Accurate and efficient in vitro splicing of purified precursor RNAs specified by early region 2 of the adenovirus 2 genome

Structural insights into human exon-defined spliceosome prior to activation

Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.

Mechanism of exon ligation by human spliceosome

Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C^∗ complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C^∗-I and pre-C^∗-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C^∗-I to pre-C^∗-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C^∗-I, pre-C^∗-II, and C^∗ complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C^∗ complexes, our studies recapitulate a molecular choreography of the C-to-C^∗ transition, revealing mechanistic insights into exon ligation.

Structures of the human pre-catalytic spliceosome and its precursor spliceosome

The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (Bact complex). The pre-B-to-B and B-to-Bact transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.

Development of an in vitro pre-mRNA splicing assay using plant nuclear extract

BACKGROUND

Pre-mRNA splicing is an essential post-transcriptional process in all eukaryotes. In vitro splicing systems using nuclear or cytoplasmic extracts from mammalian cells, yeast, and Drosophila have provided a wealth of mechanistic insights into assembly and composition of the spliceosome, splicing regulatory proteins and mechanisms of pre-mRNA splicing in non-plant systems. The lack of an in vitro splicing system prepared from plant cells has been a major limitation in splicing research in plants.

RESULTS

Here we report an in vitro splicing assay system using plant nuclear extract. Several lines of evidence indicate that nuclear extract derived from Arabidopsis seedlings can convert pre-mRNA substrate (LHCB3) into a spliced product. These include: (1) generation of an RNA product that corresponds to the size of expected mRNA, (2) a junction-mapping assay using S1 nuclease revealed that the two exons are spliced together, (3) the reaction conditions are similar to those found with non-plant extracts and (4) finally mutations in conserved donor and acceptor sites abolished the production of the spliced product.

CONCLUSIONS

This first report on the plant in vitro splicing assay opens new avenues to investigate plant spliceosome assembly and composition, and splicing regulatory mechanisms specific to plants.

Proteolysis of splicing factors during rat and monkey cell fractionation

We have investigated the ability of various rat and monkey cell lines to yield nuclear extracts that would allow splicing of a model adenovirus pre-mRNA substrate. Extracts from normal FR3T3, rat-1 and CV-1 fibroblasts were unable to assemble splicing complexes and displayed a dramatic reduction in the binding activity of the splicing factor 65 kD U2AF. These results correlated with reduced levels of 65 kD U2AF and the snRNP-associated B protein. When a battery of protease inhibitors was used during cell fractionation, increased levels of 65 kD U2AF and B proteins were detected. Most importantly, U2AF binding and complex formation were dramatically improved in FR3T3, rat-1 and CV-1 extracts. Interestingly, transformation of rat and monkey cells with the SV40 large T antigen yielded extracts active in complex formation. Similar extracts were generated following transformation of rat-1 cells with the Py middle T antigen but not with the v-fos oncogene. Only SV40-transformed FR3T3 extracts displayed splicing activity. Our results indicate that proteolysis is a major obstacle encountered during the preparation of active extracts from normal rat and monkey cells and suggest that cells transformed with T antigens manifest reduced proteolysis during fractionation.

The synthesis of influenza virus negative-strand RNA takes place in insoluble complexes present in the nuclear matrix fraction

The replication of influenza virus RNA in vitro has been studied by cell fractionation of MDCK-infected cells and characterization of in vitro synthesized RNA. Analysis of the RNA product polarity by liquid hybridization to excess single-stranded DNA probes shows that only the RNP complexes present in the nuclear matrix fraction are able to synthesize negative-polarity RNA. This RNA product has been characterized as authentic vRNA by size analysis, RNase-protection by unlabelled, positive-polarity riboprobes and T1-fingerprinting. Priming the in vitro reaction with ApG stimulates preferentially the synthesis of positive-polarity RNA, while ApGpU stimulates both positive and negative-polarity RNA synthesis.

Structure and expression of the Euglena gracilis nuclear gene coding for the translation elongation factor EF-1 alpha

A cDNA library from the protist Euglena gracilis was used to isolate and sequence an ORF coding for the elongation factor protein EF-1 alpha. The decoded amino acid sequence (MW, 48'515) is to 75-80% identical with other eukaryotic EF-1 alpha sequences but only to 24% identical with the Euglena chloroplast EF-Tu. Homologous DNA probes interact with multiple fragments of Euglena nuclear restricted DNA typical for a multimembered gene family. We present the restriction sites map of four tef nuclear gene loci and postulate that the nuclear genome also contains tef related sequences (e.g. pseudogenes). Expression of tef gene(s) is monitored by Northern hybridization and the 5' end of a stable transcript (1.5 kb) is sequenced and shown to precede the start codon by 29 positions only. The steady state concentration of the 1.5 kb mRNA is not influenced by switching cell growth conditions from dark to light (chloroplast development).

The dependence of splicing efficiency on the length of 3' exon

Oligonucleotide-limited transcription has been used to prepare a series of transcripts which allowed the positions of termination by T7 RNA polymerase to be characterized. The same technique was used to prepare a set of transcripts from a rabbit beta-globin gene that extend in intervals of two nucleotides from the 3' splice site of IVS-1 into the second exon. Splicing efficiency in a HeLa cell nuclear extract decreased with decreasing length of the 3' exon, although both steps of the splicing reaction could still be detected with as few as four nucleotides in this exon. No evidence was found for a lower limit to the length of the 3' exon below which splicing would not take place. With longer substrates, the rate of the second step of splicing was increased substantially.

The secondary structure of a messenger RNA precursor probed with psoralen is melted in an in vitro splicing reaction

The secondary structure of the SP6/mouse insulin precursor RNA was determined by psoralen cross-linking experiments. A series of long-range contacts occur within the left half of the pre-mRNA that contains the intervening sequence. Multiple secondary structures for the pre-mRNA exist since some of the interactions share common sites. In splicing buffer but without the splicing extract added, many of these interactions are stable up to at least 50 degrees C. These interactions, however, are dissociated during the in vitro splicing reaction. This dissociation requires ATP and it occurs during the first 30 min. of the splicing reaction. Pre-mRNAs containing psoralen cross-links in different locations within the RNA molecule were purified and used as substrates for in vitro splicing. Psoralen cross-links at any of the double-stranded regions resulted in complete inhibition of the splicing reaction. This indicates that destabilization of the secondary structure of the SP6/mouse insulin pre-mRNA is necessary for in vitro splicing.

Euglena gracilis chloroplast DNA: the untranslated leader of tufA-ORF206 gene contains an intron

Structural features of a dicistronic 1.95 kb mRNA coding for the chloroplast specific elongation factor Tu and ORF206 are described. The unspliced pre-mRNA is composed of 2562 nucleotides and undergoes four splicing events which remove a total of 606 nucleotides. The first intron splits the untranslated leader, two introns dissect the tufA coding region and the forth intron is within ORF206, which codes for a putative protein that is to 34% homologous with the putative protein of chloroplast ORF184 of tobacco. Introns neither belong to group I nor II, and 5' and 3' intron boundaries do not follow consensus sequences. Potential ribosome binding sites are located 58 and 32 positions upstream of the tufA and ORF206 start codon, respectively.

Analysis of RNase-A-resistant regions of adenovirus 2 major late precursor-mRNA in splicing extracts reveals an ordered interaction of nuclear components with the substrate RNA

An RNase A protection assay was employed to investigate the interaction of nuclear components with a precursor-mRNA derived from the adenovirus 2 major late transcription unit in a splicing extract from HeLa cells. Upon incubation in the extract, two regions in the precursor-RNA become resistant to digestion with RNase A. After short incubation times (5 min) at 30 degrees C, fragments mapping upstream from the branch point in the intron are obtained. After ten minutes or more, additional oligonucleotides, derived from the 5' splice site, are protected. RNase A protection of different RNA substrates demonstrates that a 5' splice site is not required for the binding of components to the branch point region. For interaction with this site, the polypyrimidine stretch just upstream from the 3' splice site is essential. Binding to the 5' splice site occurs only in the presence of an intact 3' end of the intron. Preincubation of the extract with excess unlabelled RNA containing only a 3' splice site leads to efficient competition of binding, both in the branch point region and at the 5' splice site, whereas an RNA that contains only 5'-splice-site sequences has no effect on the interaction with the mRNA precursor. This indicates that stable association with the 5' splice site requires prior binding of components in the branch point region. When splicing complexes are digested with RNase A, it becomes apparent that only the branch point region is sequestered into a ribonucleoprotein (RNP) structure in the 35 S complex. The 5' splice site becomes resistant to RNase A only when a 50 S splicing complex has been assembled. Degradation of specific regions in U1, U2 and U4 RNA with complementary oligodeoxynucleotides and RNase H has been used to analyse involvement of the U small nuclear RNPs (snRNPs) in the protection reaction. The 5' end of U2 RNA is essential for protection of the branch point region. RNA sequences in a loop of U2 RNA (nucleotides 65 to 78) are required for the formation of an RNase-A-resistant structure at the 5' splice site. Taken together, these results suggest that U2 snRNP participates in the formation of a pre-splicing complex, the 5' end of its RNA being involved in the observed binding. Conversion to a 50 S splicing complex is obtained after the binding of U1 and U4/U6 snRNPs, which also requires sequences in a loop of U2 RNA. Possible interactions between the individual snRNPs and between snRNPs and precursor-mRNA are discussed.

Preferential excision of the 5' proximal intron from mRNA precursors with two introns as mediated by the cap structure

We have studied the effect of the 5' cap structure on the splicing of precursor mRNAs containing three exons and two introns within a single molecule in a HeLa nuclear extract. When a precursor mRNA was capped, the upstream intron was spliced out more efficiently than the downstream intron. The differential splicing reactions of the two introns are not due to differences in the intrinsic efficiency of splicing of each intron, since the preferential excision of the upstream intron was also observed when the positions of the two introns relative to the cap structure were reversed. When uncapped precursor mRNA was used as substrate, the downstream intron was spliced out appreciably, but splicing of the upstream intron was greatly reduced. Preincubation of the extract with cap analogues inhibited splicing of the upstream intron but not the downstream intron. Thus, the cap structure exerts its effect primarily on the 5' proximal intron.

Multiple interactions between the splicing substrate and small nuclear ribonucleoproteins in spliceosomes

Protection experiments with antibodies against small nuclear ribonucleoproteins (snRNPs) have elucidated the location of and requirements for interactions between snRNPs and human beta-globin transcripts during splicing in vitro. U2 snRNP association with the intron branch site continues after branch formation, requires intact U2 RNA, and is affected by some alterations of the 3' splice site sequence. U2 snRNP binding to the branched intermediate and U1 snRNP protection of an extended 5' splice region are detected exclusively in spliceosome fractions, indicating that both snRNPs are spliceosome components. While each snRNP associates specifically with the pre-mRNA, they also appear to interact with each other. The recovery of fragments mapping upstream of the 5' splice site suggests how the excised exon is held in the spliceosome.

Multiple interactions between the splicing substrate and small nuclear ribonucleoproteins in spliceosomes

Protection experiments with antibodies against small nuclear ribonucleoproteins (snRNPs) have elucidated the location of and requirements for interactions between snRNPs and human beta-globin transcripts during splicing in vitro. U2 snRNP association with the intron branch site continues after branch formation, requires intact U2 RNA, and is affected by some alterations of the 3' splice site sequence. U2 snRNP binding to the branched intermediate and U1 snRNP protection of an extended 5' splice region are detected exclusively in spliceosome fractions, indicating that both snRNPs are spliceosome components. While each snRNP associates specifically with the pre-mRNA, they also appear to interact with each other. The recovery of fragments mapping upstream of the 5' splice site suggests how the excised exon is held in the spliceosome.

A protein associated with small nuclear ribonucleoprotein particles recognizes the 3' splice site of premessenger RNA

A HeLa cell nuclear extract active in splicing of pre-mRNA has been fractionated to identify the component that interacts with the 3' splice site. The activity that binds this region in an RNAase T1 protection assay copurifies with a 70 kd protein which is recognized by anti-Sm antibodies. Protein blots probed with labeled mRNA precursors either containing or lacking an intact 3' splice site reveal that the 70 kd polypeptide can bind pre-mRNA after immobilization on nitrocellulose and that it shows a preference for sequences located between the 3' splice junction and the site of lariat formation. Cofractionation during chromatography and immunoprecipitation by anti-2,2,7-trimethylguanosine antibodies demonstrate that the 3' splice site binding component associates with small nuclear ribonucleoprotein particles in low (1 mM) but not high (15 mM) Mg++ concentrations.

E. coli ribosomes with a C912 to U base change in the 16S rRNA are streptomycin resistant

Resistance to streptomycin (Sm) of Euglena gracilis chloroplasts can be due to a single C to T transition of the 16S rRNA gene in an invariant position which is equivalent to C912 of the Escherichia coli 16S rRNA. Since Euglena chloroplasts cannot be transformed we introduced, by site-directed mutagenesis, a C912 to T transition in the cloned rrnB operon (pKK3535) of E. coli and used this new construct (pEM109) in transformation experiments. Transformed E. coli cells were selected for Sm resistance by colony plating and stepwise increase of Sm up to 25 micrograms/ml of culture medium. Several Sm-resistant colonies were obtained. Ribosomes were isolated from pEM109-transformed Sm-resistant and pKK3535-transformed Sm-sensitive cells. The ribosomes were assayed in vitro for Sm-induced misreading of poly(U) mRNA. We isolated 16S rRNA and sequenced the crucial RNA region by reverse transcription. The results clearly show that ribosomes from Sm-resistant cells correctly read the poly(U) mRNA in the presence of 25 micrograms Sm/ml of reaction mixture and the 16S rRNA contains the C912 to U transition. We conclude that C912 is involved in a translation step(s) which is (are) sensitive to streptomycin.

Pre-mRNA splicing in vitro requires intact U4/U6 small nuclear ribonucleoprotein

Selective cleavage of U4 or U6 RNA in a HeLa cell nuclear extract inhibits splicing of pre-mRNAs containing an adenovirus or a simian virus 40 intron. RNAs in the U4/U6 small nuclear ribonucleoprotein (snRNP) were specifically degraded with RNAase H and deoxyoligonucleotides. Two oligomers complementary to U4 RNA and two complementary to U6 RNA cleave their target RNAs and inhibit the appearance of both spliced products and reaction intermediates. Splicing is reconstituted by mixing an extract containing cleaved U4 or U6 RNA with one in which splicing has been inhibited by degrading U2 RNA. All four abundant snRNPs, containing U1, U2, U5, or U4 and U6 RNAs, are now implicated in pre-mRNA splicing. Possible interactions of the U4/U6 snRNP with other components of the splicing complex are discussed.

Assembly in an in vitro splicing reaction of a mouse insulin messenger RNA precursor into a 60-40S ribonucleoprotein complex

An SP6/mouse insulin RNA precursor containing two exons and one intron can be spliced in a partially purified nuclear extract isolated from MOPC-315 mouse myeloma cells. We have detected the putative RNA splicing intermediate (intron-3'exon) in a lariat form, the excised intron in a lariat form, and the mRNA spliced product. The in vitro splicing reaction of gel-purified RNA precursors requires ATP and Mg2+ and was accompanied by the formation of a 60-40S ribonucleoprotein complex. The formation of the 60S complex requires ATP. At least two Sm snRNPs containing U1 and U2 RNAs are components of the 60-40S complex. The assemble of those snRNPs occurs early during the splicing reaction and it requires ATP and intron containing pre-mRNAs.

Fractionation and characterization of a yeast mRNA splicing extract

We have fractionated a yeast whole cell extract that can accurately splice synthetic actin and CYH2 pre-mRNAs. Three fractions, designated I, II, and III, have been separated by use of ammonium sulfate fractionation and chromatography on heparin agarose. Each fraction alone has no splicing activity. Fractions I and II allow the first step of the splicing reaction to proceed, giving rise to the splicing intermediates, free exon 1, and intron-exon 2. Addition of fraction III completes the reaction. Micrococcal nuclease treatment of the whole cell extract or of either fraction I or II abolished splicing activity, indicating that fractions I and II have RNA moieties that are required in the splicing reaction. The nature of the RNAs was examined using antibodies directed against the trimethylated cap structure unique to small nuclear RNAs. Preincubation of the whole cell extract with protein A-Sepharose coupled to trimethylated cap antibody abolished splicing activity. This indicates that at least one essential RNA component contains a trimethyl cap. Thus, in yeast as in mammalian systems, small nuclear RNAs are involved in mRNA splicing.

Splicing of the E2A premessenger RNA of adenovirus serotype 2. Multiple pathways in spite of excision of the entire large intron

During the early period of infection, the 4.9 kb (kb = 10(3) bases) E2A premRNA of adenovirus serotype 2 is matured mainly into a 2.0 kb mRNA by excision of introns of 2233 and 626 nucleotides. In order to define all the possible steps of splicing occurring in vivo, we characterized splicing intermediates present after a limiting treatment of cells with cycloheximide. Three complementary methods of analysis were used: RNA transfer analysis, S1 nuclease mapping and complementary DNA-RNase assay. Our principal conclusions concerning the poly(A)+ species are as follows. The RNA intermediate family detected is more complex than expected, since two major RNA intermediates of 4.6 kb and 4.3 kb, two minor intermediates of 2.9 kb and 2.6 kb, and a 2.3 kb RNA, which represents a minor alternative mRNA form, are revealed. Despite its large size and the presence of multiple internal donor and acceptor signals, intron 1 is exclusively excised as a whole. Intron 2 is either primarily excised as a whole, removing the standard 626-nucleotide sequence, or a smaller sequence of 337 nucleotides is removed, generating the 2.3 kb alternative mRNA. Kinetics of the ligation reaction demonstrate that the minimal time for excision of intron 2 is no more than two minutes, indicating a high level of co-ordination of the multiple individual reactions occurring during excision of an intron. Besides the major pathway for E2A premRNA splicing, namely the excision first of intron 2, followed by the excision of intron 1 after a lag time of five minutes, a minor pathway (used with a frequency of 10%) can be detected where the order of intron excision was inverted. With the alternative variant of excision of intron 2, at least three different pathways are therefore used to mature the E2A premRNA. RNA intermediates resulting from the cleavage at the 5' end of introns and branching can be detected by S1 mapping experiments, but their low accumulative level (1% relatively to the initial premRNA) precluded their direction by RNA transfer experiments and their complete characterization.

Inhibition of splicing but not cleavage at the 5' splice site by truncating human beta-globin pre-mRNA

Human beta-globin mRNAs truncated in the second exon or in the first intron have been processed in vitro in a HeLa cell nuclear extract. Transcripts containing a fragment of the second exon as short as 53 nucleotides are efficiently spliced, whereas transcripts truncated 24 or 14 nucleotides downstream from the 3' splice site are spliced inefficiently, if at all. All of these transcripts, however, are efficiently and accurately cleaved at the 5' splice site. In contrast, RNA truncated in the first intron, 54 nucleotides upstream from the 3' splice site, is not processed at all. These findings suggest that cleavage at the 5' splice site and subsequent splicing steps--i.e., cleavage at the 3' splice site and exon ligation--need not be coupled. Anti-Sm serum inhibits the complete splicing reaction and cleavage at the 5' splice site, suggesting involvement of certain ribonucleoprotein particles in the cleavage reaction. ATP and Mg2+ are required for cleavage at the 5' splice site at concentrations similar to those for the complete splicing reaction.

Specific and stable intron-factor interactions are established early during in vitro pre-mRNA splicing

Biochemical components (splicing factors) interact with specific intron regions during pre-mRNA splicing in vitro. The pre-mRNA specifically associates with factors at both the branch point and the 5' splice site and these RNA-factor interactions are maintained in the intron-containing RNA processing products. The first detectable event, the ATP-dependent association of a factor (or factors) with the branch point, is mediated by at least one factor containing an essential nucleic acid component. Mutant RNA substrates that lack either the 5' splice site or the vast majority of exon sequences can still associate with the branch point binding factor(s). However, this branch point-factor interaction does not occur with a mutant RNA substrate that contains the branch point but that lacks the 3' splice site consensus sequence. These results suggest that selection of the 3' splice site accompanied by the association of a factor with the branch point may be the initial step in mammalian pre-mRNA splicing.

Cap-dependent RNA splicing in a HeLa nuclear extract

We have studied the involvement of the 5' cap structure in the splicing of precursor mRNAs in a HeLa nuclear extract. We show that precursor mRNAs are spliced efficiently only when they possess a cap structure and that preincubation of a HeLa nuclear extract rendered the splicing reaction highly sensitive to inhibition by cap analogues. This sensitization was dependent on exogenous Mg2+ but not exogenous ATP or GTP. These results demonstrate that splicing in a nuclear extract is highly dependent on the cap structure, as was demonstrated for the splicing process in a HeLa whole-cell extract [Konarska, M. M., Padget, R. A. & Sharp, P. A. (1984) Cell 38, 731-736], and thus support the contention that cap recognition is an important feature of eukaryotic mRNA biogenesis.

Isolation and characterization of the RNA2, RNA3, and RNA11 genes of Saccharomyces cerevisiae

Temperature-sensitive mutations in the genes RNA2 through RNA11 cause accumulation of intervening sequence containing precursor mRNAs in Saccharomyces cerevisiae. Three different plasmids have been isolated which complement both the temperature-sensitive lethality and precursor mRNA accumulation when introduced into rna2, rna3, and rna11 mutant strains. The yeast sequences on these plasmids have been shown by Southern transfer hybridization and genetic mapping to be derived from the RNA2, RNA3, and RNA11 genomic loci. Part of the RNA2 gene is homologous to more than one region of the yeast genome, whereas the RNA3 and RNA11 genes are single copy. RNAs homologous to these loci have been identified by RNA transfer hybridization, and the specific RNAs which are associated with the Rna+ phenotype have been mapped. This was done by a combination of transcript mapping, subcloning, and in vitro mutagenesis. The transcripts are found to be enriched in polyadenylated RNA and are of very low abundance (0.01-0.001% polyadenylated RNA).

The small nuclear RNAs of Drosophila

We have investigated the sequences of the major small nuclear RNAs of Drosophila cultured cells, with the objective of elucidating phylogenetically conserved primary and secondary structures by comparison of the data with previously determined sequences of these RNAs in vertebrate species. Our results reveal striking degrees of conservation between each Drosophila RNA and its vertebrate cognate, and also demonstrate blocks of homology among the Drosophila small nuclear RNAs, as previously described for vertebrates. The most conserved features include the 5' terminal region of U1 RNA, though to function in pre-mRNA splicing, most of the regions of U4 RNA recently implicated in 3' processing of pre-mRNA, and the major snRNP protein binding site ("domain A") that is also shared by vertebrate U1, U2, U4 and U5 RNAs. Several other conserved features have been revealed, suggesting additional regions of functional significance in these RNAs and also providing further insights into the evolutionary history of the small nuclear RNAs.

Isolation and characterization of the RNA2, RNA3, and RNA11 genes of Saccharomyces cerevisiae

Temperature-sensitive mutations in the genes RNA2 through RNA11 cause accumulation of intervening sequence containing precursor mRNAs in Saccharomyces cerevisiae. Three different plasmids have been isolated which complement both the temperature-sensitive lethality and precursor mRNA accumulation when introduced into rna2, rna3, and rna11 mutant strains. The yeast sequences on these plasmids have been shown by Southern transfer hybridization and genetic mapping to be derived from the RNA2, RNA3, and RNA11 genomic loci. Part of the RNA2 gene is homologous to more than one region of the yeast genome, whereas the RNA3 and RNA11 genes are single copy. RNAs homologous to these loci have been identified by RNA transfer hybridization, and the specific RNAs which are associated with the Rna+ phenotype have been mapped. This was done by a combination of transcript mapping, subcloning, and in vitro mutagenesis. The transcripts are found to be enriched in polyadenylated RNA and are of very low abundance (0.01-0.001% polyadenylated RNA).

U1 RNA-protein complex preferentially binds to both 5' and 3' splice junction sequences in RNA or single-stranded DNA

We have investigated factors that recognize the splice junctions for mRNA by means of a rapid and sensitive filter binding assay using chemically synthesized single-stranded (ss) DNA (16-21 nucleotides) that includes a splice junction sequence or using RNA transcribed from the DNA. When small nuclear RNA-protein complexes from HeLa cells or rat liver were separated by a DEAE-Sepharose column, U1 RNA-protein complex fractions showed strong binding to ss DNA including a 5' or 3' consensus splice junction sequence. This binding took place in the presence of a large excess of Escherichia coli denatured DNA or RNA, but it was significantly reduced when conserved G-T or A-G within the splice junction was altered. In contrast, the U2 RNA-protein complex fractions did not show significant binding. We also have prepared RNA carrying the splice junction sequence by in vitro transcription of double-stranded splice junction DNA, which was linked to the E. coli lac promoter. By using this RNA, preferential binding to both 5' and 3' splice junction sequences has been confirmed with the partially purified U1 RNA-protein complex fraction described above. When the U1 RNA-protein complex is highly purified, it always retains a strong binding activity for a 5' splice junction. The binding activity for a 3' splice junction is partly or mostly lost during purification. These results strongly suggest that the U1 RNA-protein complex and/or an associated factor participates in the recognition of both 5' and 3' splice junctions.

High Specificity of the cDNA-RNase Assay to Detect Accurate SplicingIn Vitro

e previously developed a splicing assay (Keohavong et al., 1982) that we designated as a cDNA-RNase assay to analyze the ligation reaction between exons of premessenger RNA during in vivo or in vitro splicing. It was important to determine the specificity of this splicing assay, since the accuracy of in vitro splicing must always be demonstrated clearly. To do this, we constructed DNA probes derived from adenovirus E1A cDNA carrying deletions or insertions of 2-6 bases. After hybridizing them to the wild-type mRNA, the ability of single-strand-specific RNases to detect small mismatches of the RNA-DNA hybrids was examined. The demonstration that an imprecision in the splicing reaction of as little as 2 nucleotides can be detected with an efficiency of 99% indicates the high specificity of the splicing assay and its usefulness for the verification of accurate splicing in in vitro systems.

Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro

To study the mechanisms of RNA splicing we have analyzed the products generated by in vitro processing of a truncated 32P-labeled human beta-globin RNA precursor that contains the first two exons and the first intervening sequence (IVS1). Six major RNA products were detected and characterized. The first detectable RNA processing event is cleavage at the 5' GT of IVS1. Subsequently, accurately spliced RNA and the excised, intact IVS1 are simultaneously observed. The IVS1-containing RNA processing products have several unusual properties, which include: anomalous electrophoretic mobilities on polyacrylamide gels; a block to reverse transcription near the 3' end of IVS1; the presence of a nuclease-resistant component within IVS1. The block to reverse transcription and the nuclease-resistant component map to the same site near the 3' end of IVS1. The nuclease-resistant component appears to be a modified adenosine residue that contains an RNA branch. Based upon these and other structural studies we propose that the 5' end of IVS1 is joined by a 2'-5' phosphodiester linkage to the A residue in the RNAase T1 oligonucleotide ACTCTCTCTG located 28-37 nucleotides upstream from the IVS1 3' end. The IVS1 is therefore in the form of a lariat. These results imply that sequences within IVS1 actively participate in splicing.

In vitro-synthesized adenovirus 2 messenger RNA precursors are accurately spliced by nuclear extracts

Precursor mRNAs were synthesized in vitro from a plasmid in which the early region 2 gene of adenovirus 2 is fused to an efficient bacteriophage promoter (Salmonella phage 6). The RNAs were purified and used as substrates for in vitro splicing in the presence of nuclear extracts prepared from MOPC-315 mouse myeloma cells. The in vitro splicing was accurate at the nucleotide level. The reaction occurs rapidly and without any detectable lag. The concentration of the pre-mRNA precursor during incubation appears to be an important factor for high efficiency (60%-80%) of in vitro RNA splicing. Fractionation of the splicing components as well as modifications of the DNA template to study the nucleotide-sequence requirement for in vitro splicing can now be accomplished with this system.

Characterization of the newly-formed internucleotide bond of in vitro spliced mRNAs

Precursor RNAs were synthesized in vitro from a plasmid in which the early region 2 (E2) of adenovirus 2 is fused to an efficient bacteriophage promoter (Salmonella phage 6). The RNAs were purified and utilized as substrates for in vitro splicing in the presence of nuclear extracts prepared from MOPC-315 mouse myeloma cells. We have shown previously (Goldenberg, C.J., PNAS, August, in press, 1984) that in vitro splicing in those extracts was accurate at the nucleotide level. We now show that: i) the new internucleotide bond at the splice junction generated in vitro is a 3',5'-phosphodiester bond; and ii) the phosphate that forms the splice between the exons is derived from the pre-mRNA.

Efficient coupled transcription and mRNA splicing in vitro using plasmids derived from early region 3 of adenovirus 2 and a nondefective adenovirus-simian virus 40 hybrid

Accurate and highly efficient (80%) splicing of a single mRNA precursor to processed products was achieved using HeLa cell extracts to synthesize and process RNA in vitro from recombinant plasmids containing specific DNA segments from adenovirus 2 (Ad2) and the nondefective adenovirus-simian virus 40 (Ad+2ND1) hybrid. One plasmid, pRID, contains a segment of Ad2 DNA spanning chromosome map coordinates 75.9-83.4. The other plasmid, pRW9, contains the analogous viral region from Ad+2ND1. RNA synthesis from pRID in vitro occurs for more than 60 min and is directed by RNA polymerase II. RNA products consistent in size with the expected precursor and the two processed mRNAs are made. RNA blot hybridization analyses showed that these products are complementary to the Ad2 insert in the plasmid and that the appropriate intervening sequence was absent from the smallest processed mRNA. Comparison of the splice patterns of RNA made in vitro to those of RNAs taken from infected cells using the nuclease S1 technique demonstrated the accuracy of intron removal.

Normal and mutant human beta-globin pre-mRNAs are faithfully and efficiently spliced in vitro

Human beta-globin mRNA precursors (pre-mRNAs) synthesized in vitro from a bacteriophage SP6 promoter/beta-globin gene fusion are accurately and efficiently spliced when added to a HeLa cell nuclear extract. Under optimal conditions, the first intervening sequence (IVS 1) is removed by splicing in up to 90% of the input pre-mRNA. Splicing requires ATP and in its absence the pre-mRNA is neither spliced nor cleaved at splice junctions. Splicing does not require that the pre-mRNA contain a correct 5' or 3' end, a 3' poly A tail, or a 5'-terminal cap structure. However, capping of the pre-mRNA significantly affects the specificity of in vitro processing. In the absence of a cap approximately 30%-40% of the pre-mRNA is accurately spliced, and a number of aberrantly cleaved RNAs are also detected. In contrast, capped pre-mRNAs are spliced more efficiently and produce fewer aberrant RNA species. The specificity of splice-site selection in vitro was tested by analyzing pre-mRNAs that contain beta-thalassemia splicing mutations in IVS 1. Remarkably, these mutations cause the same abnormal splicing events in vitro and in vivo. The ability to synthesize mutant pre-mRNAs and study their splicing in a faithful in vitro system provides a powerful approach to determine the mechanisms of RNA splice-site selection.

The duck alpha A globin but not the yeast actin gene is transcribed by a HeLa cell extract

We have investigated the transcription in a HeLa whole-cell extract of two evolutionary widely separated structural genes coding for duck alpha A globin and yeast actin. Transcription of isolated DNA fragments of the duck alpha A globin gene increases linearly up to relatively high concentrations of DNA. Size analyses and S1 mapping of the transcripts synthesized in vitro on either linear DNA fragments or supercoiled templates reveal that the alpha A globin RNA is initiated at the in vivo cap site and remains unspliced. The same assay conditions were used to transcribe the yeast actin gene. In contrast to the duck gene, size analyses and S1 mapping of the RNA products synthesized on both linear DNA fragments and the supercoiled template containing the actin gene show that the transcripts found in vitro do not stem from the in vivo cap site. The promoter of the yeast actin gene is not recognized in this system in vitro.

Splicing of in vitro synthesized messenger RNA precursors in HeLa cell extracts

Using a whole cell extract of HeLa cells, we synthesized unspliced RNAs containing the first two leaders and the first intervening sequence of the adenovirus 2 major late transcription unit. Upon incubation of these pre-mRNAs in reaction mixtures containing a nuclear extract and a postnuclear fraction (S100), removal of the first intervening sequence and concomitant joining of the first leader to the second leader was observed. This splicing reaction requires proteins, Mg2+ ions, and ATP. The S100 fraction alone has no splicing activity but stimulates splicing when added to the nuclear extract. Upon fractionation of the postnuclear S100 by chromatography on ion exchange and gel filtration columns, the stimulatory activity copurifies with small ribonucleoprotein particles.

Microinjected simian virus 40 cRNA is spliced, as evidenced by electron microscopy

Simian virus 40 cRNA was transcribed in vitro from the early viral DNA strand. The RNA was injected through glass capillaries into the nuclei of monkey cells. After a 2-h incubation, the RNAs were extracted and hybridized to single-stranded simian virus 40 DNA sequences contained in a bacteriophage M13 vector. Electron microscopy revealed processed cRNAs with splice loops in the region of the intron of large T antigen.