Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro

To study the role of base-pairing between the mammalian U7 snRNA and the highly variable histone downstream element (HDE) during the 3'-end maturation of mammalian histone pre-mRNAs, we mutated the HDE of the mouse H2A-614 gene and assayed processing in HeLa cells both in vivo and in vitro. Either a 9-nucleotide deletion or a block substitution of pyrimidines for 6 purines within the HDE abolished all 3'-end processing. Compensatory changes were introduced into a synthetic human U7 gene, whose transcripts assemble into Sm snRNPs in vivo. Suppression of the 6-purine substitution as well as a 3-purine substitution within the HDE was obtained in vivo by coexpressing the corresponding U7 suppressor RNAs and in vitro by using nuclear extracts prepared from HeLa cells containing U7 suppressor genes. Our results not only provide genetic evidence for base-pairing between the U7 snRNP and the HDE of mammalian histone pre-mRNAs but reveal an unexpected tolerance to drastic changes in the nature of the base-paired region.

Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function

The human 7SK ribonucleoprotein (RNP) has been analyzed to determine its RNA secondary structure and protein constituents. HeLa cell 7SK RNA alone and within its RNP have been probed by chemical modification and enzymatic cleavage, and sites of modification or cleavage have been mapped by primer extension. The resulting secondary structure suggests that structural determinants necessary for capping (a 5' stem followed by the sequence AUPuUPuC) and nuclear migration (the sequence AUPuUPuC) of 7SK RNA may be similar to those for U6 small nuclear RNA (snRNA). It also supports existence of a 3' stem structure which could serve to self-prime cDNA synthesis during pseudogene formation. Oligonucleotide-directed RNase H digestion indicated regions of 7SK RNA capable of base pairing with other nucleic acids. Antisense 2'-O-methyl RNA oligonucleotides were used to affinity select the 7SK RNP from an in vivo 35S-labeled cell sonic extract and identify eight associated proteins of 83, 48, 45, 43, 42, 21, 18, and 13 kDa. 7SK RNA has extensive sequence complementarity to U4 snRNA, within the U4/U6 base pairing domain, and also to U11 snRNA. The possibility that the 7SK RNP is an unrecognized component of the pre-mRNA processing machinery is discussed.

EAP, a highly conserved cellular protein associated with Epstein-Barr virus small RNAs (EBERs)

Human B lymphocytes latently infected with Epstein-Barr virus (EBV) synthesize very large amounts (5 x 10(6)/cell) of two small nuclear RNAs called EBERs (Epstein-Barr encoded RNAs). These RNAs are of unknown function and, like many RNA polymerase III (Pol III) transcripts, bind the La autoantigen. We have discovered that the EBERs also associate with a second highly abundant host-encoded protein designated EAP (EBER associated protein). Human EAP is a small (14,777 dalton, 128 amino acid) polypeptide that binds both EBER 1 and EBER 2. EAP is also found in association with one or both of two analogous virally-encoded RNAs found in baboon cells infected with herpesvirus papio (HVP). We have devised a purification procedure for EAP and have cloned its cDNA from a human placental cDNA library using amino acid sequence data and the polymerase chain reaction (PCR). The predicted amino acid sequence of EAP shows a strong resemblance (77% identity) to an endodermal, developmentally regulated sea urchin protein called 217 (Dolecki et al., 1988). EAP contains a potential nuclear localization signal and a highly acidic carboxy terminus, but does not display marked similarity to any other RNA binding proteins.

Spliced leader RNA sequences can substitute for the essential 5' end of U1 RNA during splicing in a mammalian in vitro system

L. collosoma or C. elegans SL RNA sequences joined to an adenovirus intron and 3' exon are spliced highly efficiently and accurately in HeLa nuclear extract. After inactivation of U1 snRNPs using RNAase H and a deoxyoligonucleotide complementary to the first 12 nucleotides of U1, splicing of SL RNA-containing constructs continues undiminished, whereas control substrates no longer splice. Since neither binding of U1 snRNPs nor inhibition of splicing is detected using anti-(U1)RNP antibodies, splicing of SL RNA-containing constructs may be entirely U1 snRNP independent. Analyses of altered L. collosoma constructs revealed that the sequence surrounding the 5' splice site is not sufficient to confer U1-independent splicing; the smallest U1-independent region identified so far retains only the first stem-loop of the SL RNA. That sequences responsible for recognition of the 5' splice site can be relocated within the splicing substrate itself reinforces the similarity between group II self-splicing and spliceosome-mediated pre-mRNA splicing.

Herpesvirus saimiri U RNAs are expressed and assembled into ribonucleoprotein particles in the absence of other viral genes

Marmoset T lymphocytes transformed by herpesvirus saimiri contain a set of five virally encoded U RNAs called HSUR1 through HSUR5. HSUR genes have been individually transfected into a nonlymphoid, nonsimian cell line (HeLa cells) in the absence of any other coding regions of the herpesvirus saimiri genome. The levels of HSUR1 through HSUR4 in HeLa transient-expression systems are comparable to those found in virally transformed T cells (23 to 91%). In contrast, HSUR5 is expressed at ninefold-higher levels in transfected HeLa cells. Immunoprecipitation experiments show that HSURs expressed in transfected cells bind proteins with Sm determinants and acquire a 5' trimethylguanosine cap structure, as they do in transformed T cells. HSUR1 or HSUR4 particles from transfected HeLa cells migrate between 10S and 15S in velocity gradients, identical to the sedimentation of "monoparticles" produced in virally transformed lymphocytes. We conclude from these transfection experiments that no other herpesvirus saimiri or host-cell-specific gene products appear to be required for efficient expression of the HSUR genes or for subsequent assembly of the viral U RNAs into small nuclear ribonucleoprotein particles. In lymphocytes transformed by herpesvirus saimiri, HSUR small nuclear ribonucleoprotein particles are involved in higher-order complexes that sediment between 20S and 25S. HSUR1, HSUR2, and HSUR5 dissociate from such complexes upon incubation at 30 degrees C, whereas the complex containing HSUR4 is stable to incubation.

The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing

The first cleavage in mammalian pre-rRNA maturation occurs near the 5' end within the 5' external transcribed spacer. Using mouse cell extracts, we show that this processing is abolished by micrococcal nuclease pretreatment. Autoantibodies that recognize the U3, U8, and U13 snRNPs (anti-fibrillarin) deplete processing activity from the extract and selectively immunoprecipitate both rRNA substrates and processing products from the reaction. Specific involvement of the U3 snRNP is demonstrated by native gel electrophoresis of the processing reaction followed by Northern blotting and by oligonucleotide-directed RNAase H abolition of processing activity. Our identification of U3 function is discussed with respect to the molecular basis of pre-rRNA recognition by the U3 snRNP, possible roles of U3 and other nucleolar snRNPs in rRNA processing, and the morphological organization of the nucleolus and the ribosomal transcription complex.

The mammalian analogue of the yeast PRP8 splicing protein is present in the U4/5/6 small nuclear ribonucleoprotein particle and the spliceosome

HeLa cell nuclear extracts contain a protein reactive with antibodies against PRP8, a polypeptide essential for pre-mRNA splicing in yeast and a specific component of the yeast U5 small nuclear ribonucleoprotein (snRNP) [Lossky, M., Anderson, G. J., Jackson, S. P. & Beggs, J. (1987) Cell 51, 1019-1026]. The mammalian protein appears as a doublet at approximately 200 kDa, smaller than the 260-kDa yeast protein, and possesses an Sm epitope as determined by immunoblotting. Its association with a snRNP of the Sm class other than U1 or U2 is indicated by its immunoprecipitation by anti-Sm and anti-trimethylguanosine antibodies but not by anti-(U1) or anti-(U2) RNP sera. Gradient fractionation of splicing extracts demonstrates that the 200-kDa protein is a component of the U4/5/6 snRNP complex and of U5 snRNPs. It is also present in affinity-purified spliceosomes.

U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus

Using anti-(U3)RNP autoantibodies, we have isolated and characterized two additional small nucleolar RNAs from HeLa cells, which are less abundant than U3 RNA. Both RNAs possess a trimethylguanosine cap as judged by precipitation with anti-TMG antibody, but are not precipitated by either anti-Sm or anti-La antibodies. In addition, both RNAs are not precipitable by anti-Th serum, which recognizes another nucleolar RNP autoantigen. Sequence analysis revealed that one of these RNAs, 136 nucleotides long, is the human U8 homolog; while the other, 105 nucleotides long, represents a novel species which we designate U13. Both RNAs share with U3 two conserved sequences (boxes C and D). The role of one or both of these boxes in binding the common 34 kd antigenic protein, otherwise known as fibrillarin, is discussed. Fractionation of HeLa cells revealed that U8 and U13, like U3, reside in the nucleolus. In glycerol gradients both RNAs cosediment with larger structures possibly representing ribosomal precursors. We propose that U3, U8 and U13 comprise a new subset of mammalian snRNPs whose roles in ribosome biogenesis are discussed.

Each of the conserved sequence elements flanking the cleavage site of mammalian histone pre-mRNAs has a distinct role in the 3'-end processing reaction

To study the substrate requirements for the histone 3'-end processing reaction of mammalian histone pre-mRNAs, we created a set of mutations in the sequences flanking the processing site of a mouse H3 gene. We found that deletion of the downstream purine-rich element hypothesized to interact with U7 small nuclear RNA abolishes in vitro 3'-end processing. Somewhat surprisingly, however, mutations in the hairpin loop element which destabilize or destroy the secondary structure reduce but do not abolish 3'-end processing. This is in apparent contrast to results obtained for the sea urchin system, where both sequence elements appear to be absolutely required for 3'-end formation.

The RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro

The autoantigen La binds the U-rich 3' ends of all nascent RNA polymerase III transcripts. Here, we demonstrate that this abundant nuclear phosphoprotein not only binds these RNAs but appears to be required for their synthesis. HeLa cell extracts immunochemically depleted of La by either patient or mouse monoclonal antibodies lose greater than 99% of their transcription activity on class III genes. The few transcripts synthesized in the absence of La have fewer uridylate residues at their 3' ends than those made in its presence. Reconstitution of La-depleted extracts with biochemically purified HeLa La protein stimulates transcription levels and completely restores transcript length. A model coupling transcription levels to the action of La at the RNA polymerase III termination signal is presented.

Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III

We have tested the hypothesis that the mammalian La protein, which appears to be required for accurate and efficient RNA polymerase III transcription, is a transcription termination factor. Our data suggest that 3' foreshortened transcripts generated in La's absence are components of a novel transcription intermediate containing a paused polymerase. These transcripts are produced by fractionated transcription complexes, are synthesized with kinetics different from full-length transcripts, and are chasable to completion from the stalled transcription complexes. Together, these findings argue that termination by RNA polymerase III requires auxilliary factor(s) and implicate La as such a factor. Since La appears to facilitate transcript completion and release and also binds the resulting RNA product, it may be a regulator of RNA polymerase III transcription.

An in vitro interaction between the human U3 snRNP and 28S rRNA sequences near the alpha-sarcin site

Model transcripts containing mammalian pre-rRNA sequences were incubated with a HeLa cell extract, digested with T1 RNase, and immunoprecipitated with anti-(U3)RNP or control antibodies. Two overlapping fragments derived from the 3' domain of human 28S rRNA were specifically immunoprecipitated although transcripts which spanned the transcription initiation site, the ETS processing site, the 5' end of 18S, and both termini of 5.8S yielded no protected fragments. The sequence of these fragments was determined using a novel technique in which the [32P]-labeled fragment was co-finger-printed with [3H]-labeled total transcript serving as an internal marker. The fragments immunoprecipitated derive from nucleotides 4570-4590 and 4575-4590 of human 28S and are adjacent to the alpha-sarcin site. Protection most likely involves the U3 RNA since it is sensitive to pretreatment of the extract with micrococcal nuclease. Complementarity between U3 and this rRNA region is phylogenetically conserved in species ranging from human to S. cerevisiae. The possible significance of this finding is discussed.

Correct in vivo splicing of the mouse immunoglobulin kappa light-chain pre-mRNA is dependent on 5' splice-site position even in the absence of transcription

In transcripts from the rearranged mouse immunoglobulin kappa light-chain locus, the intron separating the variable (V) plus joining (J) exon from the constant (C) exon contains up to three additional J regions, each with a functional 5' splice site. Previously, HeLa cells transfected with DNA encoding kappa light chains have been shown to mimic kappa-producing lymphocytes in splicing exclusively to the upstream-most 5' splice site, whereas selectivity is lost when kappa transcripts containing two more J regions are incubated in HeLa cell or lymphocyte nuclear extracts. Here we demonstrate that the fidelity of in vivo splicing depends on neither V-J rearrangement, the instability of erroneously splicing transcripts, nor a hierarchy of J-region 5' splice site utilization. Analysis of the splicing of presynthesized kappa transcripts injected into Xenopus oocytes demonstrates the correct 5' splice-site selection is independent of transcription. Implications for in vitro studies of regulated splice-site pairing are discussed.

Four novel U RNAs are encoded by a herpesvirus

Marmoset T lymphocytes transformed by herpesvirus saimiri contain the first virally encoded U RNAs (called HSURs) to be identified. HSURs assemble into small nuclear ribonucleoproteins of low abundance (less than or equal to 2 x 10(4) copies/cell). They bind proteins with Sm determinants and acquire a 5' trimethylguanosine cap structure. The sequences of HSUR 1 (143 nucleotides), HSUR 2 (115 nucleotides), HSUR 3 (76 nucleotides), and HSUR 4 (106 nucleotides) are related to each other but are distinct from any previously characterized cellular U RNA. The viral genes encoding the HSURs possess conserved enhancer, promoter, and 3' end formation signals unique to U RNA genes. HSUR 1 and HSUR 2 have a similar 5' end sequence that exhibits perfect complementarity to the highly conserved AAUAAA polyadenylation signal. Oligonucleotide directed RNAase H degradation indicates that this 5' end region is available for base pairing interactions within the HSUR 1 and HSUR 2 snRNP particles.

Subjective age, age identity, and middle-age adults

A casual model of subjective age among middle-age working adults is proposed. Determinants of subjective age include chronological age, education, health, self-esteem, financial satisfaction, and job satisfaction. Life satisfaction is used as an explanatory outcome. Using a sample of middle-age men, the results indicate that self-esteem and financial satisfaction were important mediators between chronological age and subjective age. In turn, positive and negative characteristics were associated with both a "younger" and "older" subjective age. The results contribute to the further understanding of adult development and the meaning of subjective age.

Structural analyses of EBER1 and EBER2 ribonucleoprotein particles present in Epstein-Barr virus-infected cells

The ribonucleoprotein (RNP) particles containing the Epstein-Barr virus-associated small RNAs EBER1 and EBER2 were analyzed to determine their RNA secondary structures and sites of RNA-protein interaction. The secondary structures were probed with nucleases and by chemical modification with single-strand-specific reagents, and the sites of modification or cleavage were mapped by primer extension. These data were used to develop secondary structures for the two RNAs, and likely sites of close RNA-protein contact were identified by comparing modification patterns for naked RNA and RNA in RNP particles. In addition, sites of interaction between each Epstein-Barr virus-encoded RNA (EBER) and the La antigen were identified by analyzing RNA fragments resistant to digestion by RNase A or T1 after immunoprecipitation by an anti-La serum sample from a lupus patient. Our results confirm earlier findings that the La protein binds to the 3' terminus of each molecule. Possible functions for the EBER RNPs are discussed.

A 5S rRNA/L5 complex is a precursor to ribosome assembly in mammalian cells

A novel 5S RNA-protein (RNP) complex in human and mouse cells has been analyzed using patient autoantibodies. The RNP is small (approximately 7S) and contains most of the nonribosome-associated 5S RNA molecules in HeLa cells. The 5S RNA in the particle is matured at its 3' end, consistent with the results of in vivo pulse-chase experiments which indicate that this RNP represents a later step in 5S biogenesis than a previously described 5S*/La protein complex. The protein moiety of the 5S RNP has been identified as ribosomal protein L5, which is known to be released from ribosomes in a complex with 5S after various treatments of the 60S subunit. Indirect immunofluorescence indicates that the L5/5S complex is concentrated in the nucleolus. L5 may therefore play a role in delivering 5S rRNA to the nucleolus for assembly into ribosomes.

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.

Human acidic ribosomal phosphoproteins P0, P1, and P2: analysis of cDNA clones, in vitro synthesis, and assembly

cDNA clones encoding three antigenically related human ribosomal phosphoproteins (P-proteins) P0, P1, and P2 were isolated and sequenced. P1 and P2 are analogous to Escherichia coli ribosomal protein L7/L12, and P0 is likely to be an analog of L10. The three proteins have a nearly identical carboxy-terminal 17-amino-acid sequence (KEESEESD(D/E)DMGFGLFD-COOH) that is the basis of their immunological cross-reactivity. The identities of the P1 and P2 cDNAs were confirmed by the strong similarities of their encoded amino acid sequences to published primary structures of the homologous rat, brine shrimp, and Saccharomyces cerevisiae proteins. The P0 cDNA was initially identified by translation of hybrid-selected mRNA and immunoprecipitation of the products. To demonstrate that the coding sequences are full length, the P0, P1, and P2 cDNAs were transcribed in vitro by bacteriophage T7 RNA polymerase and the resulting mRNAs were translated in vitro. The synthetic P0, P1, and P2 proteins were serologically and electrophoretically identical to P-proteins extracted from HeLa cells. These synthetic P-proteins were incorporated into 60S but not 40S ribosomes and also assembled into a complex similar to that described for E. coli L7/L12 and L10.