The 3' splice site of pre-messenger RNA is recognized by a small nuclear ribonucleoprotein

Unusual branch point selection in processing of human growth hormone pre-mRNA

Intron A of the human growth hormone gene does not contain an A residue within 56 nucleotides preceding the 3' splice site. The analysis of the excised intron lariat revealed a C residue 28 nucleotides upstream from the 3' splice site as the major branch acceptor nucleotide. Two additional minor branched nucleotides were identified as U residues at positions -22 and -36. An adenosine substitution at position -22 results in lariat formation solely to this nucleotide. Therefore, C and U residues can function efficiently as natural branch acceptors, but an A residue is preferred if available in the proper region. In addition, the data strongly reinforce the importance of the distance constraint for lariat formation. To explain selection of the branch acceptor nucleotide, potential base-pairing interactions of branch point sequences with the U2 RNA are discussed.

H-2K molecules have two different C-termini, one of which is K-region specific

Amino acid sequences encoded by exon 8 of the H-2K and H-2D/L genes appear to be locus specific. The majority of H-2Kb molecules contain 10 amino acids that are derived from exon 8. In contrast, the H-2Db, -Dd and -Ld molecules contain only one amino acid which is encoded by exon 8, even though the genetic information exists to encode 10 amino acids analogous to those encoded by the majority of H-2Kb transcripts. We have produced a rabbit anti-peptide serum reactive with the exon 8 encoded sequence of H-2Kb (alpha K-C) that specifically immunoprecipitates a molecule of 45 K mol. wt from spleen cell lysates of b, d, p, q and k haplotype mice. Further analysis by Western blots indicated that virtually all mouse strains express a 45 K protein reactive with alpha K-C. In sequential immunoprecipitations of spleen cell lysates from b, q, p and d haplotype mice using alpha K-C followed by H-2K or H-2D private specificity alloantisera, the anti-peptide serum removed nearly all of the molecules reactive with the anti-H-2K alloantisera (except in the k haplotype) and none of the molecules reactive with the anti-H-2D serum. In addition, no D-region molecules possessing a long C-terminal sequence were detected with an antiserum directed against a representative D-region long C-terminal peptide. We conclude that even though the genetic information for an extended exon 8 exists in K, D and L locus genes, apparently only K-region molecules are expressed with such a C-terminus. Furthermore, in most haplotypes the great majority of H-2K molecules are produced using long exon 8; however, H-2Kk is produced mostly from short exon 8. The absence or presence of key adenosine residues is predicted to be responsible for the variability in class I exon 8 splicing.

Multiple functional motifs in the chicken U1 RNA gene enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

Nucleotide sequence determination and secondary structure of Xenopus U3 snRNA

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.

Functional analysis of the sea urchin U7 small nuclear RNA

U7 small nuclear RNA (snRNA) is an essential component of the RNA-processing machinery which generates the 3' end of mature histone mRNA in the sea urchin. The U7 small nuclear ribonucleoprotein particle (snRNP) is classified as a member of the Sm-type U snRNP family by virtue of its recognition by both anti-trimethylguanosine and anti-Sm antibodies. We analyzed the function-structure relationship of the U7 snRNP by mutagenesis experiments. These suggested that the U7 snRNP of the sea urchin is composed of three important domains. The first domain encompasses the 5'-terminal sequences, up to about nucleotides 7, which are accessible to micrococcal nuclease, while the remainder of the RNA is highly protected and hence presumably bound by proteins. This region contains the sequence complementarities between the U7 snRNA and the histone pre-mRNA which have previously been shown to be required for 3' processing (F. Schaufele, G. M. Gilmartin, W. Bannwarth, and M. L. Birnstiel, Nature [London] 323:777-781, 1986). Nucleotides 9 to 20 constitute a second domain which includes sequences for Sm protein binding. The complementarities between the U7 snRNA sequences in this region and the terminal palindrome of the histone mRNA appear to be fortuitous and play only a secondary, if any, role in 3' processing. The third domain is composed of the terminal palindrome of U7 snRNA, the secondary structure of which must be maintained for the U7 snRNP to function, but its sequence can be drastically altered without any observable effect on snRNP assembly or 3' processing.

Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicing

To study the determinants of splice site selection, we have inserted synthetic 5' and 3' splice sites at different positions within beta-globin genes and analyzed the resultant RNA substrates for in vitro splicing, factor binding, and complex assembly. We show that consensus 5' and 3' splice site sequences are insufficient to determine splice site utilization; in the presence or absence of the authentic site, the synthetic sites are variably active in a position-dependent manner. However, regardless of position or utilization, the synthetic 5' and 3' splice sites are bound by the appropriate splicing factors. Thus, binding of splicing factors is necessary but not sufficient for splice site utilization. Finally, we demonstrate that a block to efficient splicing can occur at multiple steps in the pathway of normal splicing complex assembly.

The length of the downstream exon and the substitution of specific sequences affect pre-mRNA splicing in vitro

We have shown previously that truncation of the human beta-globin pre-mRNA in the second exon, 14 nucleotides downstream from the 3' splice site, leads to inhibition of splicing but not cleavage at the 5' splice site. We now show that several nonglobin sequences substituted at this site can restore splicing and that the efficiency of splicing depends on the length of the second (downstream) exon and not a specific sequence. Deletions in the first exon have no effect on the efficiency of in vitro splicing. Surprisingly, an intron fragment from the 5' region of the human or rabbit beta-globin intron 2, when placed 14 nucleotides downstream from the 3' splice site, inhibited all the steps in splicing beginning with cleavage at the 5' splice site. This result suggests that the intron 2 fragment carries a "poison" sequence that can inhibit the splicing of an upstream intron.

Gel electrophoretic isolation of splicing complexes containing U1 small nuclear ribonucleoprotein particles

Assembly of splicing precursor RNAs into ribonucleoprotein particle (RNP) complexes during incubation in in vitro splicing extracts was monitored by a new system of RNP gel electrophoresis. The temporal pattern of assembly observed by our system was identical to that obtained by other gel and gradient methodologies. In contrast to the results obtained by other systems, however, we observed requirements of U1 small nuclear RNPs (snRNPs) and 5' splice junction sequences for formation of specific complexes and retention of U1 snRNPs within gel-fractionated complexes. Single-intron substrate RNAs rapidly assembled into slow-migrating complexes. The first specific complex (A) appeared within a minute of incubation and required ATP, 5' and 3' precursor RNA consensus sequences, and intact U1 and U2 RNAs for formation. A second complex (B) containing precursor RNA appeared after 15 min of incubation. Lariat-exon 2 and exon 1 intermediates first appeared in this complex, operationally defining it as the active spliceosome. U4 RNA was required for appearance of complex B. Released lariat first appeared in a complex of intermediate mobility (A') and subsequently in rapidly migrating diffuse complexes. Ligated product RNA was observed only in fast-migrating complexes. U1 snRNPs were detected as components of gel-isolated complexes. Radiolabeled RNA within the A and B complexes was immunoprecipitated by U1-specific antibodies under gel-loading conditions and from gel-isolated complexes. Therefore, the RNP antigen remained associated with assembled complexes during gel electrophoresis. In addition, 5' splice junction sequences within gel-isolated A and B complexes were inaccessible to RNase H cleavage in the presence of a complementary oligonucleotide. Therefore, nuclear factors that bind 5' splice junctions also remained associated with 5' splice junctions under our gel conditions.

A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly

Pre-mRNA splicing complex assembly is mediated by two specific pre-mRNA-snRNP interactions: U1 snRNP binds to the 5' splice site and U2 snRNP binds to the branch point. Here we show that unlike a purified U1 snRNP, which can bind to a 5' splice site, a partially purified U2 snRNP cannot interact with its target pre-mRNA sequence. We identify a previously uncharacterized activity, U2AF, that is required for the U2 snRNP-branch point interaction and splicing complex formation. Using RNA substrate exclusion and competition assays, we demonstrate that U2AF binds to the 3' splice site region prior to the U2 snRNP-branch point interaction. This provides an explanation for the necessity of the 3' splice site region in U2 snRNP binding and, hence, the first step of splicing.

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.

In vitro splicing of mRNA precursors: 5' cleavage site can be predicted from the interaction between the 5' splice region and the 5' terminus of U1 snRNA

Combinations of different mutations within the 5' splice region of the rabbit beta-globin large intron were analyzed for their effect on in vitro splicing. Based upon the complementarity of the 5' splice region to the 5' terminal region of the U1 snRNA, the exact location of the 5' cleavage site of different mutants could be predicted and was experimentally confirmed. These findings add further strong support to the hypothesis (1) that the exact location of the 5' cleavage site in pre-mRNA splicing of higher eukaryotes is determined by the overall 5' splice region via the complementarity to the 5' end of the U1 snRNA, and not by the strongly conserved GU dinucleotide.

Identification of the human U7 snRNP as one of several factors involved in the 3' end maturation of histone premessenger RNA's

In eukaryotic cells, the conversion of gene transcripts into messenger RNA's involves multiple factors, including the highly abundant small nuclear ribonucleoprotein (snRNP) complexes that mediate the splicing reaction. Separable factors are also required for the 3' end processing of histone pre-mRNA's. The two conserved signals flanking the 3' cleavage site are recognized by discrete components present in active HeLa cell extracts: the upstream stem loop associates with a nuclease-insensitive factor, while binding to the downstream element is mediated by a component having the properties of a snRNP. The sequence of the RNA moiety of the low abundance human U7 snRNP suggests how the relatively degenerate downstream element of mammalian pre-mRNA's could be recognized by RNA base-pairing.

Identification of a complex associated with processing and polyadenylation in vitro of herpes simplex virus type 1 thymidine kinase precursor RNA

Cleavage and polyadenylation of substrate RNAs containing the herpes simplex virus type 1 (HSV-1) thymidine kinase (tk) gene polyadenylation signal region were examined in HeLa cell nuclear extract. 3'-End RNA processing was accurate and efficient and required ATP and Mg2+. Cleavage, but not polyadenylation, occurred in the presence of EDTA or when ATP was replaced with 3' dATP (cordycepin) or AMP(CH2)PP, a nonhydrolyzable analog of ATP. Processing in vitro and in vivo showed the same signal element requirements: a series of substrates containing linker scanning, internal deletion, and small insertion mutations was processed with the same relative efficiencies and at the same sites in vitro and in vivo. A complex involved in 3'-end RNA processing was identified by gel mobility shift analysis. This complex formed rapidly, reached a maximum level after 20 to 30 min, and was much reduced after 2 h. Very little complex was formed at 0 degree C or with substrates lacking a polyadenylation signal. Entry of 32P-labeled tk substrate into the complex could be prevented by addition of excess 35S-labeled tk or adenovirus L3 precursor RNAs. Competition was not observed with tk RNAs lacking a complete polyadenylation signal.

Accurate and efficient 3' processing of U2 small nuclear RNA precursor in a fractionated cytoplasmic extract

The small nuclear RNAs U1, U2, U4, and U5 are cofactors in mRNA splicing and, like the pre-mRNAs with which they interact, are transcribed by RNA polymerase II. Also like mRNAs, mature U1 and U2 RNAs are generated by 3' processing of their primary transcripts. In this study we have investigated the in vitro processing of an SP6-transcribed human U2 RNA precursor, the 3' end of which matches that of authentic human U2 RNA precursor molecules. Although the SP6-U2 RNA precursor was efficiently processed in an ammonium sulfate-fractionated HeLa cytoplasmic S100 extract, the product RNA was unstable. Further purification of the processing activity on glycerol gradients resolved a 7S activity that nonspecifically cleaved all RNAs tested and a 15S activity that efficiently processed the 3' end of pre-U2 RNA. The 15S activity did not process the 3' end of a tRNA precursor molecule. As demonstrated by RNase protection, the processed 3' end of the SP6-U2 RNA maps to the same nucleotides as does mature HeLa U2 RNA.

Self-splicing of group II introns in vitro: lariat formation and 3' splice site selection in mutant RNAs

Deletion or substitution of the branch A residue in group II intron bl1 significantly reduces splicing activity; yet, residual exon ligation is correct, and lariats have their branch points at the normal distance from the 3' end of the intron. Mutations in the sequence facing the branch point also allow residual lariat formation; however, free 3' exons are generated with false 5' termini, all of which are within a UCACA consensus sequence located upstream or downstream of the normal 3' splice site. These results indicate that both the conserved 3' splice site APy and the spatial arrangements in stem 6 are crucial for correct 3' splice site selection.

U1 small nuclear ribonucleoproteins are required early during spliceosome assembly

U1 small nuclear ribonucleoproteins (snRNPs) are required for in vitro splicing of pre-mRNA. Sequences within U1 RNA hybridize to, and thus recognize, 5' splice junctions. We have investigated the mechanism of association of U1 snRNPs with the spliceosome. U1-specific antibodies detected U1 association with precursor RNA early during assembly. Removal of the 5' terminal sequences of U1 RNA by oligo-directed cleavage or removal of U1 snRNPs by immunoprecipitation prior to the addition of precursor RNA depressed the association of all snRNPs with precursor RNA as detected by immunoprecipitation of splicing complexes by either Sm or U1-specific antibodies. Assembly of the spliceosome as monitored by gel electrophoresis was also depressed after cleavage of U1 RNA. The dependency of Sm precipitability of precursor RNA upon the presence of U1 snRNPs suggests that U1 snRNPs participate in the early recognition of substrate RNAs by U2 to U6 snRNPs. Although removal of the 5'-terminal sequences of U1 depressed U1 snRNP association with precursor RNA, it did not eliminate it, suggesting semistable association of U1 snRNPs with the assembling spliceosome in the absence of U1 RNA hybridization. This association was not dependent upon 5' splice junction sequences but was dependent upon 3' intronic sequences, indicating that U1 snRNPs interact with factors recognizing 3' intronic sequences. Mutual dependence of 5' and 3' recognition factors suggests significant snRNP-snRNP communication during early assembly.

Heat-labile regulatory factor is required for 3' processing of histone precursor mRNAs

In addition to Sm antigen-type small nuclear ribonucleoprotein particle(s) [snRNP(s)], at least one more factor is involved in the in vitro 3' processing of histone precursor mRNAs (pre-mRNAs) in a HeLa cell nuclear extract. This factor can be completely inactivated by mild heat treatment but is resistant to digestion by micrococcal nuclease and is not immunoprecipitated by antisera of the Sm serotype. Both snRNP (the presumed human homologue of the U7 snRNP of the sea urchin) and the heat-labile factor described above show closely similar properties when fractionated on DEAE, heparin, and Mono Q columns. Fractions, after extensive purification, still contain both heat-labile factor and snRNP activity. When analyzed by gel filtration, the heat-labile component distributes bimodally, the smaller component possessing an apparent molecular weight on the order of 40,000, and the larger, of ca. 300,000.

Multiple functional motifs in the chicken U1 RNA gene enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

Identification of a novel sequence that governs both polyadenylation and alternative splicing in region E3 of adenovirus

Region E3 encodes four major overlapping mRNAs with different splicing patterns. There are two poly(A) sites, an upstream site called E3A and a downstream site called E3B. We have analyzed virus mutants with deletions or insertions in E3 in order to identify sequences that function in the alternative processing of E3 pre-mRNAs, and to understand what determines which poly(A) sites and which splice sites are used. In previous studies we established that the 5' boundary of the E3A poly(A) signal is at an ATTAAA sequence. We now show, using viable virus mutants, that the 3' boundary of the E3A signal is located within 47-62 nucleotides (nt) downstream of the ATTAAA (17-32 nt downstream of the last microheterogenous poly(A) addition site). Our data further suggest that the spacing between the ATTAAA, the cleavage sites, and the essential downstream sequences may be important in E3A 3' end formation. Of particular interest, these mutants suggest a novel mechanism for the control of alternative pre-mRNA processing. Mutants which are almost completely defective in E3A 3' end formation display greatly increased use of a 3' splice site located 4 nt upstream of the ATTAAA. The mRNA that uses this 3' splice site is polyadenylated at the E3B poly(A) site. We suggest, for this particular case, that alternative pre-mRNA processing could be determined by a competition between trans-acting factors that function in E3A 3' end formation or in splicing. These factors could compete for overlapping sequences in pre-mRNA.

Transcriptional signals of a U4 small nuclear RNA gene

The signals controlling the expression of a chicken U4 small nuclear RNA (snRNA) gene have been studied by microinjection into Xenopus oocytes. At least two distinct regions in the 5'-flanking DNA contribute to U4B RNA gene expression. The proximal regulatory element, which is inactivated by a 5'-flanking DNA deletion to position -38, provides a basal level of U4B RNA synthesis. The distal regulatory region, centered near position -200, acts as a transcriptional enhancer. It provides a 4-5 fold stimulation of U4B RNA gene expression above the basal level, and, like mRNA enhancers, is composed of multiple functional motifs. One of these, the octamer sequence ATGCAAAG, has previously been recognized as an important element of U1 and U2 snRNA gene enhancers, as well as being involved in the expression of a number of mRNA genes. However, the octamer sequence is not sufficient for U4B enhancer activity. An additional element, an "Sph motif," is located 12 base pairs downstream of the octamer and is an essential component of the U4B enhancer. Transcriptional competition studies indicate that the U4B and U1 snRNA genes utilize a common set of transcription factors.

Spliceosome assembly in yeast

Precursors to mRNA become substrates for splicing by being assembled into a complex multisubunit structure, the spliceosome. To study the assembly of the yeast spliceosome, intermediate complexes were separated by electrophoresis on nondenaturing polyacrylamide gels. Four splicing-dependent complexes, A1, A2-1, A2-2, and B, were observed. The order of assembly of these complexes was determined to be B----A2-1----A1----A2-2. The assembly process can be blocked at complex A1 by addition of 5 mM EDTA or by carrying out the assembly process in heat-inactivated rna2 extracts. The snRNA composition of the complexes was determined by hybridization with probes for five yeast snRNAs. snR14 (U4) was only found in complex A2-1, snR6 (U6) and snR7 (U5) were in complexes A1, A2-1, and A2-2, whereas snR20 (U2) was in all four of the complexes. snR19 (U1) was not present in any of the complexes. Hybridization with these probes was also employed to detect snRNPs present in yeast splicing extracts. We found that snR6, snR7, and snR14 were present together in a large complex. This complex underwent an ATP-dependent dissociation to give snR7 and snR6-snR14 complexes. snR19 and snR20 are present in distinct RNPs but the mobility of these is not affected by ATP. A mechanism for spliceosome assembly is proposed.

In vitro processing of the human growth hormone primary transcript

To study the sequence of events during processing of primary RNA transcripts and to gain more insight into the mechanism of splice site selection, the in vitro processing of a 2.5 kb human growth hormone (hGH) pre-mRNA containing four introns and an alternative 3' splice site for intron B was analysed. In order to process the hGH pre-mRNA the preparation of the HeLa cell nuclear extract had to be modified, indicating differences in factor requirement for processing this pre-mRNA. After an unusual long lag phase of one hour splicing intermediates begin to accumulate. Intron A and D are removed with correct ligation of exons 1/2 and 4/5. Most splice sites are used--albeit with variable efficiencies--except the splice sites surrounding exon 3 and the 3' alternative splice site within exon 3; as a consequence "exon skipping" events take place. Using a pre-mRNA containing only intron B neither the 5' nor the 3' splice site is cleaved, indicating that the 3' splice site of intron B is not recognized. The results show that splice sites can differ considerably in their requirement for splicing factors.

Accurate and efficient 3' processing of U2 small nuclear RNA precursor in a fractionated cytoplasmic extract

The small nuclear RNAs U1, U2, U4, and U5 are cofactors in mRNA splicing and, like the pre-mRNAs with which they interact, are transcribed by RNA polymerase II. Also like mRNAs, mature U1 and U2 RNAs are generated by 3' processing of their primary transcripts. In this study we have investigated the in vitro processing of an SP6-transcribed human U2 RNA precursor, the 3' end of which matches that of authentic human U2 RNA precursor molecules. Although the SP6-U2 RNA precursor was efficiently processed in an ammonium sulfate-fractionated HeLa cytoplasmic S100 extract, the product RNA was unstable. Further purification of the processing activity on glycerol gradients resolved a 7S activity that nonspecifically cleaved all RNAs tested and a 15S activity that efficiently processed the 3' end of pre-U2 RNA. The 15S activity did not process the 3' end of a tRNA precursor molecule. As demonstrated by RNase protection, the processed 3' end of the SP6-U2 RNA maps to the same nucleotides as does mature HeLa U2 RNA.

Identification of a complex associated with processing and polyadenylation in vitro of herpes simplex virus type 1 thymidine kinase precursor RNA

Cleavage and polyadenylation of substrate RNAs containing the herpes simplex virus type 1 (HSV-1) thymidine kinase (tk) gene polyadenylation signal region were examined in HeLa cell nuclear extract. 3'-End RNA processing was accurate and efficient and required ATP and Mg2+. Cleavage, but not polyadenylation, occurred in the presence of EDTA or when ATP was replaced with 3' dATP (cordycepin) or AMP(CH2)PP, a nonhydrolyzable analog of ATP. Processing in vitro and in vivo showed the same signal element requirements: a series of substrates containing linker scanning, internal deletion, and small insertion mutations was processed with the same relative efficiencies and at the same sites in vitro and in vivo. A complex involved in 3'-end RNA processing was identified by gel mobility shift analysis. This complex formed rapidly, reached a maximum level after 20 to 30 min, and was much reduced after 2 h. Very little complex was formed at 0 degree C or with substrates lacking a polyadenylation signal. Entry of 32P-labeled tk substrate into the complex could be prevented by addition of excess 35S-labeled tk or adenovirus L3 precursor RNAs. Competition was not observed with tk RNAs lacking a complete polyadenylation signal.

An essential snRNA from S. cerevisiae has properties predicted for U4, including interaction with a U6-like snRNA

Three yeast snRNAs (snR20, snR7, and snR14) have been implicated in pre-mRNA splicing. snR20 and snR7 contain domains of homology to U2 and U5, respectively, and each is required for viability. These RNAs are found associated with the spliceosome, as is snR14. We show here that snR14 is also an essential gene product. Sequence analysis reveals that, like snR7 and snR20, snR14 contains a consensus binding site for the Sm antigen, a feature common to all mammalian snRNAs involved in splicing. Moreover, snR14 exhibits several blocks of sequence and structural homology to U4, which in metazoans is found in association with U6. Native gel electrophoresis demonstrates that snR14 is in fact base-paired with another yeast snRNA, designated snR6, which has primary sequence homology to U6. We conclude that snR14 is the yeast analog of U4.

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.

U1 small nuclear ribonucleoproteins are required early during spliceosome assembly

U1 small nuclear ribonucleoproteins (snRNPs) are required for in vitro splicing of pre-mRNA. Sequences within U1 RNA hybridize to, and thus recognize, 5' splice junctions. We have investigated the mechanism of association of U1 snRNPs with the spliceosome. U1-specific antibodies detected U1 association with precursor RNA early during assembly. Removal of the 5' terminal sequences of U1 RNA by oligo-directed cleavage or removal of U1 snRNPs by immunoprecipitation prior to the addition of precursor RNA depressed the association of all snRNPs with precursor RNA as detected by immunoprecipitation of splicing complexes by either Sm or U1-specific antibodies. Assembly of the spliceosome as monitored by gel electrophoresis was also depressed after cleavage of U1 RNA. The dependency of Sm precipitability of precursor RNA upon the presence of U1 snRNPs suggests that U1 snRNPs participate in the early recognition of substrate RNAs by U2 to U6 snRNPs. Although removal of the 5'-terminal sequences of U1 depressed U1 snRNP association with precursor RNA, it did not eliminate it, suggesting semistable association of U1 snRNPs with the assembling spliceosome in the absence of U1 RNA hybridization. This association was not dependent upon 5' splice junction sequences but was dependent upon 3' intronic sequences, indicating that U1 snRNPs interact with factors recognizing 3' intronic sequences. Mutual dependence of 5' and 3' recognition factors suggests significant snRNP-snRNP communication during early assembly.

Both conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro

Pre-mRNA substrates containing sequences from human and mouse histone genes are accurately processed in a HeLa cell nuclear extract to generate mature 3' termini. When in vitro processing reactions containing either human histone H3 or mouse histone H3 transcripts are treated with RNase T1 and probed with antibodies specific for the Sm protein determinants or for the trimethylguanosine cap structure unique to the U RNAs present in small nuclear ribonucleoproteins, RNA fragments that encompass the site of 3' end formation on the pre-mRNA transcript are selectively recovered. Several different interactions are detected: at time zero, the protected region contains the upstream conserved hairpin loop structure; at later times during the reaction, protection extends beyond the site of 3' end formation to include the downstream conserved sequence element and the 5' cap of the transcript is bound as well. Possible interactions between Sm small nuclear ribonucleoproteins and these conserved sequence elements in histone pre-mRNAs are discussed.

Splicing of SV40 early pre-mRNA to large T and small t mRNAs utilizes different patterns of lariat branch sites

To explore the mechanism and control of alternative splicing, we have characterized the products formed by splicing of SV40 early pre-mRNA in vitro and in vivo. Large T and small t mRNAs are derived from this precursor by joining alternative 5' splice sites to a single shared 3' splice site. In contrast to pre-mRNAs studied previously, we have shown that splicing to large T RNA involves the utilization of multiple lariat branch sites, while small t splicing uses a single branch site. Interestingly, the predominant branch sites utilized in splicing of large T RNA in vitro were found to differ in nuclear extracts from HeLa and human 293 cells, correlated with previously observed differences in the ratio of large T to small t mRNAs produced in the two cell types. To test the significance of this correlation, we examined the products formed by splicing of an SV40 early precursor microinjected into X. laevis oocytes. Strikingly, both the pattern of branch sites used in large T splicing and the ratio of large T to small t mRNAs produced were found to be identical to those observed in 293 cells and extracts.

A trans-acting suppressor restores splicing of a yeast intron with a branch point mutation

Splicing of introns from Saccharomyces cerevisiae pre-mRNA requires the conserved sequence TACTAAC; the 3'-most A residue is utilized as the site of branch formation. We showed previously that the transcript from an actin-HIS4 gene fusion containing the mutation TACTAAC to TACTACC (designated C259) is spliced inefficiently, thereby preventing growth on the histidine precursor histidinol. By selecting for growth on histidinol, we have identified a mutant in which the splicing of the C259 transcript is increased fourfold; splicing of other mutated introns is not significantly improved. The mutant locus encodes a trans-acting suppressor. A single mutation, rna16-1, is sufficient for suppression; however, suppression is maximized in heterozygous diploids containing both rna16-1 and the wild-type allele RNA16. In addition, wild-type pre-mRNAs (and lariat intermediates) accumulate in rna16-1 cells. We propose that the RNA16 locus encodes a component of the splicing machinery.

Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes

Electrophoretic separation of ribonucleoprotein particles in a nondenaturing gel was used to analyze the splicing of mRNA precursors. Early in the reaction, a complex formed consisting of the U2 small nuclear ribonucleoprotein particle (snRNP) bound to sequences upstream of the 3' splice site. This complex is modeled as a precursor of a larger complex, the spliceosome, which contains U2, U4/6, and U5 snRNPs. Conversion of the U2 snRNP-precursor RNA complex to the spliceosome probably involves binding of a single multi-snRNP particle containing U4/6 and U5 snRNPs. The excised intron was released in a complex containing U5, U6, and probably U2 snRNPs. Surprisingly, U4 snRNP was not part of the intron-containing complex, suggesting that U4/6 snRNP disassembles and assembles during splicing. Subsequently, the reassembled U4/6 snRNP would associate with U5 snRNP and participate in de novo spliceosome formation. U1 snRNP was not detected in any of the splicing complexes.

An essential yeast snRNA with a U5-like domain is required for splicing in vivo

Yeast contains at least 24 snRNAs, many of which are dispensable for viability. We recently demonstrated that a small subset of these RNAs has a functional binding site for the Sm antigen, a hallmark of metazoan snRNAs involved in mRNA processing. Here we show that one of these snRNAs, snR7, is required for growth. To determine the biochemical basis of lethality in cells lacking snR7, we engineered the conditional synthesis of snR7 by fusing the snRNA coding sequences to the yeast GAL1 control region. Cells depleted for the SNR7 gene product by growth on glucose for five generations show marked accumulation of unspliced mRNA precursors from the four intron-containing genes tested. In some cases, intron-exon 2 lariats also accumulate. We have identified a 70 nucleotide domain within snR7 with limited sequence-specific but striking structural homology to the mammalian snRNA U5. We conclude that mRNA splicing in yeast requires the function of a U5-like snRNA.

Splice acceptor site for the env message of Moloney murine leukemia virus

We report the isolation and sequence of a cDNA clone containing part of the env message of the Moloney murine leukemia virus (MoMuLV). This clone was derived from a rat thymic lymphoma induced by MoMuLV. The AG acceptor site employed in this message is located at position 5490 in the MoMuLV genome. This splice site is detectable at the cDNA level by the creation of a novel SacI restriction site not present in the viral genome. In the -1 to -40 region, this AG acceptor site is preceded by four conserved heptanucleotides (PyXPyTPuAPy) that may function as acceptors for removal of the 5' end of the intron.

Molecular relationships between U snRNP proteins as investigated by rabbit antisera and peptide mapping

Each of the major U snRNP polypeptides from human cells was purified by electroelution from SDS-polyacrylamide gels. Rabbit antisera could be obtained against the individual proteins 70K, A, B', B and D, although rabbits failed to elicit antibodies against E, F and G. A strong structural homology was found between proteins B' and B, against which patients with connective tissue diseases produce predominantly anti-Sm autoantibodies. Thus, rabbit antisera against B' strongly crossreact with B and vice versa. Peptide patterns of the proteins B' and B obtained with chymotrypsin are identical with the exception of one fragment in each case. Polypeptide D, the third major Sm-antigenic protein, is structurally distinct from B' and B, as evidenced by the failure of anti-D antisera to crossreact with B' or B and vice versa, as well as by the different peptide patterns observed for proteins D and B' or B. The U1 specific polypeptide A and the U2 specific polypeptide B" share homologous regions, as indicated by the crossreactivity of anti-A antisera with protein B", and the occurrence of common fragments in the peptide patterns of the two proteins. Further homologies between other snRNP protein pairs were not detected.

Signals for the selection of a splice site in pre-mRNA. Computer analysis of splice junction sequences and like sequences

To evaluate the importance of the surrounding nucleotide sequence in the selection of a splice site for mRNA, we have carried out computer studies of eukaryotic protein genes whose entire nucleotide sequences were available. A splice site-like sequence that has a significant homology to the consensus splice junction sequences is frequently found within an intron and exon. It is found that the higher the homology of a candidate donor site sequence to the nine-nucleotide consensus sequence, the higher is its probability of being a donor site. For most of the donors, the stability of presumed base-pairing with U1-RNA is higher than that of donor-like sequences, if any, in the adjacent exon and intron. However, homology of a candidate acceptor sequence to the 15-nucleotide consensus is a poor criterion of an acceptor site. The presence of a sequence that could serve as a branch-point 18 to 37 nucleotides before an acceptor does not seem to be critical in distinguishing it from an acceptor-like sequence. For genes of human, rat, mouse and chicken, respectively, nucleotide frequencies around splice junctions of many genes have been calculated. They seem to be different at some positions around a donor site from species to species. The acceptors for these vertebrates have longer pyrimidine-rich regions than the previous consensus sequence. The newly derived nucleotide frequencies were used as the standard to calculate the weighted homology score of a candidate splice site sequence in a gene of the four species. This weighted homology score of the 40 to 60-nucleotide intron-exon sequence is a much better criterion of an acceptor. These results suggest that the most important signal in the selection of a splice resides in the surrounding nucleotide sequence. It is also suggested that the surrounding nucleotide sequence alone is not generally sufficient for the selection.

Both conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro

Pre-mRNA substrates containing sequences from human and mouse histone genes are accurately processed in a HeLa cell nuclear extract to generate mature 3' termini. When in vitro processing reactions containing either human histone H3 or mouse histone H3 transcripts are treated with RNase T1 and probed with antibodies specific for the Sm protein determinants or for the trimethylguanosine cap structure unique to the U RNAs present in small nuclear ribonucleoproteins, RNA fragments that encompass the site of 3' end formation on the pre-mRNA transcript are selectively recovered. Several different interactions are detected: at time zero, the protected region contains the upstream conserved hairpin loop structure; at later times during the reaction, protection extends beyond the site of 3' end formation to include the downstream conserved sequence element and the 5' cap of the transcript is bound as well. Possible interactions between Sm small nuclear ribonucleoproteins and these conserved sequence elements in histone pre-mRNAs are discussed.

Cytoplasmic maturation of the snRNAs

The snRNAs are abundant and stable components of the interphase nucleus. Aqueous and non-aqueous cell fractionation demonstrate that the snRNAs appear transiently in the cytoplasm shortly after transcription, before returning permanently to the interphase nucleus. In pulse label and chase experiments, the newly synthesized snRNA species appear in the cytoplasm after 1 min of labeling and then return to the interphase nucleus after approximately 15 min in the cytoplasm. In order to study the maturation and intracellular transport of these particles, a battery of metabolic inhibitors and alterations in cell culture conditions were investigated for their ability to interfere with the return of the newly synthesized snRNAs to the nucleus. A wide range of inhibitors of the cytoskeleton did not interfere with this process. Only the inhibition of protein synthesis and exposure of cells to medium of at least twice the normal tonicity block the return of the snRNAs to the nucleus. Immunofluorescent staining of cells exposed to hypertonic medium identifies discrete foci in the cytoplasm that stain with the Sm antiserum, directed against proteins associated with the snRNAs. Using a detergent extraction procedure that preserves the cytoskeleton, the newly synthesized snRNAs in the cytoplasm fractionate as soluble complexes. These data are consistent with the hypothesis that the snRNAs partition into the interphase nucleus because of a preferential solubility and the existence of specific binding sites.

The indirect flight muscle of Drosophila accumulates a unique myosin alkali light chain isoform

Mapping of the 5' and 3' ends of the Drosophila myosin alkali light chain (MLC-ALK) mRNA by S1 nuclease and primer extension assays has shown that the primary transcripts are identical irrespective of the time in development that the RNA was prepared. As shown by S1 nuclease experiments these transcripts are alternatively spliced in a tissue-specific fashion generating mRNAs that encode tissue-specific protein isoforms. Antibodies were raised to synthetic peptides identical in sequence to the unique portion of each protein. Western blots of one-dimensional polyacrylamide gels using the type-specific antibodies confirmed and extended the results obtained from the S1 nuclease experiments. The indirect flight muscle is the only tissue in the adult that accumulates the alternatively spliced mRNA. The choice between splicing pathways involves the use of a nonconsensus 3' splice junction in larvae and in the tubular muscles of adults, whereas in the indirect flight muscle of the adult only consensus sequences are utilized. The involvement of a trans-acting factor to activate the nonconsensus splice site in the myotubes of larvae and the tubular myotubes of adults is proposed.

A novel role for the 3' region of introns in pre-mRNA splicing of Saccharomyces cerevisiae

To investigate the importance of sequences between the yeast (Saccharomyces cerevisiae) branch point (TACTAAC box) and 3' splice site (AG), we generated a series of pre-mRNA substrates that differed in the length of RNA retained on the 3' side of the TACTAAC box. These pre-mRNAs were compared as substrates for the first step of in vitro splicing (5' cleavage and lariat formation) and in vitro spliceosome assembly (complex formation) in a whole-cell yeast extract. The results indicate that for rp51A pre-mRNA at least 29 nucleotides of RNA on the 3' side of the TACTAAC box are required for 5' cleavage and lariat formation, as smaller substrates fail to manifest any detectable cleavage or ligation events. Analysis of splicing complex assembly indicates that these smaller substrates undergo efficient yet incomplete complex formation; they are blocked at a late stage of spliceosome assembly, the complex I to complex II transition (Pikielny et al. 1986), a result which suggests that the failure to form lariats is due to a specific assembly defect. The lariat formation block (and assembly defect) can be relieved by the addition of ribohomopolymer "tails" to the 3' end of the shortened rp51A pre-mRNAs, and similar results were obtained with shortened actin pre-mRNAs. The results of this study indicate that this region of the pre-mRNA serves a specific function late in in vitro spliceosome assembly.

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.

Pre-mRNA splicing and the nuclear matrix

We examined the relationship between pre-mRNA splicing and the nuclear matrix by using an in vivo system that we have developed. Plasmids containing the inducible herpesvirus tk gene promoter linked to an intron-containing segment of the rabbit beta-globin gene were transfected into HeLa cells, and then the promoter was transactivated by infection with a TK- virus. Northern analysis revealed that the globin pre-mRNA and all its splicing intermediates and products are associated with the nuclear matrix prepared from such transfected cells. When the nuclear matrix was incubated with a HeLa cell in vitro splicing extract in the presence of ATP, the amount of matrix-associated precursor progressively decreased without a temporal lag in the reaction, with a corresponding increase in free intron lariat. Thus, most of the events of the splicing process (endonucleolytic cuts and branching) occur in this in vitro complementation reaction. However, ligation of exons cannot be monitored in this system because of the abundance of preexisting mature mRNA. Since the matrix is not a self-splicing entity, whereas the in vitro splicing system cannot process efficiently deproteinized matrix RNA, we conclude from our in vitro complementation results (which can be reproduced by using micrococcal nuclease-treated splicing extract) that the nuclear matrix preparation retains parts of preassembled ribonucleoprotein complexes that have the potential to function when supplemented with soluble factors (presumably other than most of the small nuclear ribonucleoproteins known to participate in splicing) present in the HeLa cell extract.

Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA

The U2 snRNP binds to the site of branch formation during splicing of mammalian pre-mRNA in vitro. In Saccharomyces cerevisiae the branch site is within the so-called TACTAAC box (UACUAAC box), an absolutely conserved intron sequence required for splicing. Based on the identification and sequence of a U2 analogue in yeast, a specific base pairing interaction between the UACUAAC box and a highly conserved region of this snRNA can be proposed. To test this hypothesis, we have taken advantage of two mutations constructed previously in the UACUAAC box of an actin-HIS4 fusion. These mutant strains were transformed with stable plasmids bearing U2-like snRNAs into which changes predicted to restore base pairing had been introduced. Allele-specific suppression of biological and biochemical phenotypes was observed in both cases. Recognition of the UACUAAC box thus relies, at least in part, on Watson-Crick base pairing with the yeast U2 analogue.

Recognition of mutant and cryptic 5' splice sites by the U1 small nuclear ribonucleoprotein in vitro

We examined the ability of U1 small nuclear ribonucleoproteins (U1 snRNPs) to recognize mutant and cryptic 5' splice sites on beta-globin pre-mRNA substrates using an RNase T1 protection assay. When U1 snRNPs were prebound to anti-(U1)RNP antibodies, we detected binding to mutant but not to cryptic 5' splice sites on several substrates. By contrast, in a splicing extract at 0 degree C, neither the mutated nor cryptic 5' splice sites of a human beta-globin transcript were selected as protected fragments with the same antibodies. However, after incubation of the transcript in the extract to yield splicing intermediates, fragments that included a cryptic 5' splice site were detected. The results of our analyses suggest that U1 snRNPs are involved in recognizing cryptic 5' splice sites but that interactions with other splicing components are required to stabilize the association.

Factors influencing alternative splice site utilization in vivo

To study factors that influence the choice of alternative pre-mRNA splicing pathways, we introduced plasmids expressing either wild-type or mutated simian virus 40 (SV40) early regions into tissue culture cells and then measured the quantities of small-t and large-T RNAs produced. One important element controlling splice site selection was found to be the size of the intron removed in the production of small-t mRNA; expansion of this intron (from 66 to 77 or more nucleotides) resulted in a substantial increase in the amount of small-t mRNA produced relative to large-T mRNA. This suggests that in the normal course of SV40 early pre-mRNA processing, large-T splicing is at a competitive advantage relative to small-t splicing because of the small size of the latter intron. Several additional features of the pre-mRNA that can influence splice site selection were also identified by analyzing the effects of mutations containing splice site duplications. These include the strengths of competing 5' splice sites and the relative positions of splice sites in the pre-mRNA. Finally, we showed that the ratio of small-t to large-T mRNA was 10 to 15-fold greater in human 293 cells than in HeLa cells or other mammalian cell types. These results suggest the existence of cell-specific trans-acting factors that can dramatically alter the pattern of splice site selection in a pre-mRNA.

The length but not the sequence of the polyoma virus late leader exon is important for both late RNA splicing and stability

Polyoma virus late RNA processing provides a convenient model system in which to study the mechanics of splicing in vivo. In order to understand further the role of the untranslated "late leader" unit in late RNA processing we have constructed a group of polyoma viruses with deletions and substitutions in the leader exon. This has allowed us to determine that there is a minimum exon size required for both pre-mRNA splicing and stability in this system. We show here that the non-viability of a mutant (ALM) with a 9 base late leader unit is due to a general defect in late RNA splicing. In addition, ALM-infected cells show at least 40-fold depression in the accumulation of late nuclear RNA (spliced or unspliced). The ALM late promoter, however, functions nearly normally. Substituted leader variants with 51- to 96-base long exons of unrelated sequence are viable (G. Adami and G. Carmichael, J. Virol. 58, 417-425, 1986). We show here that late RNA from one of these substituted leader mutants (containing a 51-base leader exon) is spliced at wild type levels, with virtually no defect in accumulation. Thus, in the polyoma system, splice sites separated by only 9 bases can inhibit each others usage, presumably by steric interference. We suggest that this type of inhibition leads to extreme RNA instability.