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

Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity

The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5' end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We report that in mouse embryonic stem cells, expression of a transgene comprising the first two kilobases of Xist (Xist-2kb) causes transcriptional readthrough of downstream polyadenylation sequences. Readthrough required Repeat A and the ∼750 nucleotides downstream, did not require SPEN, and was attenuated by splicing. Despite associating with SPEN and chromatin, Xist-2kb did not robustly silence transcription, whereas a 5.5-kb Xist transgene robustly silenced transcription and read through its polyadenylation sequence. Longer, spliced Xist transgenes also induced robust silencing yet terminated efficiently. Thus, in contexts examined here, Xist requires sequence elements beyond its first two kilobases to robustly silence transcription, and the 5' end of Xist harbors SPEN-independent transcriptional antiterminator activity that can repress proximal cleavage and polyadenylation. In endogenous contexts, this antiterminator activity may help produce full-length Xist RNA while rendering the Xist locus resistant to silencing by the same repressive complexes that the lncRNA recruits to other genes.

Sequence determinants of polyadenylation-mediated regulation

The cleavage and polyadenylation reaction is a crucial step in transcription termination and pre-mRNA maturation in human cells. Despite extensive research, the encoding of polyadenylation-mediated regulation of gene expression within the DNA sequence is not well understood. Here, we utilized a massively parallel reporter assay to inspect the effect of over 12,000 rationally designed polyadenylation sequences (PASs) on reporter gene expression and cleavage efficiency. We find that the PAS sequence can modulate gene expression by over five orders of magnitude. By using a uniquely designed scanning mutagenesis data set, we gain mechanistic insight into various modes of action by which the cleavage efficiency affects the sensitivity or robustness of the PAS to mutation. Furthermore, we employ motif discovery to identify both known and novel sequence motifs associated with PAS-mediated regulation. By leveraging the large scale of our data, we train a deep learning model for the highly accurate prediction of RNA levels from DNA sequence alone (R = 0.83). Moreover, we devise unique approaches for predicting exact cleavage sites for our reporter constructs and for endogenous transcripts. Taken together, our results expand our understanding of PAS-mediated regulation, and provide an unprecedented resource for analyzing and predicting PAS for regulatory genomics applications.

A history of poly A sequences: from formation to factors to function

Biological polyadenylation, first recognized as an enzymatic activity, remained an orphan enzyme until poly A sequences were found on the 3' ends of eukarvotic mRNAs. Their presence in bacteria viruses and later in archeae (ref. 338) established their universality. The lack of compelling evidence for a specific function limited attention to their cellular formation. Eventually the newer techniques of molecular biology and development of accurate nuclear processing extracts showed 3' end formation to be a two-step process. Pre-mRNA was first cleaved endonucleolytically at a specific site that was followed by sequential addition of AMPs from ATP to the 3' hydroxyl group at the end of mRNA. The site of cleavage was specified by a conserved hexanucleotide, AAUAAA, from 10 to 30 nt upstream of this 3' end. Extensive purification of these two activities showed that more than 10 polypeptides were needed for mRNA 3' end formation. Most of these were in complexes involved in the cleavage step. Two of the best characterized are CstF and CPSF, while two other remain partially purified but essential. Oddly, the specific proteins involved in phosphodiester bond hydrolysis have yet to be identified. The polyadenylation step occurs within the complex of poly A polymerase and poly A-binding protein, PABII, that controls poly A length. That the cleavage complex, CPSF, is also required for this step attests to a tight coupling of the two steps of 3' and formation. The reaction reconstituted from these RNA-free purified factors correctly processes pre-mRNAs. Meaningful analysis of the role of poly A in mRNA metabolism or function was possible once quantities of these proteins most often over-expressed from cDNA clones became available. The large number needed for two simple reactions of an endonuclease, a polymerase and a sequence recognition factor, pointed to 3' end formation as a regulated process. Polyadenylation itself had appeared to require regulation in cases where two poly A sites were alternatively processed to produce mRNA coding for two different proteins. The 64-KDa subunit of CstF is now known to be a regulator of poly A site choice between two sites in the immunoglobulin heavy chain of B cells. In resting cells the site used favors the mRNA for a membrane-bound protein. Upon differentiation to plasma cells, an upstream site is used the produce a secreted form of the heavy chain. Poly A site choice in the calcitonin pre-mRNA involves splicing factors at a pseudo splice site in an intron downstream of the active poly site that interacts with cleavage factors for most tissues. The molecular basis for choice of the alternate site in neuronal tissue is unknown. Proteins needed for mRNA 3' end formation also participate in other RNA-processing reactions: cleavage factors bind to the C-terminal domain of RNA polymerase during transcription; splicing of 3' terminal exons is stimulated port of by cleavage factors that bind to splicing factors at 3' splice sites. nuclear ex mRNAs is linked to cleavage factors and requires the poly A II-binding protein. Most striking is the long-sought evidence for a role for poly A in translation in yeast where it provides the surface on which the poly A-binding protein assembles the factors needed for the initiation of translation. This adaptability of eukaryotic cells to use a sequence of low information content extends to bacteria where poly A serves as a site for assembly of an mRNA degradation complex in E. coli. Vaccinia virus creates mRNA poly A tails by a streamlined mechanism independent of cleavage that requires only two proteins that recognize unique poly A signals. Thus, in spite of 40 years of study of poly A sequences, this growing multiplicity of uses and even mechanisms of formation seem destined to continue.

The ability of the HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure

The 5' and 3' ends of HIV-1 transcripts are identical in sequence. This repeat region (R) folds a stem-loop structure that is termed the poly(A) hairpin because it contains polyadenylation or poly(A) signals: the AAUAAA hexamer motif, the cleavage site and part of the GU-rich downstream element. Obviously, HIV-1 gene expression necessitates differential regulation of the two poly(A) sites. Previous transfection experiments indicated that the wild-type poly(A) hairpin is slightly inhibitory to the process of polyadenylation, and further stabilization of the hairpin inhibited polyadenylation completely. In this study, we tested wild-type and mutant transcripts with poly(A) hairpin structures of differing thermodynamic stabilities for the in vitro binding of polyadenylation factors. Mutant transcripts with a destabilized hairpin efficiently bound the polyadenylation factors, which were provided either as purified proteins or as nuclear extract. The RNA mutant with a stabilized hairpin did not form this 'poly(A) complex'. Additional mutations that repair the stability of this hairpin restored the binding capacity. Thus, an inverse correlation was measured between the stability of the poly(A) hairpin and its ability to interact with polyadenylation factors. The wild-type HIV-1 transcript bound the polyadenylation factors suboptimally, but full activity was obtained in the presence of the USE enhancer element that is uniquely present upstream of the 3' poly(A) site. We also found that sequences of the HIV-1 leader, which are uniquely present downstream of the 5' poly(A) site, inhibit formation of the poly(A) complex. This inhibition could not be ascribed to a specific leader sequence, as we measured a gradual loss of complex formation with increasing leader length. We will discuss the regulatory role of RNA structure and the repressive effect of leader sequences in the context of differential HIV-1 polyadenylation.

trans-Activation by the hnRNP K protein involves an increase in RNA synthesis from the reporter genes

The function of many of the pre-mRNA-binding proteins in mRNA biogenesis is unclear. We have analyzed the biochemical function of the hnRNP K protein by using a mouse cDNA clone. A previous study indicated that the expression of hnRNP K activates c-myc promoter in transient transfection assays. We show that the expression of hnRNP K results in a trans-activation of a variety of RNA polymerase II promoters. The trans-activation function depends on the sequences of hnRNP K that are also necessary for RNA binding. However, the RNA binding motifs are not sufficient for trans-activation. We could identify a mutant that bound RNA in vitro but was impaired in its ability to trans-activate the reporter genes. The trans-activation was not a result of the stabilization of the reporter mRNA, because hnRNP K increased the steady-state level of the reporter mRNA without altering its decay rate. By doing nuclear run-on assays, we provide evidence that the hnRNP K protein trans-activates the reporter genes by increasing the level of transcription.

Human adenovirus type 5 variants with sequence alterations flanking the E2A gene: effects on E2 expression and DNA replication

The human adenovirus type 5 (Ad5) E2 transcription unit is divided into a promoter-proximal region, E2A, and a distal region, E2B, each with its own polyadenylation site. Together these regions encode the three virus-derived proteins necessary for genome replication. Ad5 variants were produced that carried linker insertion mutations immediately 5' and/or 3' to the coding sequence for the E2A gene DNA binding protein (DBP). Two variants carrying solely a 5' lesion showed decreased usage of the adjacent 3' splice site, via which the DBP mRNA is produced, and an increased usage of the alternative downstream splice sites in the E2B region, wherein viral DNA polymerase and terminal protein precursor are encoded; these viruses showed somewhat reduced growth. A variant carrying a 3' lesion showed a marginal increase in DBP expression and slightly accelerated growth. When lesions 5' and 3' to the DBP coding sequence were combined in cis, the resulting virus was severely defective for growth and expressed E2B products to the virtual exclusion of E2A DBP. These data indicate that interactions must occur between the E2A 3' splice site and polyadenylation site before this region can be treated as an exon by the RNA processing machinery, and that a sequence alteration at the polyadenylation site that alone has only minor effects on the pattern of RNA processing can drastically affect terminal exon usage when placed in cis with a mutation that reduces splicing efficiency at the upstream 3' splice site. The data further indicate that, in vivo, Ad5 DNA replication is limited by prevailing DBP levels rather than by levels of polymerase or terminal protein precursor.

The end of the message: 3'-end processing leading to polyadenylated messenger RNA

Almost all messenger RNAs carry a polyadenylate tail that is added in a post-transcriptional reaction. In the nuclei of animal cells, the 3'-end of the RNA is formed by endonucleolytic cleavage of the primary transcript at the site of poly(A) addition, followed by the polymerisation of the tail. The reaction depends on specific RNA sequences upstream as well as downstream of the polyadenylation site. Cleavage and polyadenylation can be uncoupled in vitro. Polyadenylation is carried out by poly(A) polymerase with the aid of a specificity factor that binds the polyadenylation signal AAUAAA. Several additional factors are required for the initial cleavage. A newly discovered poly(A)-binding protein stimulates poly(A) tail synthesis and may be involved in the control of tail length. Polyadenylation reactions different from this scheme, either in other organisms or under special physiological circumstances, are discussed.

Transcriptional regulation of a Bacillus subtilis dipeptide transport operon

The Bacillus subtilis dciA operon, which encodes a dipeptide transport system, was induced rapidly by several conditions that caused the cells to enter stationary phase and initiate sporulation. The in vivo start point of transcription was mapped precisely and shown to correspond to a site of transcription initiation in vitro by the major vegetative form of RNA polymerase. Post-exponential expression was prevented by a mutation in the spo0A gene (whose product is a known regulator of early sporulation genes) but was restored in a spo0A abrB double mutant. This implicated AbrB, another known regulator, as a repressor of dciA. In fact, purified AbrB protein bound to a portion of the dciA promoter region, protecting it against DNase I digestion. Expression of dciA in growing cells was also repressed independently by glucose and by a mixture of amino acids; neither of these effects was mediated by AbrB.

The exon-intron organization of the human erythrocyte alpha-spectrin gene

The human erythrocyte alpha-spectrin gene which spans 80 kbp has been cloned from human genomic DNA as overlapping lambda recombinants. The exon-intron junctions were identified and the exons mapped. The gene is encoded by 52 exons whose sizes range from 684 bp to the smallest of 18 bp. The donor and acceptor splice site sequences match the splice site consensus sequences, with the exception of one splice site where a donor sequence begins with -GC. The size and location of exons do not correlate with the 106-amino-acid repeat, except in three locations where the surrounding codons are conserved as well. The lack of correspondence between exons and 106-amino-acid repeat is interpreted to reflect the appearance of a spectrin-like gene from a minigene early in the evolution of eukaryotes. Since current evidence indicates that introns were present in genes before the divergence of prokaryotes and eukaryotes, it is possible that the original distribution of introns within the minigene has been lost by the random deletion of introns from the spectrin gene.

Sequence and polyadenylation site determination of the murine immunoglobulin gamma 2a membrane 3' untranslated region

We have determined the nucleotide sequence of the murine immunoglobulin gamma 2a membrane 3' untranslated region (1413 nucleotides) and approximately 679 nucleotides of downstream sequence. Two AATAAA hexanucleotide sequences are present in the 2092 nucleotide interval. The first one functions as the major polyA signal, directing cleavage and polyadenylation at a site 20 nucleotides downstream. Within 41 nucleotides downstream of the major membrane polyA signal are two sequences with 75% homology to the consensus sequence, (C/T)GTGTT(C/T)(C/T), identified by McLauchlan et al. [Nucl. Acids Res. 13, 1347-1365 (1985)]. An 80% homology match to the Berget consensus sequence, CA(C/T)TG, begins five nucleotides 3' of the major polyA site (used 20 times more than the second, downstream polyA site) [Berget Nature 309, 179-182 (1984)]. The second AATAAA, located 73 nucleotides 3' of the first, directs cleavage and polyadenylation 18 nucleotides downstream at a minor polyA site. One match with 75% homology to the McLauchlan consensus sequence begins 17 nucleotides 3' of the second (weaker) polyA site. No matches to the Berget consensus sequence are located near this second, weaker polyA site.

Molecular analysis and rescue of a vitelline membrane mutant in Drosophila

The eggshell in Drosophila is produced by ovarian follicle cells during the later stages of oogenesis. Eggshell formation involves the ordered synthesis and assembly of several protein components. Genes encoding the most abundant eggshell proteins have been identified by molecular cloning studies. Morphological examination of eggs produced by females carrying female sterile mutations on the X and third chromosomes have revealed additional loci involved in chorion formation. In this study we screened a collection of female sterile mutants carrying EMS-induced mutations on the second chromosome for eggshell mutants. A class of six mutants with potential vitelline membrane defects was identified on the basis of the response of mutant eggs to hypochlorite solutions. Biochemical analysis showed that one mutant, fs(2)QJ42, failed to produce a major vitelline membrane protein, sV23. The mutation was mapped cytogenetically to 26A, a region previously implicated in vitelline membrane formation by molecular cloning studies. Northern blot analysis using a cloned copy of the sV23 gene as probe showed a 10- to 15-fold reduction of sV23 RNA levels in the mutant. sV23 synthesis and fertility were restored when a normal copy of the sV23 gene was introduced into the mutant via germ line transformation. Transposons carrying the sV23 gene with as little as 147 bp of 5' flanking DNA were capable of restoring fertility and sV23 protein to wild type levels.

Nucleotide sequence of the Stp-1 gene coding for rat spermatid nuclear transition protein 1 (TP1): homology with protamine P1 and assignment of the mouse Stp-1 gene to chromosome 1

Spermatid transition protein 1 (TP1) is a 54 amino acid (aa), highly basic chromosomal protein found in mammals during the brief period when histones are being replaced by protamines in the haploid phase of spermatogenesis. Using a cDNA clone as probe, we have isolated the gene (Stp-1) coding for rat TP1 from a population of recombinant bacteriophage lambda. The nucleotide (nt) sequence was established from a point 126 nt upstream from the mRNA cap site to a point about 30 nt downstream from the predicted site of polyadenylation. The gene contains a single intron separating the codon for aa 45 of the mature protein. Comparison of the nucleotide sequences for Stp-1 and the mouse gene coding for protamine P1 suggests a possible evolutionary relationship. Southern blot hybridization to genomic DNA isolated from a panel of mouse-hamster somatic cell hybrids unambiguously mapped Stp-1 to mouse chromosome 1.

Mapping of a DNA sequence that down-regulates the expression of an interferon-induced gene

Recently, an interferon response element (IRE) of approximately 24 bp has been identified by Reich et al. (7) that allows certain genes to be actively transcribed by type I interferons (IFNs). The transcription of several IFN-induced genes in some cells (human fibroblasts and melanoma cells) is inhibited by long-term exposure to IFN. This process requires the synthesis of a new protein(s). Evidence is presented that this same IRE contains the information necessary for long-term IFN treatment to down-regulate the transcription of those genes whose expression it initially activates.

Identification and characterization of cryptic polyadenylation sites in the 3' region of a pea ribulose-1,5-bisphosphate carboxylase small subunit gene

The polyadenylation signal of a pea ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene has been studied using in vitro mutagenesis and Ti plasmid-mediated transformation of tobacco. Analysis of a mutant that is lacking sequences upstream from -6 (relative to the "normal" site of polyadenylation of RNAs from the rbcS-E9 gene) reveals a number of alternate polyadenylation sites located downstream from the normal poly(A) site. Transcripts carrying these sequences end at any one of at least seven sites between 20 and 300 bases downstream from the normal site. These sites are seen in populations of transgenic plant cells, and also in independent transgenic plants.

Contrasting interactions between phorbol ester and insulin on the regulation of glycogen synthase activity and p33 mRNA accumulation in rat hepatoma cells

We have compared the effect of phorbol 12-myristate 13-acetate (PMA) with that of insulin on three targets of insulin action in H4IIEC3 (H4) rat hepatoma cells. These parameters are the phosphorylation state and tyrosine kinase activity of the insulin receptor, the activation state of glycogen synthase, and the accumulation of p33 mRNA. Under conditions where insulin treatment of H4 cells clearly activated receptor serine and tyrosine phosphorylation on the insulin receptor beta-subunit in situ, activated receptor tyrosine kinase activity in vitro, and activated glycogen synthase and p33 mRNA accumulation in situ, PMA alone did not influence the insulin receptor phosphorylation state or tyrosine kinase activity and did not affect glycogen synthase activity, but markedly increased p33 mRNA accumulation. When PMA was added in the presence of insulin, particularly if PMA was preincubated, the receptor phosphorylation state and the tyrosine kinase activity again were not affected, but insulin-activated glycogen synthase was significantly diminished or abolished. In contrast, increased p33 mRNA accumulation by PMA was additive with that of insulin. Thus, under conditions where no effect was observed on the insulin receptor phosphorylation state or the tyrosine kinase activity, PMA acted in an insulin-antagonistic manner on glycogen synthase and in an insulin-like manner on p33 mRNA accumulation, indicating that these actions of PMA are unrelated to early events in the pathway of the insulin action. Effects on glycogen synthase are most readily explained by an effect of protein kinase C-activated phosphorylation of glycogen synthase.

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.

Primary structure of an alpha-tubulin gene of Physarum polycephalum

An alpha-tubulin gene of Physarum was isolated as a phage-lambda NM1149 recombinant (designated phage-lambda N alpha Tu). Phage-lambda N alpha Tu contained a 4700 base-pair HindIII nuclear DNA fragment of an allele of the altB locus of Physarum (one of four unlinked alpha-tubulin gene loci). Subfragments of the 4700 base-pair insert of phage-lambda N alpha Tu were cloned into phage M13 and the nucleotide sequence was determined by the dideoxy chain termination method. The start point of transcription was identified by primer extension and a putative polyadenylation site was located by S1 nuclease analysis. The 4650 base-pair HindIII insert into phage-lambda N alpha Tu spans the complete gene; sequences upstream from the 5' end contain the RNA transcription promoter elements (the TATA and CCAAT boxes). The nucleotide sequence encoding alpha-tubulin contains seven intervening sequences, ranging from 63 to 222 nucleotides in size. The exons have a sequence that is identical with a Physarum alpha-tubulin cDNA clone, except for three base changes, one leading to a Val codon in place of a Met codon, another leading to a Glu codon in place of an Asp codon, and the third change is silent. The genomic clone provides the nucleotide sequence coding for the last 26 amino acid residues missing from the cDNA clone. The new sequence data indicate that the alpha-tubulin gene has a C-terminal methionine codon and not a tyrosine codon, which has been found in all alpha-tubulin genes sequenced to date.

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.

Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements

U1 and U2 snRNAs are thought to be transcribed by RNA polymerase II. A conserved sequence known as the 3' box is located just downstream from the snRNA coding region and directs formation of the 3' end of pre-U1 and pre-U2 snRNA. We show here that a U1 or U2 promoter containing an intact snRNA enhancer is required for the U1 3' box to function efficiently. Promoters for genes encoding mRNAs cannot substitute for the snRNA promoter. Thus snRNAs must be transcribed by a specialized transcription complex that differs from transcription complexes synthesizing mRNAs. Moreover, in contrast to polyadenylated and nonpolyadenylated mRNAs, the 3' ends of pre-snRNAs must be generated either by termination of transcription, or by an RNA processing event intimately coupled to transcription.

New RNA species is produced by alternate polyadenylation following rearrangement associated with CAD gene amplification

Mammalian cells selected to resist N-(phosphonacetyl)-L-aspartate (PALA) contain amplified copies of the CAD gene. While a single 7.9-kb mRNA species is detected in PALA-sensitive and most PALA-resistant cell lines, two RNA species (7.9 and 10.2 kb) are detected in two related drug-resistant mutants presumably derived from the same parental cell. In this report we show that the 10.2-kb RNA is produced as a direct consequence of a sequence rearrangement adjacent to the 3' end of the CAD gene in these cell lines. A CAD gene containing the sequence rearrangement was cloned from one of these lines and found to produce both RNA species when transfected into CAD-deficient cells. DNA sequencing and S1 analysis demonstrate that the 10.2-kb RNA is produced by alternative polyadenylation rather than by alternative splicing. Sequence analysis also reveals that several consensus poly(A) addition signals (AATAAA) were brought into close proximity to the CAD gene by virtue of the rearrangement. While sequences adjacent to each of the polyadenylation signals contain additional features postulated to be important for the selection of the site of poly(A) addition, S1 mapping analysis indicates that only one of the polyadenylation signals is used. A comparison of all of these sites suggests that multiple sequence motifs are required to form a functional polyadenylation and cleavage signal.

Splicing and polyadenylylation at cryptic sites in RNA transcribed from pSV2-neo

Mapping the structures of RNAs transcribed from the chimeric plasmid pSV2-neo in transfected COS cells revealed discontinuities within the neo portion of the transcripts. Two cryptic 5' splice sites and three cryptic 3' splice sites were identified. The cryptic 5' splice sites matched 5 or 7 bases of the 5' consensus sequence. Each cryptic 3' splice site consisted of an AG that was preceded by a 15 nucleotide region which was 73% pyrimidine. They differed from the 3' consensus sequence mainly by the presence of a purine, rather than a pyrimidine, immediately adjacent to the AG at the splice site. Greater than 99% of the transcripts were spliced at the SV40 intron. Approx. 50% of these transcripts were spliced, in a complex pattern, at the additional sites within the neo region. Deletion of the SV40 early polyadenylylation signal from pSV2-neo revealed the presence of a cryptic polyadenylylation signal in a region of pBR322 sequence. It is located in the 5' portion of the beta-lactamase gene and occurs 6 +/- 2 nucleotides downstream from the sequence AATAATAATGAA, which contains three overlapping variant hexanucleotides. The cryptic signal appears to be approx. 10-fold less efficient than the SV40 polyadenylylation signal.

Poly(A) site cleavage in a HeLa nuclear extract is dependent on downstream sequences

Efficient utilization of the early SV40 poly(A) site in vivo requires sequences between 5 bp and 18 bp downstream of the cleavage site. We have used a HeLa nuclear extract to examine the sequence requirements for in vitro cleavage. DNA segments containing the SV40 poly(A) site were cloned into an SP6 vector. SP6 RNAs, accurately cleaved and polyadenylated, were detected by primer extension. Cleavage was enhanced by the presence of a cap on the primary transcript, and was inhibited by the addition of 10 microM 7meGpppG. In close agreement with the in vivo results, efficient processing at the poly(A) site in vitro required the specific downstream sequences in the SP6 RNA transcript. These experiments indicate that the sequence in the RNA precursor downstream of the cleavage site, shown to be important for efficient processing in vivo, is recognized in vitro.