-coded small RNPs are synthesized which might play a role in the maturation and regulation of HSV-coded RNA transcripts.

Animals↗
PubMed1983

Isolation and characterization of two linked mouse U1b small nuclear RNA genes.

A 6.9 kilobase Eco R1 fragment containing genes for two U1 RNAs has been isolated from a library of mouse DNA. The two genes code for an RNA which is very similar, if not identical, to mouse U1b RNA as judged by S1 nuclease mapping. This RNA is one base longer than the mouse U1a RNA, human U1 RNA, and rat U1 RNA and differs in six nucleotide substitutions from rat U1 RNA. The two genes are five kilobases apart and the U1 RNAs are coded for on opposite strands of the DNA with the 5' ends juxtaposed. The sequences flanking the genes are identical for 700 bases 5' to the gene and at least 80 bases 3' to the gene.

Animals↗
PubMed1989

Mutational analysis of the interactions between U1 small nuclear RNA and pre-mRNA of yeast.

In recent experiments we have used the power of yeast genetics to study U1 small nuclear RNA (snRNA): pre-messenger RNA (pre-mRNA) base pairing interactions [Séraphin et al. EMBO J. 7 (1988) 2533-2538]. Here we extend these observations to other potential U1 snRNA: pre-mRNA pairings. We show that several U1 snRNA mutants are viable. Using these U1 mutant strains we demonstrate further a base-pairing interaction between U1 snRNA position 3 and intron position 6. However, this interaction is only detected with a poor splicing substrate containing branchpoint mutations. These results provide information on the mechanism of 5' splice site-branch point interaction. We also propose several models which may explain why the sequence of the 5' end of the U1 snRNA is conserved among organisms as divergent as man and yeast.

Animals↗
PubMed1992

The differential transcriptional activity of two amphibian U1 small-nuclear RNA genes correlates with structural differences in the proximal sequence element.

We previously analyzed the transcription of an axolotl U1 small-nuclear RNA (snRNA) gene (AmU1) by microinjection into Xenopus laevis oocytes. In such an assay, AmU1 showed a low template activity compared to that of an X. laevis U1 snRNA gene (XlU1B2). Swapping the proximal sequence element (PSE) with that of XlU1B2 was required for AmU1 to acquire a transcription level equal to that of XlU1B2. In the present work, we examine the functional importance of the nucleotides that are common or different in both PSEs with the aim of identifying which nucleotides within the Xenopus U1 PSE are critical for this enhancement of Ambystoma mexicanum U1 snRNA transcription. The PSE mutation analysis showed that the central, phylogenetically conserved C-58/C-57 doublet is absolutely required for U1 promoter activity. In the 3' portion of this element, a CGC to ATG change (positions -54/-52) which partially restores the XlU1B2 PSE sequence, enables the AmU1 gene to gain the same transcriptional activity as XlU1B2. Remarkably, in this clustered point mutation, the sole C-54 to A-54 change is sufficient to obtain this increased level. Therefore, the activity of the AmU1 gene in injected Xenopus oocytes is strongly affected by a single sequence difference between AmU1 and XlU1B2 PSEs. This finding underscores the crucial importance of the nucleotide identity at position -54 to the function of the Xenopus U1 PSE.

Ambystoma↗
PubMed1987

Identification of proteins interacting with the enhancer of human U2 small nuclear RNA genes.

Protein/DNA interactions in the human U2 RNA gene enhancer have been characterized by DNase I footprint and DMS methylation protection analyses. Nuclear factors present in both HeLa and B cell extracts have been shown to protect an approximately 70 bp region from DNase I digestion. DMS and DNase I footprint competition studies demonstrated that the entire footprint can be accounted for by interactions with two previously identified transcription factors. One of these recognizes the so called octanucleotide-motif ATGCAAAT (transcription factor IgNF-A) which has been shown to be essential for transcription. The other is the transcription factor Sp1 which binds to three target sequences located adjacent to the octameric motif. The Sp1 interactions appear to be required for full transcriptional activity. No differences in the DNase I footprint patterns or in the DMS methylation protections were observed when nuclear extracts from HeLa cells, two different B cell lines, or from the adenovirus-transformed 293 cell line were compared.

Base Sequence↗
PubMed2001

Characterization of a candidate Trypanosoma brucei U1 small nuclear RNA gene.

We have previously shown that the poly(A) polymerase (PAP) gene of Trypanosoma brucei is interrupted by an intervening sequence. It was postulated that removing this intron by cis-splicing requires a yet unidentified U1 small nuclear RNA (snRNA), which in other organisms engages in base-pair interactions across the 5' splice site during early spliceosome assembly. Here we present a characterization of a 75 nucleotide long candidate T. brucei U1 snRNA. Immunoprecipitation studies indicate that a trimethylguanosine cap structure is present at the 5' end and that the RNA is bound to core proteins common to spliceosomal ribonucleoprotein particles. The U1 snRNA has the potential for extensive intermolecular base pairing with the PAP 5' splice site. We used block replacement mutagenesis to identify sequences necessary for in vivo expression of U1 snRNA. We found that at least two cis-acting elements, tRNA-like A and B boxes, located in the 5'-flanking region are necessary for U1 snRNA synthesis; no internal sequences close to the transcription start site are essential, suggesting a promoter architecture distinct from other trypanosome U-snRNA genes.

5' Untranslated Regions↗