End Polyadenylation Research Articles

Analysis of transcripts expressed from the UL47 gene of human cytomegalovirus.

The UL47 gene (b 60390-b 60338) located in the unique long region of the human cytomegalovirus (HCMV) AD169 strain genome was analyzed by RNA mapping. Northern blot analysis showed that the UL47 gene was expressed at late times after infection (72 h postinfection). The 9.7-kb transcript was expressed in the infected cells but not in phosphonoformate-treated cells at 72 hpi, indicating that the UL47 gene was only expressed at late times after infection. To map the 5'-end and 3'-end of UL47 transcripts, primer extension and RNase protection analysis were performed. Primer extension analysis revealed that the transcription initiation site of UL47 was located in 27 bp downstream (b 60323) of the TATA box motif. The sizes of UL47 ORF (approximately 2.9-kb) and UL48 ORF (approximately 6.7-kb) deduced from computer sequence analysis suggest that the expressed 9.7-kb transcript of UL47 uses the 3'-end polyadenylation signal of UL48. The result of RNase protection determined that the 3'-end of UL47 RNA utilized the 3'-end polyadenylation signal of UL48, which is located in HCMV genome b 70082.

Depletion of yeast RNase III blocks correct U2 3' end formation and results in polyadenylated but functional U2 snRNA.

Yeast U2 snRNA is transcribed by RNA polymerase II to generate a single non-polyadenylated transcript. A temperature-sensitive yeast strain carrying a disruption in RNT1, the gene encoding a homolog of RNase III, produces 3'-extended U2 that is polyadenylated. The U2 3'-flanking region contains a putative stem-loop that is recognized and cleaved at two sites by recombinant GST-Rnt1 protein in vitro. Removal of sequences comprising the stem-loop structure blocks cleavage in vitro and mimics the effects of Rnt1 depletion in vivo. Strains carrying a U2 gene lacking the Rnt1 cleavage site produce only polyadenylated U2 snRNA, and yet are not impaired in growth or splicing. The results suggest that eukaryotic RNase III may be a general factor in snRNA processing, and demonstrate that polyadenylation is not incompatible with snRNA function in yeast.

Influenza Virus NS1 Protein Interacts with the Cellular 30 kDa Subunit of CPSF and Inhibits 3′ End Formation of Cellular Pre-mRNAs

Inhibition of the nuclear export of poly(A)-containing mRNAs caused by the influenza A virus NS1 protein requires its effector domain. Here, we demonstrate that the NS1 effector domain functionally interacts with the cellular 30 kDa subunit of CPSF, an essential component of the 3′ end processing machinery of cellular pre-mRNAs. In influenza virus–infected cells, the NS1 protein is physically associated with CPSF 30 kDa. Binding of the NS1 protein to the 30 kDa protein in vitro prevents CPSF binding to the RNA substrate and inhibits 3′ end cleavage and polyadenylation of host pre-mRNAs. The NS1 protein also inhibits 3′ end processing in vivo, and the uncleaved pre-mRNA remains in the nucleus. Via this novel regulation of pre-mRNA 3′ end processing, the NS1 protein selectively inhibits the nuclear export of cellular, and not viral, mRNAs.

Operons and SL2 trans-splicing exist in nematodes outside the genus Caenorhabditis.

The genomes of most eukaryotes are composed of genes arranged on the chromosomes without regard to function, with each gene transcribed from a promoter at its 5' end. However, the genome of the free-living nematode Caenorhabditis elegans contains numerous polycistronic clusters similar to bacterial operons in which the genes are transcribed sequentially from a single promoter at the 5' end of the cluster. The resulting polycistronic pre-mRNAs are processed into monocistronic mRNAs by conventional 3' end formation, cleavage, and polyadenylation, accompanied by trans-splicing with a specialized spliced leader (SL), SL2. To determine whether this mode of gene organization and expression, apparently unique among the animals, occurs in other species, we have investigated genes in a distantly related free-living rhabditid nematode in the genus Dolichorhabditis (strain CEW1). We have identified both SL1 and SL2 RNAs in this species. In addition, we have sequenced a Dolichorhabditis genomic region containing a gene cluster with all of the characteristics of the C. elegans operons. We show that the downstream gene is trans-spliced to SL2. We also present evidence that suggests that these two genes are also clustered in the C. elegans and Caenorhabditis briggsae genomes. Thus, it appears that the arrangement of genes in operons pre-dates the divergence of the genus Caenorhabditis from the other genera in the family Rhabditidae, and may be more widespread than is currently appreciated.

Polyadenylation and transcription termination in gene constructs containing multiple tandem polyadenylation signals.

The processes of pre-mRNA 3'-end cleavage and polyadenylation have been closely linked to transcription termination by RNA polymerase II. We have studied the relationship between polyadenylation and transcription termination in gene constructs containing tandem poly(A) signals, at least one of which is the inefficient polyomavirus late poly(A) site. When identical tandem viral signals were separated by fewer than 400 bp, they competed for polyadenylation. The upstream site was always chosen preferentially, but relative site choice was influenced by the distance between the signals. All of these constructs showed the same low level of transcription termination as wild type polyomavirus, which contains a single late poly(A) site. When tandem poly(A) signals were not identical, a stronger downstream signal could outcompete a weaker upstream signal for polyadenylation without altering the efficiency of transcription termination characteristic for use of the upstream signal. Thus, if a weak polyoma virus late poly(A) signal (associated with inefficient transcription termination) preceded a strong rabbit beta-globin signal (associated with efficient transcription termination), termination remained inefficient, but the distal signal was most often chosen for polyadenylation. These results are consistent with independent regulation of polyadenylation and transcription termination in this system and are discussed in light of current models for the dependence of transcription termination on a functional poly(A) site.

The biochemistry of 3'-end cleavage and polyadenylation of messenger RNA precursors.

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More

The Biochemistry of 3'-End Cleavage and Polyadenylation of Messenger RNA Precursors

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More

An intact histone 3'-processing site is required for transcription termination in a mouse histone H2a gene.

A transcription termination site has been characterized between the mouse histone H2a-614 and H3-614 genes. There is a poly(A)- RNA present in small amounts in the nucleus which ends 600 nucleotides 3' to the H2a-614 gene. Nuclear transcription studies demonstrate that transcription extends at least 600 nucleotides 3' to the gene but is greatly reduced 700 nucleotides 3' to the gene. If all or part of the normal 3'-processing signal, consisting of the stem-loop and the U7 small nuclear ribonucleoprotein binding site, is deleted, transcription then continues past the putative termination site and RNAs which end at the 3' end of the downstream H3-614 gene accumulate. Insertion of a 150-nucleotide fragment containing the termination site between the histone 3' end and downstream polyadenylation sites reduces usage of polyadenylation sites 85 to 90%. Taken together these results suggest there is a transcription termination site which requires an intact histone 3'-processing signal to function.

An Intact Histone 3′-Processing Site Is Required for Transcription Termination in a Mouse Histone H2a Gene

A transcription termination site has been characterized between the mouse histone H2a-614 and H3-614 genes. There is a poly(A)- RNA present in small amounts in the nucleus which ends 600 nucleotides 3' to the H2a-614 gene. Nuclear transcription studies demonstrate that transcription extends at least 600 nucleotides 3' to the gene but is greatly reduced 700 nucleotides 3' to the gene. If all or part of the normal 3'-processing signal, consisting of the stem-loop and the U7 small nuclear ribonucleoprotein binding site, is deleted, transcription then continues past the putative termination site and RNAs which end at the 3' end of the downstream H3-614 gene accumulate. Insertion of a 150-nucleotide fragment containing the termination site between the histone 3' end and downstream polyadenylation sites reduces usage of polyadenylation sites 85 to 90%. Taken together these results suggest there is a transcription termination site which requires an intact histone 3'-processing signal to function.

Ordered splicing of thymidine kinase pre-mRNA during the S phase of the cell cycle.

Concomitant with the onset of S phase, a series of thymidine kinase (TK) splicing intermediates as well as mature TK mRNA accumulates in the nucleus of BALB/c 3T3 cells. Most of the TK splicing intermediates are retained by oligo(dT)-cellulose chromatography, and, therefore, 3' end formation and polyadenylation probably precede the splicing of TK pre-mRNAs. We have further characterized the TK pre-mRNAs that are present in the nuclei of S-phase cells by using specific probes derived from each of the six TK intervening sequences. Based on the sizes of the pre-mRNAs and their patterns of hybridization with these intron probes, we propose a pathway for intron removal from nascent TK transcripts. Intron excision occurred by a preferred, but not necessarily obligatory, order which appears to have been conserved in mouse and Chinese hamster cells.

Ordered Splicing of Thymidine Kinase Pre-mRNA during the S Phase of the Cell Cycle

Concomitant with the onset of S phase, a series of thymidine kinase (TK) splicing intermediates as well as mature TK mRNA accumulates in the nucleus of BALB/c 3T3 cells. Most of the TK splicing intermediates are retained by oligo(dT)-cellulose chromatography, and, therefore, 3' end formation and polyadenylation probably precede the splicing of TK pre-mRNAs. We have further characterized the TK pre-mRNAs that are present in the nuclei of S-phase cells by using specific probes derived from each of the six TK intervening sequences. Based on the sizes of the pre-mRNAs and their patterns of hybridization with these intron probes, we propose a pathway for intron removal from nascent TK transcripts. Intron excision occurred by a preferred, but not necessarily obligatory, order which appears to have been conserved in mouse and Chinese hamster cells.

New vectors for the efficient expression of mammalian genes in cultured cells

We have constructed a new pair of plasmid vectors for the efficient expression of mammalian genes. The first of the new plasmids, pAVE1, was derived from pCMVcat [Foecking and Hofstetter, Gene 45 (1986) 101–105] by replacing the chloramphenicol acetyltransferase-encoding sequences in the latter for a multiple cloning site. Since it possesses the powerful enhancer-promoter unit of the immediate early gene of human cytomegalovirus, pAVE1 is ideal for the expression of mammalian genes. The second expression vector, pAVE2, resulted when the 3′ -end flanking region from the human growth hormone-encoding gene ( hGH) was incorporated in pAVE1. This region provides sequences for 3′-end processing and polyadenylation of primary transcripts. Thus, pAVE2 is suitable for expression of cDNAs in cultured cells, where introns have little effect on gene expression. To test our new vectors, we inserted the structural region of the chromosomal ( hGH) gene into pAVE1, and its cDNA into pAVE2. By independently transfecting the resulting recombinant plasmids into COS-7 cells, we have achieved high levels of hGH transient expression with both vectors.

Identification and functional analysis of mammalian splicing factors.

In eukaryotic cells most primary transcripts of protein-coding genes are processed through a variety of post-transcriptional modification reactions to yield mature mRNA. One of these processing reactions termed pre-mRNA splicing involves the accurate excision of intron RNA sequences and the coordinate ligation of exon RNA sequences. In addition, there are post-transcriptional modifications at the 5’ end (capping) and at the 3’ end (polyadenylation). A systematic biochemical study of premRNA splicing began with the development of efficient in vitro splicing systems [reviewed in (1)] that accurately splice synthetic pre-mRNAs in nuclear extracts prepared from cultured mammalian cells. In most cases, relatively short model substrates consisting of two exons and one intron were used for these studies (see Figure 1 for a schematic representation). The biochemical analysis of this highly complex RNA processing reaction has since made rapid progress. Initial studies revealed a two-step mechanism involving the three conserved splicing signals (Figure 1). First, cleavage at the 5’ splice site occurs concomitantly with lariat formation at the intron branch point. Second, the RNA intermediates, exon 1 and intron lariat-exon 2, are cleaved at the 3’ splice site, and the two exon RNA sequences are ligated together. The intron RNA sequences are thereby released in the form of a lariat. Soon after the establishment of in vitro splicing systems it became clear that this complex series of reactions occurs in large ribonucleoprotein (RNP) structures of the pre-mRNA called splicing complexes or spliceo­somes (2–7). The ordered assembly of splicing complexes is a prerequisite of the pre-mRNA splicing reaction and requires the coordinate action of small nuclear ribonucleoproteins (snRNPs) and of additional proteins, so-called non-snRNP splicing factors.

Genomic differences between the diabetogenic and nondiabetogenic variants of encephalomyocarditis virus

Plaque purification of the M variant of encephalomyocarditis (EMC-M) virus resulted in the isolation of two stable variants. One is a highly diabetogenic D variant (EMC-D) and the other is a nondiabetogenic B variant (EMC-B). The cDNA of EMC-D and EMC-B genomes were cloned and seven overlapping cDNA clones were selected to cover the entire genome except the 5′-end 310 bases which were determined by RNA-dependent DNA sequencing and enzymatic RNA sequencing. Each clone was restriction-mapped, subcloned, and sequenced. The genomes of EMC-D and EMC-B are composed of 7829 and 7825 bases, respectively. Both genomes contain a long open reading frame of 6876 nucleotides starting at position 830 on the consensus sequence, which encodes a polyprotein of 2292 amino acids. The sequences of EMC-D and EMC-B differ by two deletions, one insertion, and eight point mutations. The first deletion of 3 nucleotides is located in the 5′ poly(C) tract where EMC-B has 127 nucleotides compared with 130 nucleotides in EMC-D. The second deletion in EMC-B involves 2 nucleotides at the 3′-end polyadenylation site. A single base insertion of U occurs at the 5′ noncoding region of EMC-B. The eight point mutations are located in the polyprotein coding region. Two are silent and are each located in the structural gene 1B and in the nonstructural gene 2B. The remaining six mutations, one on the L gene and the other five on the 1D gene, introduce respective amino acid changes. It is concluded that the diabetogenic EMC-D viral genome (7829 bases) differs from the nondiabetogenic EMC-B viral genome (7825 bases) by 14 nucleotides out of 7829.

Molecular Identification of Diabetogenic Viral Gene

The best evidence that viruses have a causative role in the pathogenesis of insulin-dependent diabetes mellitus comes from experiments in mice infected with encephalomyocarditis (EMC) virus. When SJL/J male mice were inoculated with a highly diabetogenic EMC-D virus, diabetes developed in 95% of the animals. In contrast, none of the mice inoculated with a nondiabetogenic EMC-B virus became diabetic. Tissue culture experiments showed that EMC-B induces considerable amounts of interferon, whereas EMC-D does not. Despite these differences, EMC-D and EMC-B could not be distinguished antigenically by a sensitive plaque-neutralization assay. Furthermore, the buoyant density in CsCl density gradients and the capsid proteins of these two variants on polyacrylamide gels could not be distinguished. Molecular-hybridization studies with radiolabeled DNA complementary to EMC-D and EMC-B RNAs failed to distinguish them. Determination of complete nucleotide sequences of EMC-D and EMC-B revealed that EMC-D (7829 bases) differs from EMC-B (7825 bases) by only 14 nucleotides. The differences consist of two deletions of five nucleotides, one base insertion, and eight point mutations. The first deletion of three nucleotides and the second deletion of two nucleotides are located in the 5'-poly(C) tract and the 3'-end polyadenylation site, respectively. One base insertion in EMC-B occurs in the 5'-noncoding region. The eight point mutations are located in the polyprotein-coding region. Two of them are silent, whereas the other six mutations, one located on the L gene and five on the VP1 gene, introduce amino acid changes.(ABSTRACT TRUNCATED AT 250 WORDS)

Poladenylated H3 histone transcripts and H3 histone vairants in alfalfa

Histone H3 mRNAs were found in polyA(+) fractions of total RNA prepared from alfalfa plants, calli and somatic embryos. The sequence analysis of cDNAs revealed the presence of a polyA tail on independent alfalfa H3 mRNAs. A highly conserved sequence motif AAUGAAA identified about 20bp upstream from the 3' ends of the alfalfa H3 cDNAs was suggested to be one of the possible regulatory elements in the 3' end formation and polyadenylation. Three out of the four analysed H3 cDNAs have more than 97% homology with a genomic clone and encode the same protein. While the fourth represents a minor species with only 78.8% homology to the coding region of the genomic clone and encodes a H3 histone with four amino acid replacements. On the basis of compilation analysis we suggest a consensus sequence for plant H3 histones which differs from that of animal's by four amino acid changes.

Transient expression in mammalian cells of the bacterial reporter gene encoding mercuric reductase: effects of various regulatory elements

The effect of several transcriptional regulatory elements on gene expression in mammalian cells was investigated. As a reporter gene we have used the bacterial gene merA coding for the enzyme mercuric reductase. Several plasmids were constructed with different promoter/enhancer sequences ( p sv/E, P sv/l, p mt, p rsv or p ad) at the 5' end and different splicing (small intron of the T antigen of SV40 or the second intron of the rabbit β-globin gene) and/or polyadenylation signals (A E n, A L n or A RβG n) at the 3' end of the merA gene. Expression was measured in five different mammalian cell lines. In COS cells the highest level of expression is obtained with p SV/L and the lowest level with p sv/e. In HeLa, CV-1, L tk −, and CHO cells merA expression is relatively high, under control of p RSV and p MT and relatively low under control of p SV/L and p Ad. The introns studied have a negative effect on the expression of merA. The presence of a polyadenylation signal downstream from the gene is essential for its expression. The three different polyadenylation signals studied give a similar stimulatory effect on the level of expression of the merA gene.

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.

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.

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.