Nuclear RNA is spliced in the absence of poly(A) addition

ANTITUMOUR ACTIVITY OF CORDYCEPIN IN MICE

1. The antitumour effect of orally administered cordycepin, a component isolated from water extracts of Cordyceps sinensis, was examined in mice inoculated with B16 melanoma (B16-BL6) cells. 2. B16-BL6 (1 x 10(6)) cells were inoculated subcutaneously into the right footpad of mice. At 2 weeks after the cell inoculation, the enlarged primary tumour lump was weighed. Cordycepin (0, 5 and 15 mg/kg per day) was administered orally to the mice for 2 weeks from the date of tumour inoculation. Cordycepin (15 mg/kg per day) significantly reduced by 36% the wet weight of the primary tumour lump compared to that of the untreated control mice, without any loss of bodyweight or systemic toxicity. 3. Cordycepin (15 mg/kg per day) administered orally for 2 weeks inhibited the tumour enlargement in the right thigh inoculated with B16-BL6 cells premixed with extracellular matrix (Matrigel). 4. These results indicate that orally administered cordycepin inhibits melanoma cell growth in mice with no adverse effects.

Cordycepin in Schizosaccharomyces pombe: effects on the wild type and phenotypes of mutants resistant to the drug

The adenosine analogue cordycepin (3'-deoxyadenosine) inhibits growth and causes aberrant cell morphology in the fission yeast, Schizosaccharomyces pombe. Exogenously added thiamine, the pyrimidine moiety of the thiamine molecule, and adenine alleviate its growth-disturbing effect. At concentrations that do not inhibit growth, the drug reduces mating and sporulation and causes a decrease in the mRNA level of gene ste11 and the ste11-dependent gene, mei2. The mating- and sporulation-inhibiting effect of cordycepin is overcome by adenine. A mutant disrupted for the ado1 gene encoding adenosine kinase exhibits a cordycepin-resistant and methionine-sensitive phenotype, excretes adenosine into the medium and mates and sporulates poorly in the presence of adenine. A S. pombe mutant containing a frameshift mutation at the beginning of the carboxy-terminal half of gene ufd1 (the Saccharomyces cerevisiae UFD1 homologue) is cordycepin-resistant and sterile. Strains disrupted for the ufd1 gene only form microcolonies.

Usage of cryptic splice sites in citrullinemia fibroblasts suggests role of polyadenylation in splice-site selection during terminal exon definition

Citrullinemia is a human genetic disease caused by a deficient argininosuccinate synthetase. In fibroblasts established from a citrullinemia patient with a mutation at the 3' splice site of the terminal intron of the gene, three cryptic 3' splice sites; i.e., SA1275, SA1636, and SA1663, residing on the terminal exon were activated. The usage of the cryptic sites showed a gradient, with the most downstream site having the highest usage; i.e., SA1663 > SA1636 > SA1275. However, when these cryptic sites were relocated to the internal exon, SA1636 was used the most. The splice-site strength of SA1636 was at least 10-fold higher than that of SA1663 in this situation. The results suggest that the preferential usage of SA1663 residing on the terminal exon may depend on its proximity to the poly(A) signal rather than on the strength of the splice site. Furthermore, when the strength of the downstream-most splice site increased, almost all the RNAs spliced to this site. However, in the presence of the wild-type splice site, all the RNAs were processed to the authentic site. Apparently, the selection of splice site can be revealed only when the sites being selected do not differ too much in their strength. By using a naturally occurring human mutant gene as a model, this study reveals that polyadenylation may play an important role in the selection of splice site during terminal exon definition.

Coupling transcription to translation: a novel site for the regulation of eukaryotic gene expression

Recent experiments using Xenopus oocytes demonstrate that the history of a particular mRNA in the nucleus can influence the efficiency with which that mRNA will be utilized by the translational machinery. Individual promoter elements, specific protein-RNA interactions and the splicing process within the nucleus can all influence translational fate within the cytoplasm. Central to the regulatory mechanisms influencing the translation process is the packaging of mRNA by a highly conserved family of Y-box proteins. These Y-box proteins are found in cytoplasmic messenger ribonucleoprotein particles where they have a causal role in restricting the recruitment of mRNA to the translational machinery. Nuclear processes influence the packaging of mRNA by the Y-box proteins in the cytoplasm and in consequence mRNA translation. This functional coupling provides a novel site for the regulation of eukaryotic gene expression.

Effect of transcription inhibitors on the iron-dependent degradation of transferrin receptor mRNA

Transferrin receptor (TfR) mRNA expression is tightly linked to intracellular iron levels. Upon iron deprivation, the iron regulatory protein (IRP) stabilizes TfR mRNA by binding to stem-loop structures in its 3'-untranslated region, whereas increased iron levels result in inactivation of the mRNA-binding protein and rapid degradation of TfR mRNA. Although IRP and the regulation of its RNA binding activity have been studied intensively, little is known about the mechanism of TfR mRNA degradation. In order to get more information about factors involved in this process we investigated the in vivo IRP-RNA interaction and the effect of transcription inhibitors on the iron-dependent decay of TfR mRNA. Here we demonstrate that part of the active IRP co-localizes with TfR mRNA to the rough endoplasmic reticulum. High intracellular iron levels led to a drastic reduction of this active RNA-bound IRP in vivo, indicating that IRP dissociates prior to TfR mRNA decay. Furthermore, the transcription inhibitor actinomycin D and translation inhibitor cycloheximide suppressed TfR mRNA degradation but did not interfere with the IRP dissociation step. Other inhibitors of RNA polymerase II had no effect on iron-dependent degradation of TfR mRNA. However, high concentrations of alpha-amanitin known to block transcription by RNA polymerase III interfered with mRNA decay suggesting the involvement of polymerase III transcripts in the degradation pathway.

The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced

The largest known gene is the human dystrophin gene, which has 79 exons spanning at least 2,300 kilobases (kb). Transcript accumulation was monitored from four regions of the gene following induction of expression in muscle cell cultures. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) results indicate that approximately 12 h are required for transcription of 1,770 kb (at an average elongation rate of 2.4 kb min-1), extrapolating to a transcription time of 16 h for the complete gene. Accumulation profiles for spliced and total transcript demonstrated that transcripts are spliced at the 5' end before transcription is complete providing strong evidence for cotranscriptional splicing. The rate of transcript accumulation was reduced at the 3' end of the gene relative to the 5' end, perhaps due to premature termination of transcription complexes.

Induction of endogenous human cytomegalovirus gene expression after differentiation of monocytes from healthy carriers

Monocytes are one site of carriage of the human cytomegalovirus (HCMV) genome in healthy human carriers. However, as there are conflicting data detailing the level of HCMV gene expression during persistence in these cells, we have analyzed monocytes for evidence of viral immediate-early, early, and late transcription by using reverse transcription followed by PCR. We were unable to find evidence of HCMV lytic gene transcription in freshly isolated peripheral blood monocytes from HCMV-seropositive subjects. However, as differentiation of monocytes to monocyte-derived macrophages results in increased permissiveness to infection with HCMV in vitro, we examined whether such differentiation could result in reactivation of endogenous viral gene expression. Here we show that in vitro differentiation of monocytes does result in expression of endogenous HCMV immediate-early genes. Although this differentiation led to reactivation of endogenous viral immediate-early expression, we were unable to detect any early or late viral transcription. Cocultivation experiments correlated with this level of gene induction, as no productive infection was detected. These data strongly suggest a mechanism of persistence of HCMV in the peripheral blood that is independent of HCMV lytic gene expression and that initial phases of lytic gene expression in monocytes can be induced by differentiation of these cells to monocyte-derived macrophages.

Polyadenylation site selection cannot occur in vivo after excision of the 3'-terminal intron

Splicing of 3'-terminal introns and polyadenylation of pre-mRNAs can be coupled in an appropriate cell-free system. However, definitive evidence has been lacking as to whether these events are coupled in vivo and whether the order of these two processing events is obligatory. Here, we investigated these questions by examining the in vivo processing of transcripts that differ solely by the precise insertion of an intron within the first of two polyadenylation signals. Quantitative S1 nuclease mapping and PCR techniques were utilized to analyze the processed RNAs that accumulated in monkey cells transfected with plasmids encoding these transcripts. We found that, whereas all of the primary transcripts that lacked the inserted intron were processed via utilization of the 5'-proximal polyadenylation signal, none of the transcripts initially disrupted in this signal were processed this way even though the disrupting intron had been properly excised and excision sometimes preceded polyadenylation. In addition, deletion of the second polyadenylation signal resulted in failure of spliced transcripts to accumulate. We conclude that selection of, but not necessarily cleavage at the polyadenylation site precedes excision of the 3'-terminal intron in vivo; although coupling exists during selection of the sites to be used for polyadenylation and excision of the 3'-terminal intron, the actual order of the subsequent enzymatic reactions is probably simply a reflection of their relative kinetics.

Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns

To investigate the relationship between splicing and polyadenylation during the production of vertebrate mRNAs, we examined the effect of mutation of a poly(A) site on splicing of upstream introns. Mutation of the AAUAAA polyadenylation consensus sequence inhibited in vitro splicing of an upstream intron. The magnitude of the depression depended on the magnesium concentration. Dependence of splicing on polyadenylation signals suggests the existence of interaction between polyadenylation and splicing factors. In multi-intron precursor RNAs containing duplicated splice sites, mutation of the poly(A) site inhibited removal of the last intron, but not the removal of introns farther upstream. Inhibition of removal of only the last intron suggests segmental recognition of multi-exon precursor RNAs and is consistent with previous suggestions that signals at both ends of an exon are required for effective splicing of an upstream intron.

Splicing precedes polyadenylation during Drosophila E74A transcription

The E74 gene is one of a small set of early genes induced by the steroid hormone ecdysone at the onset of metamorphosis in the fruit fly, Drosophila melanogaster. This complex gene directs the synthesis of a 60-kilobase (kb) primary transcript that is spliced to form the 6-kb E74A mRNA. In a previous study, we found that ecdysone directly activates the E74A promoter and determined that RNA polymerase II transcribes this gene at a rate of approximately 1.1 kb/min. This elongation rate accounts for most of the 1-hour delay seen between the addition of ecdysone and the appearance of cytoplasmic E74A mRNA (C. S. Thummel, K. C. Burtis, and D. S. Hogness, Cell 61:101-111, 1990). We show here that nascent E74A transcripts are spliced, and we propose a model for the order of that splicing. This study provides, for the first time, direct biochemical evidence for splicing of a low-abundance cellular RNA before transcription termination and polyadenylation.

Splicing precedes polyadenylation during Drosophila E74A transcription

The E74 gene is one of a small set of early genes induced by the steroid hormone ecdysone at the onset of metamorphosis in the fruit fly, Drosophila melanogaster. This complex gene directs the synthesis of a 60-kilobase (kb) primary transcript that is spliced to form the 6-kb E74A mRNA. In a previous study, we found that ecdysone directly activates the E74A promoter and determined that RNA polymerase II transcribes this gene at a rate of approximately 1.1 kb/min. This elongation rate accounts for most of the 1-hour delay seen between the addition of ecdysone and the appearance of cytoplasmic E74A mRNA (C. S. Thummel, K. C. Burtis, and D. S. Hogness, Cell 61:101-111, 1990). We show here that nascent E74A transcripts are spliced, and we propose a model for the order of that splicing. This study provides, for the first time, direct biochemical evidence for splicing of a low-abundance cellular RNA before transcription termination and polyadenylation.

The regulated production of mu m and mu s mRNA is dependent on the relative efficiencies of mu s poly(A) site usage and the c mu 4-to-M1 splice

The relative abundance of the mRNAs encoding the membrane (mu m) and secreted (mu s) forms of immunoglobulin mu heavy chain is regulated during B-cell maturation by a change in the mode of RNA processing. Current models to explain this regulation involve either competition between cleavage-polyadenylation at the proximal (mu s) poly(A) site and cleavage-polyadenylation at the distal (mu m) poly(A) site [poly(A) site model] or competition between cleavage-polyadenylation at the mu s poly(A) site and splicing of the C mu 4 and M1 exons, which eliminates the mu s site (mu s site-splice model). To test certain predictions of these models and to determine whether there is a unique structural feature of the mu s poly(A) site that is essential for regulation, we constructed modified mu genes in which the mu s or mu m poly(A) site was replaced by other poly(A) sites and then studied the transient expression of these genes in cells representative of both early- and late-stage lymphocytes. Substitutions at the mu s site dramatically altered the relative usage of this site and caused corresponding reciprocal changes in the usage of the mu m site. Despite these changes, use of the proximal site was still usually higher in plasmacytomas than in pre-B cells, indicating that regulation does not depend on a unique feature of the mu s poly(A) site. Replacement of the distal (mu m) site had no detectable effect on the usage of the mu s site in either plasmacytomas or pre-B cells. These findings are inconsistent with the poly(A) site model. In addition, we noted that in a wide variety of organisms, the sequence at the 5' splice junction of the C mu 4-to-M1 intron is significantly different from the consensus 5' splice junction sequence and is therefore suboptimal with respect to its complementary base pairing with U1 small nuclear RNA. When we mutated this suboptimal sequence into the consensus sequence, the mu mRNA production in plasmacytoma cells was shifted from predominantly mu s to exclusively mu m. This result unequivocally demonstrated that splicing of the C mu 4-to-M1 exon is in competition with usage of the mu s poly(A) site. A key feature of this regulatory phenomenon appears to be the appropriately balanced efficiencies of these two processing reactions. Consistent with predictions of the mu s site-splice model, B cells were found to contain mu m precursor RNA that had undergone the C mu 4-to-M1 splice but had not yet been polyadenylated at the mu m site.

The poly(A)-poly(A)-binding protein complex is a major determinant of mRNA stability in vitro

Using an in vitro mRNA decay system, we investigated how poly(A) and its associated poly(A)-binding protein (PABP) affect mRNA stability. Cell extracts used in the decay reactions were depleted of functional PABP either by adding excess poly(A) competitor or by passing the extracts over a poly(A)-Sepharose column. Polyadenylated mRNAs for beta-globin, chloramphenicol acetyltransferase, and simian virus 40 virion proteins were degraded 3 to 10 times faster in reactions lacking PABP than in those containing excess PABP. The addition of purified Saccharomyces cerevisiae or human cytoplasmic PABP to PABP-depleted reactions stabilized the polyadenylated mRNAs. In contrast, the decay rates of nonpolyadenylated mRNAs were unaffected by PABP, indicating that both the poly(A) and its binding protein were required for maintaining mRNA stability. A nonspecific single-stranded binding protein from Escherichia coli did not restore stability to polyadenylated mRNA, and the stabilizing effect of PABP was inhibited by anti-PABP antibody. The poly(A) tract was the first mRNA segment to be degraded in PABP-depleted reactions, confirming that the poly(A)-PABP complex was protecting the 3' region from nucleolytic attack. These results indicate that an important function of poly(A), in conjunction with its binding protein, is to protect polyadenylated mRNAs from indiscriminate destruction by cellular nucleases. A model is proposed to explain how the stability of an mRNA could be affected by the stability of its poly(A)-PABP complex.

Developmental distribution of RNA and protein products of the Drosophila alpha-tubulin gene family

The developmental pattern of gene expression of the Drosophila melanogaster alpha-tubulin family has been examined in detail at both the mRNA and protein levels. Northern data from 16 stages of development have been quantified to produce estimates of pool sizes of each of the alpha-tubulin transcripts through development. The in situ pattern of alpha 67C RNA localization in developing oocytes and early embryos has also been determined. At the protein level, two of the three previously unidentified products of alpha-tubulin genes (alpha 67C and alpha 85E) have been identified. Evidence that protein from the fourth gene comigrates with the ubiquitously expressed alpha 84B is presented. In addition to the primary translational products of the alpha-tubulin genes, an elaborate series of post-translationally modified alpha-tubulins has been resolved. The developmental profiles of both synthesis and accumulation of these alpha-tubulin proteins are described.

The regulated production of mu m and mu s mRNA is dependent on the relative efficiencies of mu s poly(A) site usage and the c mu 4-to-M1 splice

The relative abundance of the mRNAs encoding the membrane (mu m) and secreted (mu s) forms of immunoglobulin mu heavy chain is regulated during B-cell maturation by a change in the mode of RNA processing. Current models to explain this regulation involve either competition between cleavage-polyadenylation at the proximal (mu s) poly(A) site and cleavage-polyadenylation at the distal (mu m) poly(A) site [poly(A) site model] or competition between cleavage-polyadenylation at the mu s poly(A) site and splicing of the C mu 4 and M1 exons, which eliminates the mu s site (mu s site-splice model). To test certain predictions of these models and to determine whether there is a unique structural feature of the mu s poly(A) site that is essential for regulation, we constructed modified mu genes in which the mu s or mu m poly(A) site was replaced by other poly(A) sites and then studied the transient expression of these genes in cells representative of both early- and late-stage lymphocytes. Substitutions at the mu s site dramatically altered the relative usage of this site and caused corresponding reciprocal changes in the usage of the mu m site. Despite these changes, use of the proximal site was still usually higher in plasmacytomas than in pre-B cells, indicating that regulation does not depend on a unique feature of the mu s poly(A) site. Replacement of the distal (mu m) site had no detectable effect on the usage of the mu s site in either plasmacytomas or pre-B cells. These findings are inconsistent with the poly(A) site model. In addition, we noted that in a wide variety of organisms, the sequence at the 5' splice junction of the C mu 4-to-M1 intron is significantly different from the consensus 5' splice junction sequence and is therefore suboptimal with respect to its complementary base pairing with U1 small nuclear RNA. When we mutated this suboptimal sequence into the consensus sequence, the mu mRNA production in plasmacytoma cells was shifted from predominantly mu s to exclusively mu m. This result unequivocally demonstrated that splicing of the C mu 4-to-M1 exon is in competition with usage of the mu s poly(A) site. A key feature of this regulatory phenomenon appears to be the appropriately balanced efficiencies of these two processing reactions. Consistent with predictions of the mu s site-splice model, B cells were found to contain mu m precursor RNA that had undergone the C mu 4-to-M1 splice but had not yet been polyadenylated at the mu m site.

The poly(A)-poly(A)-binding protein complex is a major determinant of mRNA stability in vitro

Using an in vitro mRNA decay system, we investigated how poly(A) and its associated poly(A)-binding protein (PABP) affect mRNA stability. Cell extracts used in the decay reactions were depleted of functional PABP either by adding excess poly(A) competitor or by passing the extracts over a poly(A)-Sepharose column. Polyadenylated mRNAs for beta-globin, chloramphenicol acetyltransferase, and simian virus 40 virion proteins were degraded 3 to 10 times faster in reactions lacking PABP than in those containing excess PABP. The addition of purified Saccharomyces cerevisiae or human cytoplasmic PABP to PABP-depleted reactions stabilized the polyadenylated mRNAs. In contrast, the decay rates of nonpolyadenylated mRNAs were unaffected by PABP, indicating that both the poly(A) and its binding protein were required for maintaining mRNA stability. A nonspecific single-stranded binding protein from Escherichia coli did not restore stability to polyadenylated mRNA, and the stabilizing effect of PABP was inhibited by anti-PABP antibody. The poly(A) tract was the first mRNA segment to be degraded in PABP-depleted reactions, confirming that the poly(A)-PABP complex was protecting the 3' region from nucleolytic attack. These results indicate that an important function of poly(A), in conjunction with its binding protein, is to protect polyadenylated mRNAs from indiscriminate destruction by cellular nucleases. A model is proposed to explain how the stability of an mRNA could be affected by the stability of its poly(A)-PABP complex.

Altered replicase specificity is responsible for resistance to defective interfering particle interference of an Sdi- mutant of vesicular stomatitis virus

The in vitro resistance of an Sdi- mutant of vesicular stomatitis virus to interference by wild-type defective interfering (DI) particles was expressed quantitatively in a cell-free replication system derived from mutant-infected cells. Added wild-type DI particle templates were replicated very poorly by extracts of Sdi- mutant-infected cells. However, the addition of purified viral polymerase (a complex of L and NS proteins) from wild-type vesicular stomatitis virus allowed efficient replication of wild-type DI particle genomes in these cell extracts. Added wild-type NS protein alone did not complement DI particle genome replication in these cell extracts, but it did complement a defect in the in vitro transcriptional activity of Sdi- mutant virus. These results clearly implicate the vesicular stomatitis virus polymerase complex in the inability of Sdi- mutants to replicate DI particles and in the quantitative escape from DI particle interference in evolving virus populations.

Expression of the 31-kD stress protein in rat myoblasts and hepatocytes

Rat tissue cultures cells respond to stress by inducing the synthesis of about 20 proteins, including two low-molecular-weight species of about 31 kD and 27 kD. We have cloned a cDNA for the 31-kD protein. This protein is induced in myoblasts and hepatoma cells in response to a 43 degrees C heat shock, or exposure to sodium arsenite or cadmium chloride salts. Furthermore, this protein is superinduced in hepatoma cells conditioned to grow in cadmium and zinc salts when they are exposed to a standard sodium arsenite stress. Induction of the gene encoding the 31-kD protein has been characterized as follows: (i) Transcripts accumulate maximally with similar kinetics when myoblasts are induced with either heat shock or sodium arsenite; (ii) accumulation of transcripts decays to preinduction levels within 4 hr of a heat shock, but requires more than 8 days after sodium arsenite stress; (iii) basal levels of transcript are reduced when myoblasts are cultured in the presence of steroid hormones; and (iv) stress induction is virtually abolished once myoblasts have differentiated.

Ordered processing and splicing in a polycistronic transcript in liverwort chloroplasts

From the complete sequence of the chloroplast DNA in a liverwort, Marchantia polymorpha, an unidentified open reading frame, ORF203, was found between the psbB and rps12' (trans-split) genes. ORF203 was a split gene consisting of three exons and two group II introns. Multiple transcripts for ORF203 were detected on Northern blots of the chloroplast RNA preparation. The ORF203 locus was primarily co-transcribed with the downstream genes rps12' and rpl20, and then processed into a monomeric precursor. S1 nuclease mapping gave the transcription initiation site 52 nucleotides upstream from the coding sequence of ORF203. The spliced RNA molecules were identified, as predicted, by the use of synthetic oligodeoxyribonucleotide probes specific to ligated exon sequences. The splicing reaction proceeded successively from the 5' to 3' direction. These results indicate that ordered RNA processing occurs in the chloroplast of land plants. Trans-membrane analysis by a computer indicated that ORF203 gene product could be associated with a chloroplast membrane.

Splice site selection, rate of splicing, and alternative splicing on nascent transcripts

Based on ultrastructural analysis of actively transcribing genes seen in electron micrographs, we present evidence that pre-mRNA splicing occurs with a reasonable frequency on the nascent transcripts of early Drosophila embryo genes and that splice site selection may generally precede polyadenylation. The details of the process observed are in agreement with results from in vitro splicing systems but differ in the more rapid completion of in vivo splicing. For those introns that are removed cotranscriptionally, a series of events is initiated following 3' splice site synthesis, beginning with ribonucleoprotein (RNP) particle formation at the 3' splice site within 48 sec, intron loop formation within 2 min, and splicing within 3 min. The initiation of the process is correlated with 3' splice site synthesis but is independent of 5' splice site synthesis, the position of the intron within the transcript, and the age or length of the transcript. In some cases, introns are removed from the 5' end of a transcript before introns are synthesized at the 3' end, supporting a possible role for the order of transcription in splice site pairing. In general, our observations are consistent with the 'first-come-first-served' principle of splice site selection, although an observed example of exon skipping indicates that alternative splicing possibilities can be accommodated within this general framework.

Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation

To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.

Identification and expression of the gap segmentation gene hunchback in Drosophila melanogaster

Genetic analysis has shown that the gap segmentation gene hunchback (hb) is a member of the genetic hierarchy involved in pattern formation in Drosophila. To identify the hb gene, we have mapped the position of hb mutant breakpoints within a chromosomal walk of the 85A region by genomic Southern blots and determined the transcription pattern of DNA from the walk. We detect a single gene within the domain defined by breakpoint mapping. We conclude that we have identified the hunchback gene because three mutations that inactivate hb physically interrupt or delete this gene. Northern analysis shows that the hb gene gives rise to at least five overlapping transcripts ranging in length from 2.6 to 3.5 kilobases. S1 nuclease and primer extension experiments demonstrate that the gene employs two promoters and three polyadenylation sites. The two hb promoters have different temporal specificities. Transcripts arising from the upstream promoter are detected from 0-12 hours of embryogenesis as well as in adult female and male RNA preparations. Transcripts arising from the downstream promoter accumulate only from 0-6 hours of embryogenesis. During the syncytial blastoderm stage, transcripts from the hb gene accumulate over a broad anterior and a narrow posterior domain. This pattern sharpens during the late blastoderm/early gastrula stage to produce an embryo with two stripes of hybridization anterior and one stripe posterior. Later, hb transcripts are detected within the ventral hypoderm in extended germ band stage embryos.

A small deletion distant from a splice or polyadenylation site dramatically alters pre-mRNA processing in region E3 of adenovirus

The E3 complex transcription unit of adenovirus encodes overlapping mRNAs (a to i) with different exon structures. The major mRNAs are a (approximately 40% of the total) and c (approximately 15%), which are spliced once, and f (approximately 15%) and h (approximately 25%), which are spliced twice. mRNA a uses the upstream E3A polyadenylation site, and the other mRNAs use the downstream E3B polyadenylation site. We analyzed virus deletion mutants to identify sequences important in alternative pre-mRNA processing in region E3. Our main finding is that a 64-base-pair deletion in dl742 causes mainly mRNAs f and h to be formed. mRNAs a and c are barely made. dl742 does not delete either a splice site or a polyadenylation site. Thus, the sequences deleted must function in alternative pre-mRNA processing independently of the signals at the actual splice and polyadenylation sites. The lack of synthesis of mRNA a by dl742 does not appear to result from a defect in the E3A polyadenylation signal but rather from an increase in splicing activity which results in the synthesis of doubly spliced mRNAs f and h at the expense of singly spliced mRNAs a and c. This suggests, in the wild-type situation, that the frequency of use of the E3A versus the E3B polyadenylation site may be determined by the rate of splicing, as well as, presumably, the rate of cleavage-polyadenylation at the E3A site.

Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation

To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.

Formation of the triple-stranded polynucleotide helix, poly(A.A.U)

A polynucleotide helical structure containing two strands of poly(A) and one of poly(U) is reported. As shown by spectroscopic observations, the complex only forms when the poly(A) strands are of Mr between 9000 and 50,000 (degree of polymerization congruent to 28-150), whereas the size of the poly(U) strand has no effect. This limitation may explain why poly(A.A.U) was not seen in previous investigations. The potential of the poly(A) tails of mRNA for formation of this triple helix and of A.A.U or/and A.A.T triplet formation to contribute to the binding of specific RNA strands to gene-encoding nucleic acid double helices are noted.

Translation of ferritin light and heavy subunit mRNAs is regulated by intracellular chelatable iron levels in rat hepatoma cells

Acute administration of iron to rats has been previously shown to induce liver ferritin synthesis by increasing the translation of inactive cytoplasmic ferritin mRNAs for both heavy (H) and light (L) subunits by mobilizing them onto polyribosomes. In this report rat hepatoma cells in culture are used to explore the relationship of this response to intracellular iron levels. After adding iron as ferric ammonium citrate to the medium, latent ferritin H- and L-mRNAs were extensively transferred to polyribosomes, accompanied by increased uptake of [35S]methionine into ferritin protein. Because total cellular levels of L- and H-mRNA were not significantly changed by exposure to iron, the increased ferritin mRNAs on polyribosomes most probably come from an inactive cytoplasmic pool, consistent with the inability of actinomycin-D and of cordycepin to inhibit iron-induced ferritin synthesis. When deferoxamine mesylate, an intracellular iron chelator, was added after the addition of iron to the medium, ferritin mRNA on the polyribosomes was reduced, while the free messenger pool increased, and ferritin synthesis diminished. In contrast, the extracellular iron chelator diethylenetriaminepentaacetic acid failed to inhibit the induction of ferritin protein synthesis. Addition of iron in the form of hemin also caused translocation of mRNA to polyribosomes, a response that could be similarly quenched by deferoxamine. Because hemin does not release chelatable iron extracellularly, we conclude that the level of chelatable iron within the cell has a regulatory role in ferritin synthesis through redistribution of the messenger RNAs between the free mRNA pool and the polyribosomes.

Estrogen induction of sexual behavior in female rats and synthesis of polyadenylated messenger RNA in the ventromedial nucleus of the hypothalamus

To test the hypothesis that estrogen stimulates sexual behavior by inducing transcription of polyadenylated messenger RNA, we studied the effects of cordycepin, an adenosine analog that disrupts polyadenylation, on the lordotic responses of ovariectomized female rats made sexually receptive with systemic injections of estradiol benzoate (EB) and progesterone (P). Cordycepin inhibited lordosis when infused into the ventromedial nucleus of the hypothalamus within an hour before the females received EB; its effectiveness varied linearly with dose. It did not significantly alter sexual behavior when infused into the medial preoptic area. A dose of cordycepin that decreased lordosis when infused 1 h before injection of 0.5 microgram EB did not affect the behavior when infused 1 h before injection of 500 micrograms P. Cordycepin does not suppress behavior by blocking estrogen uptake since it did not alter estrogen accumulation by hypothalamic cell nuclei. Cordycepin inhibits ribosomal RNA (rRNA) synthesis as well as polyadenylation. While this probably contributes to cordycepin's inhibitory effects on lordosis, it cannot fully account for them since a cytidine analog that inhibits rRNA synthesis without inhibiting polyadenylation did not mimic cordycepin's behavioral effects. Cordycepin may suppress synthesis of P receptors; however, this could not fully account for its behavioral effects since cordycepin also inhibited lordosis when the P receptor was bypassed by substituting methysergide for P. As assessed by protein synthesis autoradiography, cordycepin's effects are highly localized. The data support the notion that estrogen facilitates female sexual behavior by altering gene expression in the brain.

Genetic analysis of mRNA synthesis in adenovirus region E3 at different stages of productive infection by RNA-processing mutants

Region E3 of adenovirus encodes about nine overlapping mRNAs (a to i) with different spliced structures and with two major RNA 3' end sites termed E3A and E3B. Synthesis of E3 mRNAs was examined by the nuclease-gel procedure at early and late stages of infection by wild-type virus (rec700) and by several E3 deletion mutants. Our results, together with those obtained by electron microscopy (L. T. Chow, T. R. Broker, and J. B. Lewis, J. Mol. Biol. 134:265-303, 1979), suggest that E3 may be differentially regulated at early and late stages at both the promoter and RNA-processing levels. Early after infection, the E3 promoter is used to make mainly mRNAs a and h. Late after infection, the E3 promoter appears to be shut off and the major late promoter is used to make mainly mRNAs d and e. The late L4 mRNA 3' end site is not used early even though early E3 pre-mRNAs transcribe through the L4 RNA 3' end site. The nucleotide 768-951 exon, which is the y leader on many L5 mRNAs, is very abundant late. (Nucleotide +1 is the major E3 transcription initiation site.) Early after infection, the 951 5' splice site is enhanced 5- to 10-fold in the dl712 (delta 1691 to 2122) group of mutants; late after infection, these mutants resemble the wild type. We speculate that the activity of the 951 5' splice site is regulated at early and late stages; it is suppressed early to permit synthesis of mRNA a, and it is activated late to permit synthesis of mRNAs d, e, and L5. With dl719 (delta 2173 to 2237), the 951----2157 splice is enhanced both early and late; we suggest that this deletion enhances the 2157 3' splice site.

A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression

Nuclear and cytoplasmic poly(A)-binding proteins have been purified from Saccharomyces cerevisiae, and antisera have been used to isolate a gene that encodes them. The gene occurs in a single copy on chromosome 5 and gives rise to a unique, unspliced 2.1 kb transcript. The nuclear protein appears to be derived from the cytoplasmic one by proteolytic cleavage into 53 and 17 kd polypeptides that remain associated during isolation. DNA sequence determination reveals four tandemly arrayed 90 amino acid regions of homology that probably represent poly(A)-binding domains. A 55 residue A-rich region upstream of the initiator methionine codon in the mRNA shows an affinity for poly(A)-binding protein comparable to that of poly(A)180-220, raising the possibility of feedback regulation of translation.

RNA-binding proteins of coronavirus MHV: detection of monomeric and multimeric N protein with an RNA overlay-protein blot assay

RNA-binding proteins of coronavirus MHV-A59 were identified using an RNA overlay-protein blot assay (ROPBA). The major viral RNA-binding protein in virions and infected cells was the phosphorylated nucleocapsid protein N (50K). A new 140K virus structural protein was identified as a minor RNA-binding protein both in virions and in infected cells. The 140K protein was antigenically related to N, and upon reduction, yielded only 50K N. Thus, the 140K protein is probably a trimer of N subunits linked by intermolecular disulfide bonds. Several cellular RNA-binding proteins were also detected. RNA-binding of N was not nucleotide sequence specific. Single-stranded RNA of MHV, VSV, or cellular origin, a DNA probe of the MHV leader sequence, and double-stranded bovine rotavirus RNA could all bind to N. Binding of MHV RNA was optimal between pH 7 and 8, and the RNA could be eluted in 0.1 M NaCl. The ROPBA is a useful method for the initial identification of RNA-binding proteins, such as N and the 140K protein of murine coronavirus.

Adenovirus mutants with splice-enhancing mutations in the E3 complex transcription unit are also defective in E3A RNA 3'-end formation

Region E3 of adenovirus encodes about 10 overlapping mRNAs with different spliced structures. The mRNAs are 5' coterminal and form two major 3'-coterminal families termed E3A and E3B. As a group, the mRNAs have two 5' splice sites and four or five 3' splice sites. We previously described a novel class of virus mutants with deletions that enhance distant upstream and downstream 5' and 3' splice sites in region E3 (S. L. Deutscher, B. M. Bhat, M. H. Pursley, C. Cladaras, and W. S. M. Wold, Nucleic Acids Res. 13:5771-5788, 1985). We now report that two of these mutants, dl710 and dl712, are defective in RNA 3'-end formation at the E3A site. This result was surprising because the deletions in dl710 and dl712 are upstream of the putative signal for E3A RNA 3'-end formation. The explanation that we favor for this result is that the enhanced splicing activity in these mutants results in the splicing out of the E3A 3'-end site from the RNA precursor before the E3A 3' ends have a chance to form.

Differential polyadenylation pattern of ovalbumin precursor RNAs during development

The expression of the ovalbumin gene encoding for the major hen oviduct protein slows down with age. Analysis of Northern blots of electrophoretically separated total and poly(A) + RNA from oviducts of hens of different age with an ovalbumin-specific probe (nick-translated 9.5 kb ovalbumin gene DNA cloned into pBR322) revealed that the largest high molecular weight ovalbumin RNA precursor (7.9 kb band, representing the putative primary transcript of the ovalbumin gene) was most intense if total RNA from non-egg-laying old hen oviduct was checked as compared to that from egg-laying mature animals. On the other side, the 7.9 kb RNA precursor band was readily detected in the poly(A) + RNA from mature hen oviduct whereas it was invisible in the old hen oviduct poly(A) + RNA fraction. The lack of detection of the 7.9 kb RNA species within the poly(A) + RNA fraction and its increased concentration within the total oviduct RNA, both from old animals, suggest that age-dependent impairment of ovalbumin mRNA processing may be caused by altered polyadenylation of distinct RNA precursors.

Nuclei of adenovirus 2-infected cells contain an RNA species that corresponds to an intron excised intact from mRNA precursors

We used Northern and S1 nuclease analyses to identify a nuclear RNA species of the structure predicted for an intron excised from the precursor of adenovirus 2 E2A early mRNA. The structure of this excised intron demonstrated that the splicing of E2A mRNA can involve the removal of the intron sequences as single intact molecules. The concentration of the excised intron is 30 copies per nuclei, comparable to the levels of E2A polyadenylated splicing precursors, but 30-fold less than nuclear E2A mRNA. Late in infection, when the production of E2A early mRNA is dramatically elevated (Goldenberg et al., J. Virol. 38:932-939, 1981), the excess intron was not detected, indicating that either its stability or the mechanism of splicing is altered. We also identified a spliced nonpolyadenylated E2A nuclear RNA species with a structure similar to the mRNA, indicating that splicing may normally occur in the absence of polyadenylation.

Dissociation of cells from sea urchin embryos alters the synthesis of actins and other proteins

The effects of altered cellular microenvironments on patterns of protein synthesis at various periods during sea urchin development were quantitated by comparing the relative incorporation of [35S]methionine into selected polypeptides of intact embryos and cells dissociated from them. The effects of increasing times of reassociation were also determined. Quantitative, but not qualitative, differences in incorporation were noted. Actins, as well as heterogeneous acidic polypeptides with an Mr of about 80 kDa, showed increased incorporation in dissociated cells labeled at the time control embryos were recently hatched blastulae. Labeling of another acidic group of polypeptides with an Mr of about 100 kDa was decreased. Possible mechanisms regulating these shifts in incorporation were investigated by the use of inhibitors. The dissociation-triggered changes were insensitive to actinomycin D, cordycepin, dibutyryl cAMP, 3-isobutyl-1-methylxanthine, and trifluoperazine; however, the latter two stimulated incorporation into some polypeptides in intact blastulae. Age-dependent shifts in incorporation were also detected in both intact embryos and dissociated/reassociating cells.

Nuclei of adenovirus 2-infected cells contain an RNA species that corresponds to an intron excised intact from mRNA precursors

We used Northern and S1 nuclease analyses to identify a nuclear RNA species of the structure predicted for an intron excised from the precursor of adenovirus 2 E2A early mRNA. The structure of this excised intron demonstrated that the splicing of E2A mRNA can involve the removal of the intron sequences as single intact molecules. The concentration of the excised intron is 30 copies per nuclei, comparable to the levels of E2A polyadenylated splicing precursors, but 30-fold less than nuclear E2A mRNA. Late in infection, when the production of E2A early mRNA is dramatically elevated (Goldenberg et al., J. Virol. 38:932-939, 1981), the excess intron was not detected, indicating that either its stability or the mechanism of splicing is altered. We also identified a spliced nonpolyadenylated E2A nuclear RNA species with a structure similar to the mRNA, indicating that splicing may normally occur in the absence of polyadenylation.

Splicing in adenovirus and other animal viruses

Splicing provides viruses with great genetic versatility. It is still too early to say whether this versatility is derived from ingeneous mechanisms evolved by necessity by the viruses, or whether the viruses indeed mimic cellular mechanisms. In any event, it is unlikely that cells will provide a single genomic cluster of genes that utilize splicing in such diverse ways as adenovirus, or the other viruses discussed here. And we may speculate that when the full role of splicing in adenovirus gene expression program is known, its import will continue to be a source of amazement!

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

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

Nuclear RNA metabolism in rat hippocampal slices incubated in vitro

Rat hippocampal slices were incubated with [3H]uridine in vitro to analyze the metabolism of nuclear RNA and the RNA precursor fractions. Labeling of total nuclear RNA was linear for 4 h of incubation and proportional to the concentration of labeled uridine in the incubation medium. Addition of 3.5 X 10(-8) M corticosterone to the incubation medium produced an enhancement of nuclear RNA labeling with no significant effect on the labeling of the RNA precursor fraction. Progesterone and dexamethasone, at the same concentration, had no effect on either variable. Labeling of RNA by cerebellar slices under the same conditions was approximately one-half the value obtained using hippocampal slices and the cerebellar RNA precursor fraction accumulated only 65% of the radioactivity from [3H]uridine found in the hippocampal pool. Corticosterone had no effect on the labeling of total nuclear RNA in cerebellar slices. Nuclear poly(A)-containing RNA constituted 19% of the total labeled nuclear RNA in these incubations, as estimated by oligo (dT)-cellulose chromatography. Cordycepin (3'-deoxyadenosine) at a concentration of 25 micrograms/ml inhibited to some extent the labeling of total nuclear RNA and the RNA precursor fraction, but preferentially diminished the amount of labeled RNA bound to oligo (dT)-cellulose. Corticosterone increased the amount of [3H]RNA which bound to oligo (dT)-cellulose, while progesterone had no effect. These results show that hippocampal slices maintained in vitro, can be used to analyze nuclear RNA metabolism, one positive regulator of which in the rat hippocampus is the adrenal steroid, corticosterone.

S1 mapping of purified nascent transcripts of simian virus 40

We purified nascent simian virus 40 late transcripts by incubating viral transcriptional complexes, isolated from infected BSC-1 cells, in a reaction mixture that contained mercurated CTP; RNA molecules that had incorporated mercurated residues in vitro were isolated by sulfhydrylcellulose affinity chromatography. The nascent RNA was hybridized to an end-labeled HindIII C probe fragment (0.646 to 0.86 map unit), and the hybrids were analyzed by S1 mapping. Most of the products of digestion corresponded to unspliced transcripts with 5' ends mapping at nucleotides 325, 260, and 195, which are positions of the 5' ends of mature, cytoplasmic late mRNA species. In addition, two minor products diagnostic of splicing at the acceptor junctions mapping at nucleotides 556 and 443 were detected. Because the abundance of these products was not diminished by repurifying the nascent RNA through a second round of sulfhydrylcellulose chromatography, these products did not originate from contaminating non-nascent RNA. Moreover, the generation of these products was not affected when a higher salt concentration and lower temperature were used for S1 digestion, conditions that should decrease artifactual cleavage by S1 in A + U-rich regions of colinear hybrids. Therefore, it is likely that some simian virus 40 RNA chains are spliced before release from the template.

RNA splicing in Neurospora mitochondria: nuclear mutants defective in both splicing and 3' end synthesis of the large rRNA

We have identified nuclear mutants of Neurospora that are defective in splicing the mitochondrial large rRNA and that accumulate unspliced pre-rRNA (35S RNA). In cyt-4 mutants, the unspliced pre-rRNA contains short 3' end extensions (110 nucleotides) that are not present in pre-rRNAs from the other mutants. This and other characteristics suggest that the cyt-4 mutants may be primarily defective in 3' end synthesis and the RNA splicing defect occurs secondarily as a result of impaired RNA folding. The cyt-4 mutants also accumulate a "short" intron RNA and small exon RNAs that may reflect aberrant RNA cleavages. The 5' end of the short intron is about 285 nucleotides downstream from the 5' splice site at or near the base of the "central hairpin", a putative intermediate in folding of the pre-rRNA. Furthermore, the aberrant cleavage sites are immediately after a six nucleotide sequence (GAUAAU) homologous to the final splice junction (GAU/AAC).

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

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

Identification of thyroglobulin mRNA sequences in the nucleus and the cytoplasm of cultured thyroid cells: a post-transcriptional effect of thyrotropin

Cytoplasmic and nuclear RNA were isolated from porcine thyroid cells cultured with or without thyrotropin. After denaturation by glyoxal-DMSO treatment, the RNAs were analyzed on agarose gels, transferred onto nitrocellulose filters and hybridized with a [32P]-labelled thyroglobulin cDNA clone. In the cytoplasmic RNA a single mature thyroglobulin mRNA molecule (9 Kb) was present whereas in the nuclear RNA several molecular species (24 to 3.3 Kb) were identified. In the nucleus only the 9 Kb mRNA was polyadenylated. In cytoplasmic preparations the level of mature thyroglobulin mRNA was two-fold higher when cells were cultured with thyrotropin. In nuclear preparations only the level of the mature transcript was affected by the presence of thyrotropin, increasing relative to the concentration of the higher molecular weight species. These results suggest a hormonal effect at the post-transcriptional level that may serve to stabilize the mature mRNA molecule.

Inhibition of RNA cleavage but not polyadenylation by a point mutation in mRNA 3' consensus sequence AAUAAA

A single U leads to G transversion in the 3' consensus sequence AAUAAA of the adenovirus early region 1A gene was constructed and the effect of this mutation on processing of the 3' end of the nuclear early region 1A RNAs was analysed. The results demonstrate that the intact AAUAAA is not required for RNA polyadenylation but is required for the cleavage step preceding polyadenylation to occur efficiently.

Polyadenylic acid addition sites in the adenovirus type 2 major late transcription unit

The cytoplasmic mRNAs which are transcribed from the major late adenovirus promoter can be arranged into five 3'-coterminal families, L1 to L5. We have defined the polyadenylation sites of the mRNAs that belong to the five families at the nucleotide level. From the results, the following conclusions can be made. (i) The hexanucleotide sequence AAUAAA is present at the 3' end of all late adenovirus type 2 mRNAs and precedes the site of polyadenylation by 12 to 30 nucleotides. (ii) Between one and three A residues are present in the genomic sequence at the polyadenylation site. (iii) A sequence with the composition (T)n (A)p (T)q (n, p, q greater than or equal to 1) is found 4 to 24 nucleotides beyond all the adenovirus-specific polyadenylation sites except the 3'-coterminal family L4. This sequence is also found beyond many cellular polyadenylation sites. (iv) The L1 and L2 polyadenylation sites are very similar in structure. The other polyadenylation sites show no apparent sequence relationship, except for the hexanucleotide sequence.

Possible involvement of poly(A) in protein synthesis

The experiments of this paper have re-evaluated the possibility that poly(A) is involved in protein synthesis by testing whether purified poly(A) might competitively inhibit in vitro protein synthesis in rabbit reticulocyte extracts. We have found that poly(A) inhibits the rate of translation of many different poly(A)+ mRNAs and that comparable inhibition is not observed with other ribopolymers. Inhibition by poly(A) preferentially affects the translation of adenylated mRNAs and can be overcome by increased mRNA concentrations or by translating mRNPs instead of mRNA. The extent of inhibition is dependent on the size of the competitor poly(A) as well as on the translation activity which a lysate has for poly(A)+ RNA. In light of our results and numerous experiments in the literature, we propose that poly(A) has a function in protein synthesis and that any role in the determination of mRNA stability is indirect.