Inhibition of mammalian spliceosome assembly and pre-mRNA splicing by peptide inhibitors of protein kinases

Four peptides are shown to block mammalian spliceosome assembly and pre-mRNA splicing in vitro. Previously, these peptides have been shown to inhibit Ca2+-dependent calmodulin kinase II (CaMK II) via distinct mechanisms. One is a competitive inhibitor of the kinase, two interfere with autophosphorylation events, and one competes for binding to calmodulin, a CaMK II-activating protein. However, because EGTA does not inhibit splicing, the involvement of CaMK II itself in splicing is unlikely; rather, a protein similar to CaMK II may be involved in spliceosome assembly and splicing. Two of the inhibitory peptides, the calmodulin binding domain (CBD) and glycogen synthase (GS) fragment, block assembly of spliceosomal complex C. These peptides inhibited splicing if they were added to reactions any time within the first 10 min of splicing assays. No inhibition of spliceosome assembly or splicing occurred in the presence of randomized versions of the CBD or GS peptide. Additionally, the GS peptide inhibited splicing when added to assays at later time points, despite the fact that spliceosomal complex C had formed. Cumulatively, these analyses suggest that the peptides inhibit at least two distinct events in the spliceosomal cycle. The first event occurs early during in vitro splicing. For this event, prolonged incubations of splicing reactions do not result in a recovery of splicing activity. The second event occurs later and represents a slowing of an essential step, because splicing activity can be recovered in prolonged incubations. Peptides known to inhibit protein kinase A and protein kinase C had no effect on pre-mRNA splicing, underscoring the specificity of the observed inhibitory effects.

AU-rich elements target small nuclear RNAs as well as mRNAs for rapid degradation

AU-rich elements (AREs, usually containing repeated copies of AUUUA), when present in the 3'-untranslated regions (UTRs) of many mammalian mRNAs, confer instability on their host RNA molecules. The viral small nuclear RNA (snRNA) Herpesvirus saimiri U RNA 1 (HSUR 1) also contains an AUUUA-rich sequence. Here, we report that this ARE induces rapid degradation of HSUR 1 itself and of other snRNAs including HSUR 2 and cellular U1. Mutational analyses of the viral ARE establish that sequence requirements for mRNA and snRNA decay are the same, suggesting a similar mechanism. Moreover, the in vivo degradation activity of mutant AREs correlates with their in vitro binding to the HuR protein, implicated previously as a component of the mRNA degradation machinery. Our results suggest that ARE-mediated instability can be uncoupled from both ongoing translation and deadenylation of the target RNA.

A new strategy for introducing photoactivatable 4-thiouridine ((4S)U) into specific positions in a long RNA molecule

We describe a new protocol, which does not require (4S)UpG, for introducing (4S)U into specific sites in a pre-mRNA substrate. A 5'-half and a full-length RNA are first synthesized by phage RNA polymerase. p(4S)Up, which is derived from (4S)UpU and can therefore be 32P-labeled, is then ligated to the 3' end of the 5'-half RNA with T4 RNA ligase. The 3' phosphate of the ligated product is removed subsequently by CIP (calf intestinal alkaline phosphatase) to produce a 3'-OH group. The 3'-half RNA with a 5' phosphate is produced by site-specific RNase H cleavage of the full-length pre-mRNA directed by a 2'-O-methyl RNA-DNA chimera. The two half RNAs are then aligned with a bridging oligonucleotide and ligated with T4 DNA ligase. Our results show that 32P-p(4S)Up ligation to the 3' end of the 5'-half RNA is comparable to 32P-pCp ligation. Also, the efficiency of the bridging oligonucleotide-mediated two-piece ligation is quite high, approximately 30-50%. This strategy has been applied to the P120 pre-mRNA containing an AT-AC intron, but should be applicable to many other RNAs.

Site-specific crosslinking of mammalian U11 and u6atac to the 5' splice site of an AT-AC intron

A rare class of introns with AT-AC at their termini recently has been identified in metazoan genes. Splicing of these introns requires a different set of small nuclear ribonucleoprotein particles (snRNPs) (U11, U12, U5, and U4atac/U6atac) compared with the snRNPs (U1, U2, U5, and U4/U6) required for splicing the majority of pre-mRNA introns, but otherwise little is known regarding the excision of AT-AC introns. Here we use site-specific 4-thiouridine (4SU) crosslinking analysis to dissect the mechanism of 5' splice site recognition during in vitro splicing of the AT-AC intron from the P120 pre-mRNA. Upon irradiation with 365-nm UV light, three P120 substrates, each with a single 4SU substitution near the 5' splice site (at position +2, +4, or +7), produce two early ATP-independent crosslinks with similar kinetics. For one of the substrates, P120-4SU+2, a third ATP-requiring crosslink forms as the two early crosslinks diminish. RNase H digestion coupled with Northern blotting indicates that the two early crosslinks generated with P120-4SU+2 contain the U11 small nuclear RNA. Reverse transcription-PCR followed by cloning and sequencing demonstrates that the third crosslink involves U6atac. The dynamic appearance of the three crosslinks correlates with the kinetics of the splicing reaction and suggests that the 5' splice site is recognized first by U11 and then by U6atac. Our results argue that the splicing of AT-AC introns is mechanistically similar to the splicing of the major class of introns and that the U11 and U6atac snRNPs in the AT-AC spliceosome fulfill analogous roles to U1 and U6, respectively, in the major spliceosome.

Identification of HuR as a protein implicated in AUUUA-mediated mRNA decay

Expression of many proto-oncogenes, cytokines and lymphokines is regulated by targeting their messenger RNAs for rapid degradation. Essential signals for this control are AU-rich elements (AREs) in the 3' untranslated region (UTR) of these messages. The ARE is loosely defined as the five-nucleotide sequence AUUUA embedded in a uracil-rich region. A transacting factor, presumably a protein, binds the ARE and initiates recognition by the destabilization machinery. Numerous candidate ARE-binding proteins have been proposed. We show that a 32 kDa protein in HeLa nuclear extracts characterized previously has RNA-binding specificity that correlates with the activity of an ARE in directing mRNA decay. Purification and subsequent analyses demonstrate that this 32 kDa protein is identical to a recently identified member of the Elav-like gene family (ELG) called HuR. The in vitro binding selectivity of HuR is indicative of an ARE sequence's ability to destabilize a mRNA in vivo, suggesting a critical role for HuR in the regulation of mRNA degradation.

Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge

A rare class of pre-mRNA introns with non-canonical consensus sequences has been identified in metazoan genes. The novel, low-abundance spliceosome that excises these introns contains one small nuclear ribonucleoprotein (snRNP) in common with the major spliceosome (U5) and four snRNPs that are distinct from, but structurally and functionally analogous to U1, U2 and U4-U6. The architecture of RNA components at the presumptive core of the AT-AC splicesome supports current models of the spliceosomal active center and raises tantalizing questions about spliceosome evolution.

Curricular track, career choice, and androgyny among adolescent females

This study investigated psychological androgyny among 40 high school girls from a college preparatory upper-level mathematics class and from a vocational track cosmetology class. It was hypothesized that the choice of curricular track would correspond to traditional sex-role stereotypes and that there would be a significant difference between the two groups in terms of feminine orientation. Neither hypothesis was supported. The cosmetology group was significantly more androgynous than was the upper-level mathematics group. The results are discussed in terms of implications for the prevailing perspective that career choices are linked to traditional sex-role stereotypes.

A new method for detecting sites of 2'-O-methylation in RNA molecules

2'-O-methylation of eukaryotic ribosomal RNAs occurs in the cell nucleoli. At least 100 modification sites that are highly conserved among vertebrate rRNAs have been mapped. However, in part because of the insensitivity of current approaches, there are 2'-O-methylated sites that remain unidentified. We have developed an extremely sensitive method for detecting 2'-O-methylated residues that are predicted within a long RNA molecule. Utilizing RNase H cleavage directed by a 2'-O-methyl RNA-DNA chimeric oligonucleotide, this method has allowed identification of two methylated nucleotides, G1448 in Xenopus 18S rRNA and A394 in Xenopus 28S rRNA. The latter (A394 in 28S) had not been detected before. We have confirmed that the methylation at G1448 in 18S is dependent upon Xenopus U25 snoRNA and have demonstrated that the methylation at A394 in 28S requires U26 snoRNA. One advantage of this technique is that it can examine specific rRNA and precursor molecules. We show that about 30% of the 40S pre-rRNA has been methylated at these two sites and their methylation is complete at the stage of 20S (immediate precursor to 18S) and 32S (immediate precursor to 28S). We also show that methylation at these two sites is not essential for rRNA transport from the nucleus to the cytoplasm.

More Sm snRNAs from vertebrate cells

There are a number of low-abundance small nuclear RNAs (snRNAs) in eukaryotic cells. Many of them have been assigned functions in the biogenesis of cellular RNAs, such as splicing and 3' end processing. Here, we present the sequence of Xenopus U12 snRNA and compare the secondary structures of the low-abundance U11 and U12 with those of the high-abundance U1 and U2, respectively. The data suggest functional parallels between these two pairs of snRNAs in pre-mRNA splicing. Using a highly sensitive method, we have identified several new low-abundance snRNAs from HeLa cells. These include five U7 snRNA variants and six novel snRNAs. One of the six novel RNAs is an Sm snRNA, whereas the rest are not immunoprecipitable by either anti-Sm antibodies or anti-trimethylguanosine antibodies. The discovery of these new RNAs suggests that there may be yet more low-abundance snRNAs in the nuclei of eukaryotic cells.

A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus

Vertebrate cells contain a large number of small nucleolar RNA (snoRNA) species, the vast majority of which bind fibrillarin. Most of the fibrillarin-associated snoRNAs can form 10- to 21-nt duplexes with rRNA and are thought to guide 2'-O-methylation of selected nucleotides in rRNA. These include mammalian UHG (U22 host gene)-encoded U25-U31 snoRNAs. We have characterized two novel human snoRNA species, U62 and U63, which similarly exhibit 15- (with one interruption) and 12-nt complementarities and are therefore predicted to direct 2'-O-methylation of A590 in 18S and A4531 in 28S rRNA, respectively. To establish the function of antisense snoRNAs in vertebrates, we exploited the Xenopus oocyte system. Cloning of the Xenopus U25-U31 snoRNA genes indicated that they are encoded within multiple homologs of mammalian UHG. Depletion of U25 from the Xenopus oocyte abolished 2'-O-methylation of G1448 in 18S rRNA; methylation could be restored by injecting either the Xenopus or human U25 transcript into U25-depleted oocytes. Comparison of Xenopus and human U25 sequences revealed that only boxes C, D, and D', as well as the 18S rRNA complement, were invariant, suggesting that they may be the only elements required for U25 snoRNA stability and function.

Length suppression in histone messenger RNA 3'-end maturation: processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA

Efficient 3'-end processing of cell cycle-regulated mammalian histone premessenger RNAs (pre-mRNAs) requires an upstream stem-loop and a histone downstream element (HDE) that base pairs with the U7 small ribonucleoprotein. Insertions between these elements have two effects: the site of cleavage moves in concert with the HDE and processing efficiency declines. We used Xenopus oocytes to ask whether compensatory length insertions in the human U7 RNA could restore the fidelity and efficiency of processing of mouse histone insertion pre-mRNAs. An insertion of 5 nt into U7 RNA that extends its complementary to the HDE compensated for both defects in processing of a 5-nt insertion substrate; a noncomplementary insertion into U7 did not. Yet, the noncomplementary insertion mutant U7 was shown to be active on insertion substrates further mutated to allow base pairing. Our results suggest that the histone pre-mRNA becomes rigidified upstream of its HDE, allowing the bound U7 small ribonucleoprotein to measure from the HDE to the cleavage site. Such a mechanism may be common to other RNA measuring systems. To our knowledge, this is the first demonstration of length suppression in an RNA processing system.

Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns

Removal of a rare class of metazoan precursor messenger RNA introns with AU-AC at their termini is catalyzed by a spliceosome that contains U11, U12, and U5 small nuclear ribonucleoproteins. Two previously unidentified, low-abundance human small nuclear RNAs (snRNAs), U4atac and U6atac, were characterized as associated with the AT-AC spliceosome and necessary for AT-AC intron splicing. The excision of AT-AC introns therefore requires four snRNAs not found in the major spliceosome. With the use of psoralen crosslinking, a U6atac interaction with U12 was identified that is similar to a U6-U2 helix believed to contribute to the spliceosomal active center. The conservation of only limited U6atac sequences in the neighborhood of this interaction and the potential of U6atac to base pair with the 5' splice site consensus for AT-AC introns provide support for current models of the core of the spliceosome.

A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro

A minor class of introns with noncanonical splice (AT-AC) and branch site sequences exists in metazoan protein coding genes. We have established a HeLa cell in vitro system that accurately splices a pre-mRNA substrate containing such an intron from the human P120 gene. Splicing occurs via a lariat intermediate whose branch site A residue is predicted to bulge from a duplex formed with the low abundance U12 small nuclear ribonucleoprotein (snRNP), which we confirm by psoralen cross-linking. Native gel electrophoresis reveals that U11, U12, and U5 snRNPs assemble onto the P120 pre-mRNA to form splicing complexes. Inhibition of P120 splicing by 2'-O-methyl oligonucleotides complementary to U12 or U5 demonstrates that U12 and U5 snRNPs perform essential roles in the AT-AC spliceosome.

A mammalian gene with introns instead of exons generating stable RNA products

The nucleoli of eukaryotic cells are the sites of ribosomal RNA transcription and processing and of ribosomal subunit assembly. They contain multiple small nucleolar RNAs (snoRNAs), several of which are essential for rRNA maturation. The U3, U8 and U13 snoRNA genes are transcribed independently, whereas U14-U24, as well as E3, are located within introns of protein-coding genes, most of whose functions are linked to translation. These snoRNAs are co-transcribed with their host pre-mRNAs and released by processing from excised introns. Here we show that, in addition to U22, seven novel fibrillarin-associated snoRNAs, named U25-U31, are encoded within different introns of the unusually compact mammalian U22 host gene (UHG). All seven RNAs exhibit extensive (12-15 nucleotides) complementarity to different segments of the mature rRNAs, followed by a C/AUGA ('U-turn') sequence. The spliced UHG RNA, although it is associated with polysomes, has little potential for protein coding, is short-lived, and is poorly conserved between human and mouse. Thus, the introns rather than the exons specify the functional products of UHG.

Decreasing the distance between the two conserved sequence elements of histone pre-messenger RNA interferes with 3' processing in vitro

Histone mRNA 3' end formation requires the presence of two cis-acting conserved sequence elements: a stem-loop structure upstream from the site of cleavage and a purine-rich region downstream from the site of cleavage called the histone downstream element (HDE). Possible interactions between these two elements and their respective binding factors were investigated by a series of deletions (1-7 nt) in the region between the two. The efficiency of processing decreased as the stem-loop and the HDE were moved closer together. In contrast with the documented ability of the U7 snRNP to direct cleavage at a fixed distance from the HDE in insertion mutants (Scharl & Steitz, 1994), all deletion substrates for which processing was observed were cleaved at or 1-nt upstream from the wild-type site. The reason for the inability of the system to cleave closer to the stem-loop remains unclear, but the removal of stem-loop binding protein(s) (SLBP) did not activate upstream cleavage events. Thus, although the processing machinery measures the distance between the cleavage site and the HDE of mammalian histone pre-mRNAs, there is a barrier limiting how far upstream cleavage can occur. These data allow a reevaluation of the sites of 3' end processing in known histone pre-mRNAs.

U12 snRNA in vertebrates: evolutionary conservation of 5' sequences implicated in splicing of pre-mRNAs containing a minor class of introns

A minor class of introns with noncanonical splice sites has been identified in both vertebrate and invertebrate genomes. The divergent consensus sequences within these introns suggest that splicing might be via a mechanism distinct from that used by the major class of introns. The low abundance U12 snRNA has been proposed to base pair with the predicted branch site sequence of these minor class introns, probably bulging out an adenosine to act as the nucleophile in the first step of splicing. We have identified homologues of the previously characterized human U12 snRNA in both mouse and chicken, where the minor class of introns has also been found. The U12 sequences that potentially base pair with the putative branch site are invariant. Additional conserved sequences at the 5' end of U12 snRNA could dynamically base pair with U6 snRNA sequences flanking the hexanucleotide ACAGAG to form structures analogous to those of three U2-U6 interactions genetically defined as important in the major class of spliceosome. We have also isolated two human U12 snRNA genes. One gene is functional for transcription of U12 snRNA, whereas the other appears to be a pseudogene. Sequences of the 3' box in both U12 snRNA genes are strikingly similar and bear high resemblance to those of U1 and U2 genes. Upstream elements, including the PSE and the DSE, have been identified and characterized in the functional gene. These features indicate that transcription of U12 snRNA is driven by RNA polymerase II.

Site-specific crosslinking of 4-thiouridine-modified human tRNA(3Lys) to reverse transcriptase from human immunodeficiency virus type I

We have mapped specific RNA-protein contacts between human immunodeficiency virus (HIV) type I reverse transcriptase (RT) and its natural primer, human tRNA(3Lys), using a site-specific crosslinking strategy. Four different tRNA(3Lys) constructs with a single 32P-labeled 4-thiouridine (4-thioU) residue at positions -1, 16, 36 or 41 were synthesized. After incubation with RT followed by irradiation, crosslinks were localized to either the p66 or p51 subunit of RT by digestion with nuclease and SDS gel fractionation. 4-thioU at position -1 or 16 transferred label to the p66 subunit almost exclusively (> 90%), whereas position 36 labeled both p66 and p51 (3:1). Position 41 yielded no detectable crosslinks. The region of p66 contacted by position -1 of tRNA(3Lys) was localized to the 203 C-terminal amino acids of RT by CNBr cleavage, whereas a 127 amino acid-CNBr peptide (residues 230-357) from both p66 and p51 was labeled by position 36. Functionality of the 4-thioU-modified tRNA(3Lys)(-1) crosslinked to RT in the presence of an RNA but not a DNA template was demonstrated by the ability of the tRNA to be extended. These results localize the 5' half of the tRNA on the interface between the two RT subunits, closer to the RNase H domain than to the polymerase active site, in accord with previous suggestions. They argue further that a specific binding site for the 5' end of the primer tRNA(3Lys) may exist within the C-terminal portion of the p66 subunit, which could be important for the initiation of reverse transcription.

Isolation and characterization of a novel, low abundance hnRNP protein: A0

Pre-messenger RNA is bound by a variety of proteins to form large heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. As defined by immunoprecipitation and two-dimensional gel electrophoresis, there appear to be more than 20 abundant hnRNP proteins ranging in size from 34 kDa to 120 kDa. One major class, the A/B family, is typified by its characteristic primary structure containing two RNA binding domains followed by a glycine-rich C-terminus. We report the cloning and characterization of a novel, low-abundance member of the A/B family named hnRNP A0. This protein was affinity isolated using a biotinylated RNA probe [G4(AU3)4A] designed to select a 32-kDa protein implicated in mRNA stability in mammalian cells. hnRNP A0 is a basic protein with a predicted mass of 31.7 kDa and an isoelectric point of 10.1. Comparative protease mapping shows that it is not the AUUUA binding protein we intended to clone. A0 is present in hnRNP complexes and is encoded by a gene distinct from that of any previously cloned A/B family member.

Modulation of 5' splice site choice in pre-messenger RNA by two distinct steps

Ser/Arg-rich proteins (SR proteins) are essential splicing factors that commit pre-messenger RNAs to splicing and also modulate 5' splice site choice in the presence or absence of functional U1 small nuclear ribonucleoproteins (snRNPs). Here, we perturbed the U1 snRNP in HeLa cell nuclear extract by detaching the U1-specific A protein using a 2'-O-methyl oligonucleotide (L2) complementary to its binding site in U1 RNA. In this extract, the standard adenovirus substrate is spliced normally, but excess amounts of SR proteins do not exclusively switch splicing from the normal 5' splice site to a proximal site (site 125 within the adenovirus intron), suggesting that modulation of 5' splice site choice exerted by SR proteins requires integrity of the U1 snRNP. The observation that splicing does not necessarily follow U1 binding indicates that interactions between the U1 snRNP and components assembled on the 3' splice site via SR proteins may also be critical for 5' splice site selection. Accordingly, we found that SR proteins promote the binding of the U2 snRNP to the branch site and stabilize the complex formed on a 3'-half substrate in the presence or absence of functional U1 snRNPs. A novel U2/U6/3'-half substrate crosslink was also detected and promoted by SR proteins. Our results suggest that SR proteins in collaboration with the U1 snRNP function in two distinct steps to modulate 5' splice site selection.

Requirement for intron-encoded U22 small nucleolar RNA in 18S ribosomal RNA maturation

The nucleoli of vertebrate cells contain a number of small RNAs that are generated by the processing of intron fragments of protein-coding gene transcripts. The host gene (UHG) for intro-encoded human U22 is unusual in that it specifies a polyadenylated but apparently noncoding RNA. Depletion of U22 from Xenopus oocytes by oligonucleotide-directed ribonuclease H targeting prevented the processing of 18S ribosomal RNA (rRNA) at both ends. The appearance of 18S rRNA was restored by injection of in vitro-synthesized U22 RNA. These results identify a cellular function for an intron-encoded small RNA.

Organization of small nucleolar ribonucleoproteins (snoRNPs) by fluorescence in situ hybridization and immunocytochemistry

The organization of the U3, U8, and U13 small nucleolar ribonucleoproteins (snoRNPs) has been investigated in HeLa cells using antisense DNA and 2'-OMe RNA oligonucleotides. Oligomers corresponding to deoxynucleotides that target RNase H degradation of intact RNP particles were synthesized and used for fluorescence in situ hybridization. U3 and U13 are distributed throughout the nucleolus and colocalize with anti-fibrillarin antibodies. U8, however, is organized in discrete ring-like structures near the center of the nucleolus and surround bright punctate regions visualized with anti-RNA polymerase I and anti-UBF/NOR-90 antibodies. In decondensed nucleoli, a necklace of smaller ring-like structures of U8 RNA appear. A model for the recruitment of U8 (and presumably other processing factors) to the sites of rRNA transcription is discussed. Hybridization to mitotic cells showed that unlike pol I and NOR-90, U8 is dispersed into the cytoplasm during mitosis. The subnucleolar organization of U8 is consistent with its demonstrated participation in early intermediate steps in pre-rRNA processing. In contrast, the more dispersed intranucleolar distribution of U3 agrees with its putative involvement in both early and late steps of rRNA maturation. These studies illustrate the feasibility of mapping functional domains within the nucleolus by correlating the in vitro activities of small nuclear RNPs with their in situ locations.

SR proteins can compensate for the loss of U1 snRNP functions in vitro

SR proteins are essential splicing factors that also influence 5' splice site choice. We show that addition of excess mixed SR proteins to a HeLa in vitro splicing system stimulates utilization of a novel 5' splice site (site 125) within the intron of the standard adenovirus pre-mRNA substrate. When U1 snRNPs are debilitated by sequestering the 5' end of U1 snRNA with a 2'-O-methyl oligoribonucleotide, excess SR proteins not only rescue splicing at the normal site and site 125 but also activate yet another 5' splice site (site 47) in the adenovirus intron. One SR protein, SC35, is sufficient to exhibit the above activities. The possibility that excess SR proteins recruit residual unblocked U1 snRNPs to participate in 5' splice site recognition has been ruled out by psoralen cross-linking studies, which demonstrate that the 2'-O-methyl oligoribonucleotide effectively blocks 5' splice site/U1 interaction. Native gel analysis reveals a nearly normal splicing complex profile in the 2'-O-methyl oligoribonucleotide pretreated, SR protein-supplemented extract. These results indicate that SR proteins can replace some functions of the U1 snRNP but underscore the contribution of U1 to the fidelity of 5' splice site selection.