The Mr 70,000 protein of the U1 small nuclear ribonucleoprotein particle binds to the 5' stem-loop of U1 RNA and interacts with Sm domain proteins

Molecular analysis of eight U1 RNA gene candidates from tomato that could potentially be transcribed into U1 RNA sequence variants differing from each other in similar regions of secondary structure

From a tomato genomic library we isolated and characterized eight U1 RNA gene candidates (U1.1 to U1.8) all of which possessed the canonical plant U-snRNA transcription signals in their 5' and 3' flanking regions and exhibited nucleotide sequence conservation in the 5' splice site recognition sequence, in the Sm antigen binding site and in Loops B, C, D as well as in Stems III and IV of their coding region. Deviations from the U1 RNA consensus sequence were mainly localized to Loop A and Stems I and II, suggesting that the putative transcripts of the tomato U1.1-U1.8 genes would differ from each other in their capacity of binding to the U1 RNA-specific snRNP proteins.

U1 small nuclear ribonucleoprotein particle-specific proteins interact with the first and second stem-loops of U1 RNA, with the A protein binding directly to the RNA independently of the 70K and Sm proteins

The U1 small nuclear ribonucleoprotein particle (U1 snRNP), a cofactor in pre-mRNA splicing, contains three proteins, termed 70K, A, and C, that are not present in the other spliceosome-associated snRNPs. We studied the binding of the A and C proteins to U1 RNA, using a U1 snRNP reconstitution system and an antibody-induced nuclease protection technique. Antibodies that reacted with the A and C proteins induced nuclease protection of the first two stem-loops of U1 RNA in reconstituted U1 snRNP. Detailed analysis of the antibody-induced nuclease protection patterns indicated the existence of relatively long-range protein-protein interactions in the U1 snRNP, with the 5' end of U1 RNA and its associated specific proteins interacting with proteins bound to the Sm domain near the 3' end. UV cross-linking experiments in conjunction with an A-protein-specific antibody demonstrated that the A protein bound directly to the U1 RNA rather than assembling in the U1 snRNP exclusively via protein-protein interactions. This conclusion was supported by additional experiments revealing that the A protein could bind to U1 RNA in the absence of bound 70K and Sm core proteins.

The U1 RNA-binding site of the U1 small nuclear ribonucleoprotein (snRNP)-associated A protein suggests a similarity with U2 snRNPs

The site of interaction between human U1 RNA and one of its uniquely associated proteins, A, was examined with in vitro binding assays. The A protein bound directly to stem-loop II of U1 RNA in a region which exhibits sequence similarity to U2 RNA. The similarity with U2 RNA was in a region that has been shown to interact with a U2 RNA-associated protein. The A protein-binding site on U1 RNA overlapped a previously described epitope for an RNA-specific human autoantibody (S. L. Deutscher and J. D. Keene, Proc. Natl. Acad. Sci. USA 85:3299-3303, 1988), supporting the hypothesis that the anti-RNA antibody originated as an anti-idiotypic response to A protein-specific autoantibodies.

U2 small nuclear RNP assembly in vitro

Incubation of a SP6-transcribed human U2 RNA precursor molecule in a HeLa cell S100 fraction resulted in the formation of ribonucleoprotein complexes. In the presence of ATP, the particles that assembled had several properties of native U2 snRNP, including resistance to dissociation in Cs2SO4 gradients, their buoyant density, and pattern of digestion by micrococcal nuclease. These particles also reacted with Sm monoclonal antibody and a human autoantibody with specificity for the U2 snRNP-specific proteins A' and B", but not with antibodies for U1 snRNP-specific proteins. In contrast, the particles that formed in the absence of ATP did not have these properties. ATP analogs with non-hydrolyzable beta-gamma bonds did not substitute for ATP in U2 snRNP assembly. Additional experiments with a mutant U2 RNA confirmed that nucleotides 154-167 of U2 RNA are required for binding of the U2 snRNP-specific proteins but not of the "Sm" core proteins. Pseudouridine formation, a major post-transcriptional modification of U2 RNA, was enhanced under assembly permissive conditions.

Genetic analysis of the role of human U1 snRNA in mRNA splicing: I. Effect of mutations in the highly conserved stem-loop I of U1

The 5' splice site mutation known as hr440 can be suppressed efficiently in vivo by a compensatory base change in U1 small nuclear RNA (snRNA). We have now begun a second-site reversion analysis of this suppressor U1-4u snRNA (which has a C----U change at position 4) to identify U1 nucleotides that are essential for mRNA splicing. Point mutations in U1-4u that disrupt the structure of stem-loop I or alter phylogenetically conserved nucleotides within the loop cause loss of suppression. The level of suppressor activity observed for most mutants correlated with the abundance of the corresponding suppressor RNA, suggesting that mutations in stem-loop I cause loss of suppression by destabilizing U1 snRNA or the U1 snRNP (small nuclear ribonucleoprotein particle). We favor the interpretation that incompletely or improperly assembled U1 snRNPs are unstable, because two severe point mutations in stem-loop I were found to decrease the binding of U1 snRNP-specific proteins in vitro. In a separate set of experiments, we found that increasing the distance between stem-loop I and the 5' end of U1 snRNA also inhibited suppression but did not affect assembly or stability of the U1 snRNP. This suggests that the relationship between the 5' splice site and the body of the U1 snRNP is important for mRNA splicing.

In vitro reconstitution of snRNPs: a reconstituted U4/U6 snRNP participates in splicing complex formation

We have reconstituted in vitro the four snRNPs known to be involved in pre-mRNA splicing: U1, U2, U5, and U4/6. Reconstitution involves adding either authentic or in vitro-synthesized snRNAs to extracts enriched in snRNP structural polypeptides. The reconstituted snRNPs have the same buoyant density and are immunoprecipitated by the same antibodies as authentic snRNPs. Thus, the polypeptide composition of reconstituted snRNPs is similar, if not identical, to that of authentic snRNPs. We show further that a reconstituted U4/U6 particle is fully functional in forming splicing complexes with pre-mRNA. As is the case for the authentic U4/U6 snRNP, the reconstituted U4 snRNP, but not the U6 snRNA, dissociates from the complex prior to formation of the mature spliceosome. The ability to reconstitute snRNPs and assay their activity in spliceosome formation should provide a powerful approach to study these particles.

Loop I of U1 small nuclear RNA is the only essential RNA sequence for binding of specific U1 small nuclear ribonucleoprotein particle proteins

The binding of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins C, A, and 70K to U1 small nuclear RNA (snRNA) was analyzed. Assembly of U1 snRNAs from bean and soybean and a set of mutant Xenopus U1 snRNAs into U1 snRNPs in Xenopus egg extracts was studied. The ability to bind proteins was analyzed by immunoprecipitation with monospecific antibodies and by a protein-sequestering assay. The only sequence essential for binding of the U1-specific proteins was the conserved loop sequence in the 5' hairpin of U1. Further analysis suggested that protein C binds directly to the loop and that the assembly of proteins A and 70K into the RNP requires mainly protein-protein interactions. Protein C apparently recognizes a specific RNA sequence rather than a secondary structural element in the RNA.

A structural analysis of P. polycephalum U1 RNA at the RNA and gene levels. Are there differentially expressed U1 RNA genes in P. polycephalum? U1 RNA evolution

U1 RNAs were isolated from P. polycephalum microplasmodia nuclei and sequenced. A P. polycephalum gene coding for U1 RNA was also isolated. The coding region of this gene differs at 3 positions compared to the isolated U1 RNA species. Both isolated RNAs and the gene encoded RNA can be folded according to the secondary structure model previously proposed for U1 RNA. Putative regulatory elements very similar to those required for efficient transcription of U RNA genes from vertebrates, in particular, the -200 distal enhancer element, are present in the flanking regions of this gene. The presence of several U1 RNA genes in P. polycephalum was confirmed by Southern blot analysis of genomic DNA. In contrast to yeast S. cerevisiae U1 RNA, P. polycephalum U1 RNAs have a length similar to that of U1 RNAs from higher eukaryotes. Nevertheless, P. polycephalum U1 RNAs probably differ from these RNAs in the 5'-terminal segment supposed to base-pair with the 5'-end of introns. The results are discussed taking into account phylogenetic evolution and functional role of U1 RNA.

Direct cross-linking of snRNP proteins F and 70K to snRNAs by ultra-violet radiation in situ

Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross-linkage was demonstrated by isolating protein-oligonucleotide complexes from snRNPs containing 32P-labelled snRNAs after exhaustive digestion with a mixture of RNases of different specificities. The primary target of the UV-light induced cross-linking reaction between protein and RNA was protein F. It was also found to be cross-linked to U1 snRNA in purified U1 snRNPs. Protein F is known to be one of the common snRNP proteins, which together with D, E and G protect a 15-25 nucleotide long stretch of snRNAs U1, U2, U4 and U5, the so-called domain A or Sm binding site against nuclease digestion (Liautard et al., 1982). It is therefore likely that the core-protein may bind directly and specifically to the common snRNA domain A, or else to a sub-region of this. The second protein which was demonstrated to be cross-linked to snRNA was the U1 specific protein 70K. Since it has been shown that binding of protein 70K to U1 RNP requires the presence of the 5' stem and loop of U1 RNA (Hamm et al., 1987) it is likely that the 70K protein directly interacts with a sub-region of the first stem loop structure.

Loop I of U1 small nuclear RNA is the only essential RNA sequence for binding of specific U1 small nuclear ribonucleoprotein particle proteins

The binding of the U1 small nuclear ribonucleoprotein (snRNP)-specific proteins C, A, and 70K to U1 small nuclear RNA (snRNA) was analyzed. Assembly of U1 snRNAs from bean and soybean and a set of mutant Xenopus U1 snRNAs into U1 snRNPs in Xenopus egg extracts was studied. The ability to bind proteins was analyzed by immunoprecipitation with monospecific antibodies and by a protein-sequestering assay. The only sequence essential for binding of the U1-specific proteins was the conserved loop sequence in the 5' hairpin of U1. Further analysis suggested that protein C binds directly to the loop and that the assembly of proteins A and 70K into the RNP requires mainly protein-protein interactions. Protein C apparently recognizes a specific RNA sequence rather than a secondary structural element in the RNA.

Chemical cross-linking of Sm and RNP antigenic proteins

Nuclear extracts, competent for in vitro premessenger RNA splicing, were chemically cross-linked with thiol-reversible reagents in order to study the organization of proteins within ribonucleoprotein particles (RNPs) containing uridine-rich small nuclear RNAs (UsnRNPs). The distribution of select UsnRNP antigens within cross-linked complexes was determined by Western blotting of diagonal two-dimensional gels. On the basis of calculations from the molecular weights of cross-linked complexes containing UsnRNP common proteins B', B, and D, it is proposed that each of these proteins was associated with UsnRNP common proteins E and G. In addition, D' is proposed to be positioned close to D. The spatial distribution of UsnRNP common proteins was such that B' and B could not be cross-linked to D. The data also suggested that the 63-kDa U1 snRNP specific protein was cross-linked to other U1-specific proteins, particularly C, but not to the UsnRNP common proteins. We propose that part of the UsnRNP core of common proteins contains at least two asymmetrical copies of B':B:D:D':E:G with stoichiometries of 2:1:1:1:1:1 and 1:2:1:1:1:1.