Are U4 small nuclear ribonucleoproteins involved in polyadenylation?

Rat glycine methyltransferase. Complete amino acid sequence deduced from a cDNA clone and characterization of the genomic DNA

The amino terminus of glycine methyltransferase from rat liver is blocked. A hexapeptide containing the blocked amino-terminal residue was obtained from a tryptic digest of the purified enzyme and its amino acid sequence was determined to be Ac-Val-Asp-Ser-Val-Tyr-Arg by Edman degradation and fast-atom-bombardment mass spectrometry after fragmentation with Staphylococcus aureus protease V8. A full-length cDNA clone for the enzyme was isolated from a lambda gt11 rat liver cDNA library using the previously obtained pGMT A56 cDNA [Ogawa, H., Gomi, T., Horii, T., Ogawa, H. & Fujioka, M. (1984) Biochem. Biophys. Res. Commun. 124, 44-50] as a probe. The amino acid sequence deduced from the nucleotide sequence contained both amino- and carboxyl-terminal sequences. The predicted amino acid composition and molecular mass were also in agreement with the published data obtained with the purified protein. Five clones for the glycine methyltransferase gene were isolated from a Charon 4A library containing EcoRI digest of rat liver DNA by in situ plaque hybridization. All clones had inserts of 6500 base pairs, consistent with the size of EcoRI genomic DNA fragment determined by Southern blot hybridization. Sequence analysis of a 5400-bp fragment of the insert DNA lacking a 1100-bp 5' region and comparison of the sequence with that of the cDNA showed that the insert DNA entirely encoded glycine methyltransferase and the gene consisted of six exons and five introns. S1 nuclease protection mapping and primer extension analysis allowed us to propose that the A residue located 19 bp upstream from the translation initiation codon is the site of transcription initiation. TATA, CAAT and GC sequences, and the complementary sequence to the enhancer core element, were located upstream of the transcription initiation site.

Structure of the rat ornithine carbamoyltransferase gene, a large, X chromosome-linked gene with an atypical promoter

Rat mitochondrial ornithine carbamoyltransferase (EC 2.1.3.3) is encoded by a gene located on the X chromosome and expressed specifically in the liver and small intestine; we have cloned this gene and determined its structure. The gene is 75 kilobases long and is split into 10 exons. The introns range in length from 85 bases to 26 kilobases. The sum of the total exons is 1.5 kilobases and occupies only 2% of the gene; this value being one of the lowest among genes heretofore reported. The first exon encodes most of the NH2-terminal presequence that functions as a mitochondrial targeting signal. Putative binding sites for the two substrates of the enzyme, carbamoyl phosphate and ornithine, are encoded by exons 3 and 9, respectively. A set of "CAAT box"- and "ATA box"-like sequences is present about 200 bases upstream from the 5' end of the mRNA. About 35 bases downstream from this set of putative promoter elements, an 11-nucleotide sequence around the 5' end of the mRNA reappears, as a direct repeat. This pair of direct repeats may play a role in pulling the cap site and the promoter elements together. Upstream and downstream from the 5' end of the mRNA there are several sequences that resemble the transcription factor Sp1 binding site, the enhancer core sequence, the consensus sequence for the glucocorticoid receptor binding sites, and the putative enhancer element of the antithrombin III gene, another gene that is expressed specifically in the liver.

Polyadenylation of Chinese hamster dihydrofolate reductase genomic genes and minigenes after gene transfer

The major alternative polyadenylation sites in the Chinese hamster dihydrofolate reductase (dhfr) gene have been identified by DNA sequencing and RNase protection experiments. Comparison of the 3' gene sequence and polyadenylation sites with those of the mouse reveals that, despite an overall sequence homology, the major sites are different in the two species. A series of minigenes was constructed containing the dhfr promoter and the first intron but lacking the four large introns of the genomic sequence. These minigenes contained either all three polyadenylation sites, no polyadenylation sites, or just the first site. All of these minigenes, as well as a cosmid clone containing the full genomic sequence, could transform DHFR-deficient Chinese hamster ovary cell mutants to a DHFR-positive phenotype with approximately equal efficiencies. A minigene lacking the first intron was markedly less efficient. Analysis of dhfr mRNA from transfectant clones derived from minigenes showed that the dhfr polyadenylation sites were used when included, but novel sites were often used in addition. When endogenous polyadenylation sites were absent, new sites in flanking carrier or host DNA were recruited. Transfectants produced by the full genomic dhfr gene yielded mRNA species that were identical in size and relative abundance to the endogenous dhfr gene. The results indicate that the minimal signals for polyadenylation are not complex and can be easily acquired from foreign sequences.

Effects of UV, 4-NQO and TPA on gene expression in cultured human epidermal keratinocytes

In an approach to study effects of UV light on gene expression in human epidermal keratinocytes, a cDNA library was constructed from poly(A)RNA isolated after UV irradiation from cultured keratinocytes. The cDNA library was differentially screened with labelled cDNA probes synthesized on poly(A)RNA isolated from UV irradiated or nonirradiated keratinocytes. Forty clones were selected and subjected to further analysis, 31 of them are described in this report. Whereas total mRNA synthesis is reduced after UV irradiation or treatment with 4-NQO Northern blot analysis revealed that there is an at least relative increase in the level of mRNAs corresponding to the majority of the isolated cDNA clones. Among these 15 were identified as corresponding to mRNAs for 50K and 56K keratins and for 50K- and 46K-related keratin. In addition, clones were found corresponding to the proteinase inhibitor cystatin A and to the glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Treatment of keratinocytes with the tumor promoter TPA had no effect on the mRNA level for most of the clones except those corresponding to keratins. Our results indicate that in keratinocytes UV irradiation leads to a relative increase in the level of some mRNAs.

Phycomyces blakesleeanus TRP1 gene: organization and functional complementation in Escherichia coli and Saccharomyces cerevisiae

We have cloned the gene encoding the TRPF and TRPC functions of Phycomyces blakesleeanus by complementation of the corresponding activities of Escherichia coli. TRPF also complemented a trpl mutation in Saccharomyces cerevisiae. As in other filamentous fungi, such as Neurospora and Aspergillus spp., the P. blakesleeanus TRPF and TRPC formed part of a trifunctional polypeptide encoded by a single gene (called TRP1). Transcription of TRP1 in P. blakesleeanus did not appear to be regulated by light or by the nutritional status of the culture. The information on the structure and organization of a P. blakesleeanus gene derived from these studies should be useful in devising molecular genetic strategies to analyze the sensory physiology of this organism.

Nucleotide sequence of the gene coding for human factor VII, a vitamin K-dependent protein participating in blood coagulation

Activated factor VII (factor VIIa) is a vitamin K-dependent plasma serine protease that participates in a cascade of reactions leading to the coagulation of blood. Two overlapping genomic clones containing sequences encoding human factor VII were isolated and characterized. The complete sequence of the gene was determined and found to span about 12.8 kilobases. The mRNA for factor VII as demonstrated by cDNA cloning is polyadenylylated at multiple sites but contains only one AAUAAA poly(A) signal sequence. The mRNA can undergo alternative splicing, forming one transcript containing eight segments as exons and another with an additional exon that encodes a larger prepro leader sequence. The latter transcript has no known counterpart in the other vitamin K-dependent proteins. The positions of the introns with respect to the amino acid sequence encoded by the eight essential exons of factor VII are the same as those present in factor IX, factor X, protein C, and the first three exons of prothrombin. These exons code for domains generally conserved among members of this gene family. The comparable introns in these genes, however, are dissimilar with respect to size and sequence, with the exception of intron C in factor VII and protein C. The gene for factor VII also contains five regions made up of tandem repeats of oligonucleotide monomer elements. More than a quarter of the intron sequences and more than a third of the 3' untranslated portion of the mRNA transcript consist of these minisatellite tandem repeats.

Isolation and characterization of the active cDNA of the human cell cycle gene (RCC1) involved in the regulation of onset of chromosome condensation

The human RCC1 gene was cloned after DNA-mediated gene transfer into the tsBN2 cell line, which shows premature chromosome condensation at nonpermissive temperatures (39.5-40 degrees C). This gene codes for a 2.5-kb poly(A)+ RNA that is well conserved in hamsters and humans. We isolated 15 cDNA clones from the Okayama-Berg human cDNA library, and found two that can complement the tsBN2 mutation with an efficiency comparable to that of the genomic DNA clone. The base sequences of these two active cDNA clones differ at the 5' proximal end, yet both have a common open reading frame, encoding a protein of 421 amino acids with a calculated molecular weight of 44,847 and with seven homologous repeated domains of about 60 amino acids. This human RCC1 gene was located to human chromosome 1 using sorted chromosomal fractions.

Products of in vitro cleavage and polyadenylation of simian virus 40 late pre-mRNAs

Formation of mRNA 3' termini involves cleavage of an mRNA precursor and polyadenylation of the newly formed end. Cleavage of simian virus 40 late pre-mRNA in a crude nuclear extract generated two RNAs, 5' and 3' half-molecules. These RNAs were unmodified and linear. The 5' half-molecule contained sequences upstream but not downstream of the poly(A) site and ended in a 3'-terminal hydroxyl. The 3' half-molecules comprised a family of RNAs, each of which contains only sequences downstream of the poly(A) site, and ends in a 5'-terminal phosphate. These RNAs differed only in the locations of their 5' terminus. The 3' terminus of the 5' half-molecule was the adenosine 10 nucleotides downstream of AAUAAA, at the +1 position. The 5' terminus of the longest 3' half-molecule was at +2. Thus, these two RNAs contain every nucleoside and phosphate of the precursor. The existence of these half-molecules demonstrates that endonucleolytic cleavage occurs near the poly(A) site. 5' half-molecules generated in the presence of EDTA (which blocks polyadenylation, but not cleavage) ended at the adenosine at position +1 of the precursor. When incubated in the extract under suitable conditions, they became polyadenylated. 5' half-molecules formed in 3'-dATP-containing reactions contained a single 3'-deoxyadenosine (cordycepin) residue added onto the +1 adenosine and were poor polyadenylation substrates. We infer that the +1 adenosine of the precursor becomes the first A of the poly(A) tract and provides a 3' hydroxyl group to which poly(A) is added posttranscriptionally.

Characterization of two types of histone H2B genes from macronuclei of Tetrahymena thermophila

Two histone H2B gene clones were isolated from macronuclei of Tetrahymena thermophila. Nucleotide sequences of the two clones were highly homologous within the coding region but not in the noncoding region. Comparison of the deduced amino acid sequences between the two clones showed three differences in a total of 121 amino acids. Each of the two clones contained a TAA triplet within the coding region, which appeared to code for a glutamine residue. To demonstrate the existence of histone mRNA containing UAA triplet, nuclease P1 protection mapping using total cellular RNA and nucleotide sequencing of primer extension products were carried out. The results clearly indicated that two cloned histone H2B genes were transcribed, giving rise to the major histone H2B mRNAs with a UAA triplet sequence in frame. The tentative 5'- and 3'-ends of histone H2B mRNAs were determined.

Gerbich blood group deficiency of the Ge:-1,-2,-3 and Ge:-1,-2,3 types. Immunochemical study and genomic analysis with cDNA probes

Human erythrocytes carry several transmembrane glycoproteins, among which the two minor species associated with the blood group Gerbich (Ge) antigens, GP C and GP D, play pivotal role since they interact with the membrane cytoskeleton and contribute to maintain the normal red cell shape. On the red cells from two categories of homozygous donors lacking the Ge determinants (Ge:-1,-2,-3 and Ge:-1,-2,3), GP C and GP D are missing but instead there is a new glycoprotein, easily detected by SDS/polyacrylamide gel electrophoresis, which exhibits some properties shared by GP C and GP D. This was shown by immunochemical analyses with a murine monoclonal antibody, extraction of the glycoproteins by organic solvents and binding studies with the 125I-labelled Lens culinaris lectin. The red cells from obligate heterozygotes for the Ge:-1,-2,-3 condition also carry this new glycoprotein component but in a much lesser amount than expected on the basis of one gene dose response. Using a cDNA probe containing the coding sequence of human GP C and the entire 3' untranslated region of its mRNA, we have demonstrated by Southern analyses that the Ge:-1,-2,-3 and the Ge:-1,-2,3 conditions are associated with a constant 3-kbp deletion within the GP C gene. Similar studies indicated that this gene is present as a unique copy per haploid genome of Ge-positive control donors (Ge:1,2,3). To account for these data and for the glycoprotein profile of Ge-negative erythrocytes, it is proposed that a unique Gerbich gene encodes for GP C and GP D, either by alternative RNA splicing or by different post-translational events, and that, following a 3-kbp deletion within this gene, a new glycoprotein having properties common to GP C and GP D can be produced.

Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit beta-globin mRNA 3' end formation

We previously demonstrated that a critical 35 bp region 3' of the AAUAAA is required for rabbit beta-globin mRNA 3' end formation. Recently, we synthesized and tested sequence elements derived from this region. Here, we report that a GU-rich and a U-rich sequence element are both required for efficient rabbit beta-globin mRNA 3' end formation. The efficiency of processing is restored to the wild-type level when the two elements are placed together and is greatly diminished when only one element is present. The level of 3' end formation is also decreased when the distance between the two elements is expanded. These results demonstrate that the GU-rich and U-rich elements function synergistically to restore efficient mRNA 3' end formation and that they most likely form a single requisite sequence 3' of the AAUAAA. Furthermore, we show that the effect of the GU-rich and U-rich sequence elements is position-dependent.

Requirements for accurate and efficient mRNA 3' end cleavage and polyadenylation of a simian virus 40 early pre-RNA in vitro

Using a pre-RNA containing the simian virus 40 early introns and poly(A) addition site, we investigated several possible requirements for accurate and efficient mRNA 3' end cleavage and polyadenylation in a HeLa cell nuclear extract. Splicing and 3' end formation occurred under the same conditions but did not appear to be coupled in any way in vitro. Like splicing, 3' end cleavage and polyadenylation each required Mg2+, although spermidine could substitute in the cleavage reaction. Additionally, cleavage of this pre-RNA, but not others, was totally blocked by EDTA, indicating that structural features of pre-RNA may affect the ionic requirements of 3' end formation. The ATP analog 3' dATP inhibited both cleavage and polyadenylation even in the presence of ATP, possibly reflecting the coupled nature of these activities. A 5' cap structure appears not to be required for mRNA 3' end processing in vitro because neither the presence or absence of a 5' cap on the pre-RNA nor the addition of cap analogs to reaction mixtures had any effect on the efficiency of 3' end processing. Micrococcal nuclease pretreatment of the nuclear extract inhibited cleavage and polyadenylation. However, restoration of activity was achieved by addition of purified Escherichia coli RNA, suggesting that the inhibition caused by such a nuclease treatment was due to a general requirement for mass of RNA rather than to destruction of a particular nucleic acid-containing component such as a small nuclear ribonucleoprotein.

Structure of the rat platelet factor 4 gene: a marker for megakaryocyte differentiation

A rat platelet factor 4 (PF4) cDNA has been isolated by immunoscreening a g lambda 11 rat megakaryocyte cDNA expression library. Sequence analysis of the rat PF4 cDNA revealed that this megakaryocyte protein is composed of a leader sequence of 29 amino acid residues and a mature protein sequence of 76 amino acid residues. The structure of rat PF4 derived from its cDNA shows a marked homology with the amino acid sequence of human PF4 obtained by classical protein chemistry techniques. This observation is particularly striking with regard to the carboxy-terminal region of rat and human PF4, where 28 of the last 31 C-terminal residues are identical. The rat PF4 gene was obtained from a rat genomic library by using rat PF4 cDNA as a hybridization probe. Sequence analysis showed that the gene is constructed of three exons and two short introns. The transcriptional start site is located 73 base pairs upstream of the translational start codon as judged by S1 nuclease mapping and primer extension. The 5' noncoding region of the gene also exhibited a sequence homologous to the TATA box at -31, as well as a series of direct and inverted repeat sequences and a cluster of 26 T residues at -155 to -218. This latter domain may be involved in regulating PF4 gene expression during megakaryocytopoiesis.

Products of in vitro cleavage and polyadenylation of simian virus 40 late pre-mRNAs

Formation of mRNA 3' termini involves cleavage of an mRNA precursor and polyadenylation of the newly formed end. Cleavage of simian virus 40 late pre-mRNA in a crude nuclear extract generated two RNAs, 5' and 3' half-molecules. These RNAs were unmodified and linear. The 5' half-molecule contained sequences upstream but not downstream of the poly(A) site and ended in a 3'-terminal hydroxyl. The 3' half-molecules comprised a family of RNAs, each of which contains only sequences downstream of the poly(A) site, and ends in a 5'-terminal phosphate. These RNAs differed only in the locations of their 5' terminus. The 3' terminus of the 5' half-molecule was the adenosine 10 nucleotides downstream of AAUAAA, at the +1 position. The 5' terminus of the longest 3' half-molecule was at +2. Thus, these two RNAs contain every nucleoside and phosphate of the precursor. The existence of these half-molecules demonstrates that endonucleolytic cleavage occurs near the poly(A) site. 5' half-molecules generated in the presence of EDTA (which blocks polyadenylation, but not cleavage) ended at the adenosine at position +1 of the precursor. When incubated in the extract under suitable conditions, they became polyadenylated. 5' half-molecules formed in 3'-dATP-containing reactions contained a single 3'-deoxyadenosine (cordycepin) residue added onto the +1 adenosine and were poor polyadenylation substrates. We infer that the +1 adenosine of the precursor becomes the first A of the poly(A) tract and provides a 3' hydroxyl group to which poly(A) is added posttranscriptionally.

Human elongation factor 1 alpha: a polymorphic and conserved multigene family with multiple chromosomal localizations

One of the genes activated in human melanoma cells by the tumor-promoting phorbol ester is that of the elongation factor 1 alpha. A cDNA clone containing the complete 3'-end untranslated region and the nucleotide sequences coding for 227 carboxyterminal amino acids was isolated. Computer-assisted comparison with known sequences of elongation factors from other species revealed homologies up to 73% and 63% on amino acid and nucleotide sequences, respectively. Northern blot analysis of mRNA from unstimulated and phorbol ester-treated cells showed a 3- to 5-fold increase in cytoplasmic elongation factor 1 alpha mRNA after phorbol ester induction. When compared with the phorbol ester-inducible single-copy gene transcripts coding for the tissue-type plasminogen activator, the cellular mRNA content of elongation factor 1 alpha is 30 times higher. By Southern blot analysis experiments on human genomic DNA, a multi-gene family was found showing polymorphisms in restriction endonuclease fragment lengths (RFLP). Several polymorphisms were studied more extensively in the population on more than 100 DNA samples from normal individuals and in three-generation families. In situ hybridization of the cDNA probe to normal human metaphase chromosomes showed multiple chromosomal localizations of the elongation factor gene(s), with peak hybridization on the chromosomes 1, 2, 4, 5, 6, 7, and 15. The estimate of the gene copy number in humans is more than ten copies per (haploid) genome.

In vitro cleavage of the simian virus 40 early polyadenylation site adjacent to a required downstream TG sequence

Exogenous RNA containing the simian virus 40 early polyadenylation site was efficiently and accurately polyadenylated in in vitro nuclear extracts. Correct cleavage required ATP. In the absence of ATP, nonpoly(A)+ products accumulated which were 18 to 20 nucleotides longer than the RNA generated by correct cleavage; the longer RNA terminated adjacent to the downstream TG element required for polyadenylation. In the presence of ATP analogs, alternate cleavage was not observed; instead, correct cleavage without poly(A) addition occurred. ATP-independent cleavage of simian virus 40 early RNA had many of the same properties as correct cleavage including requirements for an intact AAUAAA element, a proximal 3' terminus, and extract small nuclear ribonucleoproteins. This similarity in reaction parameters suggested that ATP-independent cleavage is an activity of the normal polyadenylation machinery. The ATP-independent cleavage product, however, did not behave as an intermediate in polyadenylation. The alternate RNA did not preferentially chase into correctly cleaved material upon readdition of ATP; instead, poly(A) was added to the 3' terminus of the cleaved RNA during a chase. Purified ATP-independent cleavage RNA, however, was a substrate for correct cleavage when reintroduced into the nuclear extract. Thus, alternate cleavage of polyadenylation sites adjacent to a required downstream sequence element is directed by the polyadenylation machinery in the absence of ATP.

Expression of a human cytomegalovirus late gene is posttranscriptionally regulated by a 3'-end-processing event occurring exclusively late after infection

A phenomenon of posttranscriptional regulation has been previously identified in cytomegalovirus-infected human fibroblast cells (Wathen and Stinski, J. Virol. 41:462, 1982). A region typifying this phenomenon has been located within the large unique component of the viral genome (map units 0.408 to 0.423). Even though this transcriptional unit was highly transcribed at early times after infection, mRNAs from this region were only detectable on the polyribosomes after viral DNA replication. Thus, this region is believed to code for a late gene. Single-strand-specific nuclease mapping experiments of viral transcripts established that the transcriptional initiation sites and the 5' ends of a downstream exon were identical at early and late times. However, the late transcripts differed from the early transcripts by the processing of the 3' end of the viral RNAs. This involved either the removal of a distinct region of the transcript by the selection of an upstream cleavage and polyadenylation site or the differential splicing of the RNA molecule. The upstream cleavage and polyadenylation site was identified by nuclease mapping analyses and DNA sequencing. The 3'-end processing of these transcripts is necessary for the detection of these viral RNAs within the cytoplasm of the infected cell. We propose that human cytomegalovirus either codes for a factor(s) that is involved in the 3'-end-processing event at late times after infection or stimulates the synthesis of a host cell factor(s) involved in this complex regulatory event. This level of regulation may have an influence on the types of cells that permit productive cytomegalovirus replication.

Splice commitment dictates neuron-specific alternative RNA processing in calcitonin/CGRP gene expression

The calcitonin/CGRP gene is a complex transcription unit in which developmentally regulated cell-specific alternative RNA processing results in the production of CGRP mRNA in neurons, and of calcitonin mRNA in thyroid C cells. Alternative poly(A) site selection and exon splicing lead to the production of these alternative mature transcripts. The wild-type and a series of mutated calcitonin/CGRP genes were expressed in heterologous cell types, which produced predominantly calcitonin or CGRP mRNA. The results of these studies suggest that neurons express machinery or a factor that determines a specific alternative splicing pathway and consequently its associated alternative poly(A) site selection. It is hypothesized that a splice commitment regulatory factor might modulate pre-mRNA secondary structure, revealing a cryptic splice site required to generate CGRP mRNA in the brain.

Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas

A new promoter of the human c-myc gene called P0, with multiple RNA start sites, was mapped over 500 bases upstream of the two previously identified promoters, P1 and P2. Sequencing full-length cDNA clones of P0 RNAs revealed two open reading frames upstream of that for the P64c-myc protein. P0 RNA is located on polyribosomes and released by puromycin, indicating that it functions as an mRNA. In vitro translation of RNA synthesized from the cloned cDNAs predicts that P0 transcripts are translated into a novel 12.5-kilodalton protein corresponding to the first open reading frame. The regulation of P0 RNA was studied in the B-cell lymphoma cell line Manca, in which only the translocated c-myc allele lacking exon 1 was thought to be active. However, we found that P0 transcription and the DNase I-hypersensitive site associated with this promoter persist on the untranslocated allele, even though P1/P2 transcription as measured by a nuclear runoff assay was repressed. These results suggest that allelic exclusion of c-myc expression in this B-cell lymphoma is caused by a repression of transcription which is specific to the P1/P2 promoters. We previously reported a block to elongation of transcription near the 3' end of exon 1 in the wild-type c-myc gene, which results in an excess of exon 1 over exon 2 transcription (5a). In contrast, we found that in the Daudi B-cell lymphoma, which retains exon 1 in the active allele, equimolar transcription of exons 1 and 2 occurs. This result suggests a model for the activation of c-myc in B-cell lymphomas.

Structure of the rat platelet factor 4 gene: a marker for megakaryocyte differentiation

A rat platelet factor 4 (PF4) cDNA has been isolated by immunoscreening a g lambda 11 rat megakaryocyte cDNA expression library. Sequence analysis of the rat PF4 cDNA revealed that this megakaryocyte protein is composed of a leader sequence of 29 amino acid residues and a mature protein sequence of 76 amino acid residues. The structure of rat PF4 derived from its cDNA shows a marked homology with the amino acid sequence of human PF4 obtained by classical protein chemistry techniques. This observation is particularly striking with regard to the carboxy-terminal region of rat and human PF4, where 28 of the last 31 C-terminal residues are identical. The rat PF4 gene was obtained from a rat genomic library by using rat PF4 cDNA as a hybridization probe. Sequence analysis showed that the gene is constructed of three exons and two short introns. The transcriptional start site is located 73 base pairs upstream of the translational start codon as judged by S1 nuclease mapping and primer extension. The 5' noncoding region of the gene also exhibited a sequence homologous to the TATA box at -31, as well as a series of direct and inverted repeat sequences and a cluster of 26 T residues at -155 to -218. This latter domain may be involved in regulating PF4 gene expression during megakaryocytopoiesis.

The AAUAAA sequence is required both for cleavage and for polyadenylation of simian virus 40 pre-mRNA in vitro

The sequence AAUAAA is found near the polyadenylation site of eucaryotic mRNAs. This sequence is required for accurate and efficient cleavage and polyadenylation of pre-mRNAs in vivo. In this study we show that synthetic simian virus 40 late pre-mRNAs are cleaved and polyadenylated in vitro in a HeLa cell nuclear extract, and that cleavage in vitro is abolished by each of four different single-base changes in AAUAAA. In this same extract, precleaved RNAs (RNAs with 3' termini at the polyadenylation site) are efficiently polyadenylated. This in vitro polyadenylation reaction also requires the AAUAAA sequence.

Expression of hepatitis B viral core region in mammalian cells

We studied the expression of the core region of the hepatitis B virus genome in mammalian cells with recombinant plasmid vectors. Stably transformed rat fibroblast cell lines were established by transfection with vectors containing subgenomic and genome-length hepatitis B virus DNA, followed by G418 selection. The RNA transcripts directed by the core region were characterized by Northern blot hybridization and S1 nuclease mapping. Using the chloramphenicol acetyltransferase gene expression system, the promoter activity located upstream of the core open reading frame was confirmed. The synthesis of core and e polypeptides was studied with a commercial radioimmunoassay. These studies show that partial deletion of the precore sequences abolished secretion of the e antigen, but there was pronounced synthesis of the core antigen in transfected cells.

Sequences near the 3' secretion-specific polyadenylation site influence levels of secretion-specific and membrane-specific IgG2b mRNA in myeloma cells

The expressed immunoglobulin gamma 2b (IgG2b) heavy-chain gene of 4T001 was cloned into the shuttle vector pSV2-gpt and transfected into myeloma J558L and lymphoma A20.2J. Northern blots indicated that the transfected gamma 2b gene was processed in a manner similar to the endogenous heavy chain in both lymphoma and myeloma cells. To identify sequences important for immunoglobulin mRNA processing, we constructed deletions around the secretion-specific polyadenylation site and introduced the deleted genes into J558L cells. The BAL deletion lacked 670 base pairs of intervening sequence between secreted and membrane regions; the Kpn deletion lacked 830 base pairs in this region. J558L cells transfected with either the entire gamma 2b gene or the delta BAL vector produced predominantly secretion-specific gamma 2b mRNA and protein. J558L cells transfected with the delta Kpn vector produced approximately equimolar amounts of secretion-specific and membrane-specific gamma 2b mRNA. Both 55,000-dalton secreted and 62,000-dalton putative surface IgG2b proteins were detected in the delta Kpn transfectants. We conclude that sequences absent in the Kpn deletion but present in the BAL deletion exert an important role in the production of secretion-specific mRNA. The Kpn deletion removes the normal site of cleavage and poly(A) addition, and it is possible that it is the absence of this site which changes the processing pattern. Alternatively, it is possible that sequences absent in the Kpn deletion but present in the BAL deletion function in regulating the production of predominantly secretion-specific mRNA in myeloma cells. The possible role of a highly conserved sequence found in this region is discussed.

Sequence homologies among the three yolk polypeptide (Yp) genes in Drosophila melanogaster

To identify candidates for cis-acting sequences that regulate the sex-, stage-, and cell-specific expression of three coordinately regulated yolk polypeptide genes (Yp) in Drosophila melanogaster, we have mapped the Yp3 transcript, sequenced a 4278 bp DNA fragment containing the Yp3 gene, compared Yp3 region sequences to corresponding parts of Yp1 and Yp2, and compared the predicted amino acid sequence of YP3 to YP1 and YP2. The results showed that the Yps are largely homologous in translated regions, especially in the 3' half of the genes. Untranscribed flanking regions had little homology. A conserved inverted repeat (the H-box) has homology both to vertebrate steroid hormone receptor binding sites and to the ecdysone control region of Drosophila's hsp23. These results identify sequences to mutate in order to define elements that regulate Yp gene expression and govern YP polypeptide function.

Plant cells do not properly recognize animal gene polyadenylation signals

We have introduced chimeric genes containing polyadenylation signals from a human gene and two animal virus genes into tobacco cells. We see, in all three cases, inefficient and 'aberrant' utilization of the foreign polyadenylation signals. We find that a chimeric gene carrying the polyadenylation site of the human growth hormone gene is polyadenylated at three sites in the vicinity of the site that is polyadenylated in human cells. A chimeric gene containing the polyadenylation site from the adenovirus 5 E1A gene is polyadenylated at a site 11 bases downstream from that reported in animal cells. A gene carrying the polyadenylation site from the SV40 early region is polyadenylated some 80 bases upstream from the site that is polyadenylated in animal cells. In all three cases, related mRNAs ending at flanking 'authentic' plant polyadenylation sites can be detected, indicating that the foreign polyadenylation signals are inefficiently utilized in tobacco cells.

Conserved 12-bp element downstream from mRNA polyadenylation sites

Sequences downstream from the AATAAA motif in a number of cellular and viral transcription units have been compared. A 12-bp conserved element was identified in approximately half of the cases studied, and a consensus sequence TTGANNNTTTTTT was derived from a comparison of 74 such sequences. This element is located immediately (5-20 bp) downstream from the poly(A)-addition site in every case where this is known, and it is suggested that this element may be involved in the cleavage/polyadenylation reaction. This proposal is consistent with published studies on deletion mutants of downstream regions.

Requirements for accurate and efficient mRNA 3' end cleavage and polyadenylation of a simian virus 40 early pre-RNA in vitro

Using a pre-RNA containing the simian virus 40 early introns and poly(A) addition site, we investigated several possible requirements for accurate and efficient mRNA 3' end cleavage and polyadenylation in a HeLa cell nuclear extract. Splicing and 3' end formation occurred under the same conditions but did not appear to be coupled in any way in vitro. Like splicing, 3' end cleavage and polyadenylation each required Mg2+, although spermidine could substitute in the cleavage reaction. Additionally, cleavage of this pre-RNA, but not others, was totally blocked by EDTA, indicating that structural features of pre-RNA may affect the ionic requirements of 3' end formation. The ATP analog 3' dATP inhibited both cleavage and polyadenylation even in the presence of ATP, possibly reflecting the coupled nature of these activities. A 5' cap structure appears not to be required for mRNA 3' end processing in vitro because neither the presence or absence of a 5' cap on the pre-RNA nor the addition of cap analogs to reaction mixtures had any effect on the efficiency of 3' end processing. Micrococcal nuclease pretreatment of the nuclear extract inhibited cleavage and polyadenylation. However, restoration of activity was achieved by addition of purified Escherichia coli RNA, suggesting that the inhibition caused by such a nuclease treatment was due to a general requirement for mass of RNA rather than to destruction of a particular nucleic acid-containing component such as a small nuclear ribonucleoprotein.

Cloning and molecular analysis of the ornithine carbamoyl transferase gene of Aspergillus niger

We have cloned the gene encoding ornithine carbamoyl transferase (OCTase) from Aspergillus niger. The structure and complete nucleotide sequence of this gene have been determined. The gene encodes an mRNA of 1.3 kb. The transcription unit contains an open reading frame of 1110 nucleotides (nt) which shows strong homology to the OCTase of Aspergillus nidulans along most of its length. The N terminus, which shows little or no homology to other OCTases, is highly basic and is probably involved in mitochondrial targeting.

Myeloma mutant with a novel 3' flanking region: loss of normal sequence and insertion of repetitive elements leads to decreased transcription but normal processing of the alpha heavy-chain gene products

We isolated and characterized LP1.2, a mouse myeloma mutant with a deletion of at least 4 kilobases (kb) immediately 3' of the alpha gene and introduction of at least 5 kb of novel (nonimmunoglobulin) sequence in its place. A 6.2-kb genomic EcoRI fragment from the mutated allele was cloned, and a subfragment was sequenced. The deletion begins 11 base pairs (bp) beyond the normal site of cleavage and polyadenylation for the secreted form of alpha mRNA. A short direct repeat, eight copies of the 17-mer GCCT ATAGAAGTAAGGA, is located at the junction of the alpha and novel sequences. The first 4 bp of the 17-mer are identical to the last 4 bp of the alpha sequence. Novel sequences downstream of the direct repeats in LP1.2 include a low-copy-number sequence flanked by two distinct, highly repetitive elements. The low-copy-number portion of the novel sequence appears on a single 30-kb EcoRI fragment in several myelomas and in liver DNA; one copy of this fragment has rearranged in cell line W3129, and this allele has rearranged a second time in LP1.2. LP1.2 contains low levels of apparently normal alpha protein and mRNA. The S1 nuclease protection of nuclear and cytoplasmic RNAs shows that cleavage and polyadenylation are efficient and accurate and that they occur without the accumulation of aberrant transcripts. Alpha transcription in isolated nuclei is decreased sevenfold in LP1.2 relative to its parent, which accounts for the low steady-state levels of cytoplasmic alpha mRNA and protein in LP1.2. Decreased alpha transcription could result either from the deletion of a positive regulator in the 3' flanking region or from the introduction of novel sequences which exert a negative effect.

Complete nucleotide sequence and genome organization of bovine parvovirus

We determined the complete nucleotide sequence of bovine parvovirus (BPV), an autonomous parvovirus. The sequence is 5,491 nucleotides long. The terminal regions contain nonidentical imperfect palindromic sequences of 150 and 121 nucleotides. In the plus strand, there are three large open reading frames (left ORF, mid ORF, and right ORF) with coding capacities of 729, 255, and 685 amino acids, respectively. As with all parvoviruses studied to date, the left ORF of BPV codes for the nonstructural protein NS-1 and the right ORF codes for the major parts of the three capsid proteins. The mid ORF probably encodes the major part of the nonstructural protein NP-1. There are promoterlike sequences at map units 4.5, 12.8, and 38.7 and polyadenylation signals at map units 61.6, 64.6, and 98.5. BPV has little DNA homology with the defective parvovirus AAV, with the human autonomous parvovirus B19, or with the other autonomous parvoviruses sequenced (canine parvovirus, feline panleukopenia virus, H-1, and minute virus of mice). Even though the overall DNA homology of BPV with other parvoviruses is low, several small regions of high homology are observed when the amino acid sequences encoded by the left and right ORFs are compared. From these comparisons, it can be shown that the evolutionary relationship among the parvoviruses is B19 in equilibrium with AAV in equilibrium with BPV in equilibrium with MVM. The highly conserved amino acid sequences observed among all parvoviruses may be useful in the identification and detection of parvoviruses and in the design of a general parvovirus vaccine.

In vitro expression of two proteins from overlapping reading frames in a eukaryotic DNA sequence

The in vitro expression of two distinct proteins from overlapping reading frames in a sequence of rainbow trout genomic DNA has been demonstrated. In vitro transcription of DNA sequences, cloned in a plasmid under the control of Salmonella phage 6 polymerase promoter, led to the synthesis of two distinct and functional mRNAs corresponding to the protamine mRNA and also to another overlapping mRNA, termed Y. These mRNAs were translated in an mRNA-dependent rabbit reticulocyte lysate cell free system which synthesized the corresponding protein products. Similarities between the synthesized Pro-rich protein Y and three proline-rich proteins, the human salivary Pro-rich protein, the avian sarcoma virus protein P19 and the myc oncogene product, were evident and the significance of these findings is discussed. A synthetic oligonucleotide which is complementary to a sequence corresponding to a region of the Y protein mRNA, but upstream (5') of the transcribed protamine mRNA, hybridized faintly and only to trout brain RNA. However, more sensitive primer extension studies utilizing the Y-specific oligonucleotide detected several Y-related mRNAs in trout brain.

In vitro cleavage of the simian virus 40 early polyadenylation site adjacent to a required downstream TG sequence

Exogenous RNA containing the simian virus 40 early polyadenylation site was efficiently and accurately polyadenylated in in vitro nuclear extracts. Correct cleavage required ATP. In the absence of ATP, nonpoly(A)+ products accumulated which were 18 to 20 nucleotides longer than the RNA generated by correct cleavage; the longer RNA terminated adjacent to the downstream TG element required for polyadenylation. In the presence of ATP analogs, alternate cleavage was not observed; instead, correct cleavage without poly(A) addition occurred. ATP-independent cleavage of simian virus 40 early RNA had many of the same properties as correct cleavage including requirements for an intact AAUAAA element, a proximal 3' terminus, and extract small nuclear ribonucleoproteins. This similarity in reaction parameters suggested that ATP-independent cleavage is an activity of the normal polyadenylation machinery. The ATP-independent cleavage product, however, did not behave as an intermediate in polyadenylation. The alternate RNA did not preferentially chase into correctly cleaved material upon readdition of ATP; instead, poly(A) was added to the 3' terminus of the cleaved RNA during a chase. Purified ATP-independent cleavage RNA, however, was a substrate for correct cleavage when reintroduced into the nuclear extract. Thus, alternate cleavage of polyadenylation sites adjacent to a required downstream sequence element is directed by the polyadenylation machinery in the absence of ATP.

Expression of a human cytomegalovirus late gene is posttranscriptionally regulated by a 3'-end-processing event occurring exclusively late after infection

A phenomenon of posttranscriptional regulation has been previously identified in cytomegalovirus-infected human fibroblast cells (Wathen and Stinski, J. Virol. 41:462, 1982). A region typifying this phenomenon has been located within the large unique component of the viral genome (map units 0.408 to 0.423). Even though this transcriptional unit was highly transcribed at early times after infection, mRNAs from this region were only detectable on the polyribosomes after viral DNA replication. Thus, this region is believed to code for a late gene. Single-strand-specific nuclease mapping experiments of viral transcripts established that the transcriptional initiation sites and the 5' ends of a downstream exon were identical at early and late times. However, the late transcripts differed from the early transcripts by the processing of the 3' end of the viral RNAs. This involved either the removal of a distinct region of the transcript by the selection of an upstream cleavage and polyadenylation site or the differential splicing of the RNA molecule. The upstream cleavage and polyadenylation site was identified by nuclease mapping analyses and DNA sequencing. The 3'-end processing of these transcripts is necessary for the detection of these viral RNAs within the cytoplasm of the infected cell. We propose that human cytomegalovirus either codes for a factor(s) that is involved in the 3'-end-processing event at late times after infection or stimulates the synthesis of a host cell factor(s) involved in this complex regulatory event. This level of regulation may have an influence on the types of cells that permit productive cytomegalovirus replication.

Small nuclear RNAs from Saccharomyces cerevisiae: unexpected diversity in abundance, size, and molecular complexity

Previous work showed that the simple eukaryote Saccharomyces cerevisiae contains a group of RNAs with the general structural properties predicted for small nuclear RNAs (snRNAs), including possession of the characteristic trimethylguanosine 5'-terminal cap. It was also demonstrated that, unlike their metazoan counterparts, the yeast snRNAs are present in low abundance (200-500 molecules per haploid cell). We have now used antibody directed against the 5' cap to investigate the total set size of snRNAs in this organism. We present evidence that the number of distinct yeast snRNAs is on the order of several dozen, that the length of the capped RNAs can exceed 1000 nucleotides, and that the relative abundance of a subset of these RNAs is 1/5th to 1/20th that of the class of snRNAs described previously. These findings suggest that the six highly abundant species of snRNAs (U1-U6) typically reported in metazoans may represent a serious underestimation of the total diversity of snRNAs in eukaryotes.

The ATP synthase subunit 9 gene of Aspergillus nidulans: sequence and transcription

We have determined the nucleotide sequence of the Aspergillus nidulans nuclear gene oliC31, which encodes subunit 9 of mitochondrial ATP synthase. The open reading frame contains no introns and specifies a predicted protein of 143 amino acids comprising a pre-sequence of 62 residues and a mature protein of 81 residues. The amino acid homology with the equivalent Neurospora crassa protein is 50% for the pre-sequence and 80% for the mature protein. A comparison with this and other imported mitochondrial proteins has revealed conserved regions which may be important for transport or subsequent processing. Multiple transcription initiation and polyadenylation sites have been identified. The promoter region of the oliC31 gene is characterised by long pyrimidine-rich tracts preceding the transcription initiation sites.

Molecular cloning of the human T-lymphocyte surface CD2 (T11) antigen

CD2 (T11, sheep erythrocyte receptor) is a surface antigen of the human T-lymphocyte lineage. cDNA clones encoding CD2 have been isolated by using the purified, denatured CD2 to raise a rat antiserum. Positive clones were recognized in a phage lambda gt11 expression library prepared from the human leukemia T-cell line J6. The DNA sequence contained an open reading frame encoding 360 amino acids. The N-terminal 24 amino acids were characteristic of a signal peptide and were followed by a region that matched all 25 residues of the CD2 N terminus previously determined by amino acid sequencing. The predicted amino acid sequence is consistent with that of a transmembrane glycoprotein containing three potential N-glycosylation sites on the N-terminal side of a 26-amino acid hydrophobic segment. There is a large cytoplasmic domain of 125 amino acids that is rich in proline and in basic residues. RNA blot-hybridization analysis demonstrated hybridization only in those T cells that were positive for surface CD2 antigen. There are limited regions of sequence similarity to members of the immunoglobulin supergene family.

Two soybean ribulose-1,5-bisphosphate carboxylase small subunit genes share extensive homology even in distant flanking sequences

Soybean contains a multigene family which encodes the small subunit of ribulose-1,5-bisphosphate carboxylase (RuBPCss). A member of this gene family, SRS4, has been isolated from a soybean genomic DNA library. Its nucleotide sequence has been determined and compared to the sequence of SRS1, a previously characterized RuBPCss gene from soybean. Relevant regulatory sequences such as the PuPuCCAAT boxes, TATA box, the actual start of transcription and poly A addition sites are conserved between the two genes. Using a gene specific synthetic probe to the 3' flanking region the steady state mRNA levels of SRS4, like SRS1, are shown to be very high in light grown soybean seedlings and low in seedlings grown in darkness. SRS1 and SRS4 are very closely related, the three exons being 96%, 93% and 96.5% homologous in nucleotide sequence. The polypeptide sequences are nearly identical with only one amino acid change in each of the three exons encoding the 178 amino acid precursor polypeptide. The two introns are about 75% homologous and the flanking regions are more than 85% homologous (700 base pairs on the 5' end and 300 base pairs on the 3' end). Furthermore, hybridization studies between lambda clones containing the SRS1 and SRS4 genes reveal that a region of strong homology extends at least 4 kb on the 5' end and about 1.1 kb on the 3' end. We propose that these two genes may be alloalleles or homeologous alleles. This proposal is consistent with soybean having an allotetraploid origin, and would imply that the divergence of two ancient Papilionoidae species gave rise to these two genes.

Nucleotide sequence of a cDNA clone encoding Scylliorhinus caniculus protamine Z2

A cDNA library was constructed from a protamine-enriched fraction of dogfish (Scylliorhinus caniculus) mRNA. The nucleotide sequence of a 440-bp insert was determined, and its produced protein sequence confirmed its identification as a cysteine-rich protamine Z2 [Martinage, A., Gusse, M., Belaiche, D., Sautiere, P. and Chevaillier, P. (1985) Biochim. Biophys. Acta 831, 172-178]. The frequency of utilization of the different triplets coding for arginine, which represents 30-70% of the total amino acid residues for trout, mouse and dogfish protamines, is discussed. An alternative repetitive sequence of CGC-AGG was found in the N terminus of the protein. Analysis of the 3' flanking region after the mRNA-terminating TAA codon identified an inverted repeat sequence and an ACCA sequence, which may be possible vestiges of a histone-like termination signal.

Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas

A new promoter of the human c-myc gene called P0, with multiple RNA start sites, was mapped over 500 bases upstream of the two previously identified promoters, P1 and P2. Sequencing full-length cDNA clones of P0 RNAs revealed two open reading frames upstream of that for the P64c-myc protein. P0 RNA is located on polyribosomes and released by puromycin, indicating that it functions as an mRNA. In vitro translation of RNA synthesized from the cloned cDNAs predicts that P0 transcripts are translated into a novel 12.5-kilodalton protein corresponding to the first open reading frame. The regulation of P0 RNA was studied in the B-cell lymphoma cell line Manca, in which only the translocated c-myc allele lacking exon 1 was thought to be active. However, we found that P0 transcription and the DNase I-hypersensitive site associated with this promoter persist on the untranslocated allele, even though P1/P2 transcription as measured by a nuclear runoff assay was repressed. These results suggest that allelic exclusion of c-myc expression in this B-cell lymphoma is caused by a repression of transcription which is specific to the P1/P2 promoters. We previously reported a block to elongation of transcription near the 3' end of exon 1 in the wild-type c-myc gene, which results in an excess of exon 1 over exon 2 transcription (5a). In contrast, we found that in the Daudi B-cell lymphoma, which retains exon 1 in the active allele, equimolar transcription of exons 1 and 2 occurs. This result suggests a model for the activation of c-myc in B-cell lymphomas.

Primary structure of an extracellular matrix proteoglycan core protein deduced from cloned cDNA

The core protein of a small chondroitin/dermatan sulfate proteoglycan expressed by human fibroblasts and present in extracellular matrices in association with collagen has been cloned from a lambda gt11 fibroblast cDNA library. cDNA clones were isolated by use of antibodies specific for the intact proteoglycan and antibodies against a peptide synthesized on the basis of the amino-terminal sequence of the core protein. A 1.8-kilobase cDNA was found to code for a prepro core protein composed of a signal peptide, a propeptide, and a mature core protein of 329 amino acids. The amino-terminal amino acid sequence deduced from the cDNA sequence was identical to that previously obtained by protein sequencing. The core protein contains three Ser-Gly dipeptide sequences, of which one is substituted with glycosaminoglycan. A protein data base homology search established the core protein sequence is a unique sequence distinct from published amino acid sequences. RNA blot hybridizations, performed using the cloned cDNA as a probe, revealed two related transcripts of 1.6 and 1.9 kilobases in RNA from both human fibroblast and placental tissue. Hybridization of genomic DNA restriction fragments suggested that there is one gene for the core protein of this proteoglycan and possibly one other closely related gene. Availability of the cloned cDNA for the proteoglycan now makes it possible to apply methods of molecular biology to study the collagen-binding and cell attachment-inhibiting properties of this proteoglycan.

The relationship between Sm and RNP antigens

The relationship between the antigenic proteins of Sm and RNP is not clear. To further clarify their relationship, we examined sera found monospecific by counterimmunoelectrophoresis (CIEP) for anti-Sm or anti-RNP with the more sensitive techniques of immunoblotting, radioimmunoprecipitation, or enzyme immunoassay (EIA). The same eight unique problems were precipitated by both anti-Sm and anti-RNP in radioimmunoprecipitation. They had molecular weights (MWs) of 11, 13, 17, 18, 24, 26, 28, and 68 kDa. The 17, 18, and 28 kDa bands were more intense with anti-RNP. Immunoblotting with anti-Sm and anti-RNP also recognized similar proteins with MWs of 14, 17, 25, 28, 29, 30, 36, 38, and 68 kDa. Anti-Sm resulted in more intense 14, 28, 29, and 30 kDa bands, while anti-RNP gave maximum intensity of the 14, 36, 38, and 68 kDa bands. The band intensity pattern differences were more easily appreciated with immunoblotting than with radioimmunoprecipitation. RNase, heat, and urea caused a similar diminution of antigen reactivity with both anti-Sm and anti-RNP on immunoblotting, but eliminated immunoprecipitability only of RNP on immunodiffusion. The great similarities between Sm and RNP suggest several possibilities: Anti-Sm and anti-RNP antibodies coexist in the same patients; and the more sensitive techniques of immunoblotting and radioimmunoprecipitation detect both precipitating and nonprecipitating antibodies while only precipitating antibodies are detected by immunodiffusion. Sm and RNP may represent different determinants on the same macromolecular complex. Sm and RNP may be cross-reacting determinants on distinct molecules.

ATTAAA as well as downstream sequences are required for RNA 3'-end formation in the E3 complex transcription unit of adenovirus

We mapped the location of the E3A RNA 3' end site in the E3 transcription unit of adenovirus 2. The procedure used was nuclease-gel analysis with 32P-labeled RNA probes. The poly(A) addition sites were microheterogeneous and were located approximately 17 to 29 nucleotides downstream from an ATTAAA sequence. To identify the sequences that make up the E3A RNA 3' end signal, we constructed five viable virus mutants with deletions in or near the E3A RNA 3' end site. The mutants were analyzed for E3A RNA 3' end formation in vivo. No effect was observed from a 47-base-pair (bp) deletion (dl716) or a 72-bp deletion (dl714) located 22 and 19 nucleotides, respectively, upstream of the ATTAAA. In contrast, E3A RNA 3' end formation was abolished by a 554-bp deletion (dl708) that removes both the ATTAAA and the poly(A) addition sites, a 124-bp deletion (dl713) that removes the ATTAAA but leaves the poly(A) addition sites, and a 65-bp deletion (dl719) that leaves the ATTAAA but removes the poly(A) addition sites. These results indicate that the ATTAAA, as well as downstream sequences, including the poly(A) addition sites, are required for E3A RNA 3' end formation.

Definition of essential sequences and functional equivalence of elements downstream of the adenovirus E2A and the early simian virus 40 polyadenylation sites

In addition to the highly conserved AATAAA sequence, there is a requirement for specific sequences downstream of polyadenylic acid [poly(A)] cleavage sites to generate correct mRNA 3' termini. Previous experiments demonstrated that 35 nucleotides downstream of the E2A poly(A) site were sufficient but 20 nucleotides were not. The construction and assay of bidirectional deletion mutants in the adenovirus E2A poly(A) site indicates that there may be redundant multiple sequence elements that affect poly(A) site usage. Sequences between the poly(A) site and 31 nucleotides downstream were not essential for efficient cleavage. Further deletion downstream (3' to +31) abolished efficient cleavage in certain constructions but not all. Between +20 and +38 the sequence T(A/G)TTTTT was duplicated. Function was retained when one copy of the sequence was present, suggesting that this sequence represents an essential element. There may also be additional sequences distal to +43 that can function. To establish common features of poly(A) sites, we also analyzed the early simian virus 40 (SV40) poly(A) site for essential sequences. An SV40 poly(A) site deletion that retained 18 nucleotides downstream of the cleavage site was fully functional while one that retained 5 nucleotides downstream was not, thus defining sequences required for cleavage. Comparison of the SV40 sequences with those from E2A did not reveal significant homologies. Nevertheless, normal cleavage and polyadenylation could be restored at the early SV40 poly(A) site by the addition of downstream sequences from the adenovirus E2A poly(A) site to the SV40 +5 mutant. The same sequences that were required in the E2A site for efficient cleavage also restored activity to the SV40 poly(A) site.

Identification of a sequence element on the 3' side of AAUAAA which is necessary for simian virus 40 late mRNA 3'-end processing

Our previous studies of the 3'-end processing of simian virus 40 late mRNAs indicated the existence of an essential element (or elements) downstream of the AAUAAA signal. We report here the use of transient expression analysis to study a functional element which we located within the sequence AGGUUUUUU, beginning 59 nucleotides downstream of the recognized signal AAUAAA. Deletion of this element resulted in (i) at least a 75% drop in 3'-end processing at the normal site and (ii) appearance of readthrough transcripts with alternate 3' ends. Some flexibility in the downstream position of this element relative to the AAUAAA was noted by deletion analysis. Using computer sequence comparison, we located homologous regions within downstream sequences of other genes, suggesting a generalized sequence element. In addition, specific complementarity is noted between the downstream element and U4 RNA. The possibility that this complementarity could participate in 3'-end site selection is discussed.

Affinity chromatography of splicing complexes: U2, U5, and U4 + U6 small nuclear ribonucleoprotein particles in the spliceosome

The splicing process, which removes intervening sequences from messenger RNA (mRNA) precursors is essential to gene expression in eukaryotic cells. This site-specific process requires precise sequence recognition at the boundaries of an intervening sequence, but the mechanism of this recognition is not understood. The splicing of mRNA precursors occurs in a multicomponent complex termed the spliceosome. Such an assembly of components is likely to play a key role in specifying those sequences to be spliced. In order to analyze spliceosome structure, a stringent approach was developed to obtain splicing complexes free of cellular contaminants. This approach is a form of affinity chromatography based on the high specificity of the biotin-streptavidin interaction. A minimum of three subunits: U2, U5, and U4 + U6 small nuclear ribonucleoprotein particles were identified in the 35S spliceosome structure, which also contains the bipartite RNA intermediate of splicing. A 25S presplicing complex contained only the U2 particle. The multiple subunit structure of the spliceosome has implications for the regulation of a splicing event and for its possible catalysis by ribozyme or ribozymes.

U1, U2, and U6 small nuclear ribonucleoproteins (snRNPs) are associated with large nuclear RNP particles containing transcripts of an amplified gene in vivo

Nuclear ribonucleoprotein (RNP) complexes that contain intact transcripts of the amplified gene for CAD, the multifunctional protein that initiates UMP synthesis in Syrian hamster cells, have been released from nuclei of Syrian hamster cells as large particulate structures that sediment at the 200S region in a sucrose gradient. By the technique of RNA hybridization, we have shown that U1, U2, and U6 small nuclear RNAs (snRNAs) cosediment with the large RNP particles in the sucrose gradients. Autoimmune sera from systemic lupus erythematosus and mixed connective tissue disease patients, characterized as anti-(U1)RNP, have further been shown to immunoprecipitate CAD RNA along with U1 and U2 snRNAs from the fractionated nuclear 200S RNP particles. We conclude that U1, U2, and U6 snRNPs are integral constituents of the 200S RNP particles. The requirement of snRNPs for RNA processing that evidently occurs on RNP particles has been recently demonstrated. Our results thus suggest that the 200S RNPs are structurally and functionally close to the native particles on which RNA processing occurs.