Transcription termination occurs within a 1000 base pair region downstream from the poly(A) site of the mouse beta-globin (major) gene

Promoter-sharing by different genes in human genome--CPNE1 and RBM12 gene pair as an example

Background

Regulation of gene expression plays important role in cellular functions. Co-regulation of different genes may indicate functional connection or even physical interaction between gene products. Thus analysis on genomic structures that may affect gene expression regulation could shed light on the functions of genes.

Results

In a whole genome analysis of alternative splicing events, we found that two distinct genes, copine I (CPNE1) and RNA binding motif protein 12 (RBM12), share the most 5' exons and therefore the promoter region in human. Further analysis identified many gene pairs in human genome that share the same promoters and 5' exons but have totally different coding sequences. Analysis of genomic and expressed sequences, either cDNAs or expressed sequence tags (ESTs) for CPNE1 and RBM12, confirmed the conservation of this phenomenon during evolutionary courses. The co-expression of the two genes initiated from the same promoter is confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) in different tissues in both human and mouse. High degrees of sequence conservation among multiple species in the 5'UTR region common to CPNE1 and RBM12 were also identified.

Conclusion

Promoter and 5'UTR sharing between CPNE1 and RBM12 is observed in human, mouse and zebrafish. Conservation of this genomic structure in evolutionary courses indicates potential functional interaction between the two genes. More than 20 other gene pairs in human genome were found to have the similar genomic structure in a genome-wide analysis, and it may represent a unique pattern of genomic arrangement that may affect expression regulation of the corresponding genes.

Transcriptional termination sequences in the mouse serum albumin gene

Poly(A) signals are required for efficient 3' end formation and transcriptional termination of most protein-encoding genes transcribed by RNA polymerase II. However, transcription can extend far beyond the poly(A) site before termination occurs. This implies the existence of further downstream termination signals. In mammals, a variety of sequence elements, in addition to the poly(A) site, have been implicated in the termination process. For example, termination of the human beta- and epsilon-globin genes is mediated by a sequence downstream of the poly(A) site that promotes an RNA cotranscriptional cleavage (CoTC). Here we report the identification of multiple termination sequences in the mouse serum albumin (MSA) 3' flanking region. Many transcripts from this region are cleaved cotranscriptionally, implying that such cleavage of pre-mRNA may be a more general feature of transcriptional termination.

Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair

Protein clamps are ubiquitous and essential components of DNA metabolic machineries, where they serve as mobile platforms that interact with a large variety of proteins. In this report we identify residues that are required for binding of the beta-clamp to DNA polymerase III of Escherichia coli, a polymerase of the Pol C family. We show that the alpha polymerase subunit of DNA polymerase III interacts with the beta-clamp via its extreme seven C-terminal residues, some of which are conserved. Moreover, interaction of Pol III with the clamp takes place at the same site as that of the delta-subunit of the clamp loader, providing the basis for a switch between the clamp loading machinery and the polymerase itself. Escherichia coli DNA polymerases I, II, IV and V (UmuC) interact with beta at the same site. Given the limited amounts of clamps in the cell, these results suggest that clamp binding may be competitive and regulated, and that the different polymerases may use the same clamp sequentially during replication and repair.

Inducible and irreversible control of gene expression using a single transgene

Experimental or therapeutic designs involving the conditional expression of genes often require the use of two different transgenes; this can represent a major undertaking. One of these systems takes advantage of inducible recombinases. Here we show a novel use of such enzymes, in that an inducible recombinase-encoding sequence can function to both block the transcription of a gene placed downstream and, subsequently, irreversibly activate transcription of this very same gene. This double function, which circumvents the need for two transgenes, can be achieved by flanking the inducible recombinase gene by two of its target sequences. In our design we used as the inducible recombinase gene the Cre-ER(T) gene flanked by two loxP sites. This cassette was placed between a mouse phosphoglycerate kinase promoter and the enhanced green fluorescent protein (EGFP) coding sequence. Massive EGFP gene expression in BHK cells bearing this transgene was observed upon administration of 4-hydroxytamoxifen (4-OHT), the inducer of the recombinant activity of Cre-ER(T). In the absence of 4-OHT EGFP production was prevented. Because of its simplicity (only a single transgene needs to be used) this strategy is of obvious interest in certain protocols of gene or cell therapy and in a variety of experimental designs in which conditional expression of genes is required.

Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae

We have investigated transcriptional interactions between the GAL10 and GAL7 genes of Saccharomyces cerevisiae. Both genes are part of the galactose (GAL) gene cluster which is transcriptionally activated to high levels in the presence of galactose. Since GAL7 is positioned downstream of GAL10 and both genes are expressed co-ordinately at high levels, the possibility that GAL10 transcription influences GAL7 was analysed. Using transcriptional run-on assays, we show that high levels of polymerase are found in the 600 bp GAL10-7 intergenic region that accumulate over the GAL7 promoter. Furthermore, GAL7 transcription is enhanced when the GAL10 upstream activating sequence (UASG) is deleted, indicating that interference between GAL10 and GAL7 is likely to occur in the chromosomal locus. Deletions in the GAL10 poly(A) signal result in complete inactivation of the GAL7 promoter and cause a dramatic increase in bi-cistronic GAL10-7 mRNA, predominantly utilizing the downstream, GAL7 poly(A) site. These data demonstrate a pivotal role for the GAL10 poly(A) site in allowing the simultaneous expression of GAL10 and GAL7. In effect, this RNA processing signal has a direct influence on both transcriptional termination and initiation.

Regulation of c-fos expression by RNA polymerase elongation competence

The molecular mechanisms underlying transcription elongation and their role in gene regulation are poorly characterized in eukaryotes. A number of genes, however, have been proposed to be regulated at the level of transcription elongation, including c-myc, c-fos and c-myb. Here, we analyze the control of transcription elongation at the mouse c-fos gene at the nucleotide level in intact cells. We find that RNA polymerases are engaged in the promoter-proximal part of the gene in the absence of gene activation signals and mRNA synthesis. Importantly, we determine that the engaged RNA polymerases originate from a continuous initiation of transcription which, in the absence of gene activation signals, terminate close to the promoter. We also observe that the c-fos gene presents an active chromatin conformation, with the promoter and upstream regulatory sequences constitutively occupied by proteins, accounting for the continuous initiation of RNA polymerase complexes. We propose that activation of c-fos gene expression results primarily from the assembly of elongation-competent RNA polymerases that can transcribe the complete gene. Our results suggest that the engaged RNA polymerases found downstream of a number of other eukaryotic promoters may be associated with transcription termination of elongation-incompetent polymerases in the absence of activating signals.

Nascent transcription from the nmt1 and nmt2 genes of Schizosaccharomyces pombe overlaps neighbouring genes

We have determined the extent of the primary transcription unit for the two highly expressed genes nmt1 and nmt2 of Schizosaccharomyces pombe. Transcription run-on analysis in permeabilized yeast cells was employed to map polymerase density across the 3'-flanking region of these two genes. Surprisingly, polymerases were detected 4.3 kb beyond the nmt1 polyadenylation [poly(A)] site and 2.4 kb beyond the nmt2 poly(A) site, which in each case have transcribed through an entire convergent downstream transcription unit. However, the steady-state levels of both downstream genes were unaffected by the high level of nmt1 or nmt2 nascent transcription. Analysis of nmt1 and nmt2 RNA 3' end formation signals indicates that efficient termination of transcription requires not only a poly(A) signal but also additional pause elements. The absence of such pause elements close to the poly(A) sites of these genes may account for their extended nascent transcripts.

A novel transcriptional element in circular DNA monomers of the duck hepatitis B virus

We report the presence of two elements, pet and net, that are required for proper transcription of the duck hepatitis B virus (DHBV). These regions were previously identified by using plasmid clones of the virus in transient expression assays (M. Huang and J. Summers, J. Virol. 68:1564-1572, 1994). In this study, we further analyzed these regions by using in vitro-synthesized circular DHBV DNA monomers to mimic the authentic transcriptional template. We observed that pet was required for pregenome transcription from circular viral monomers, and in the absence of pet-dependent transcription, expression of the viral envelope genes was increased. We found that deletion of net in circularized DNA monomers led to the production of abnormally long transcripts due to a failure to form 3' ends during transcription. In addition, we report the presence of a net-like region in the mammalian hepadnavirus woodchuck hepatitis virus. These results are consistent with a model that net is a region involved in transcription termination and that in DHBV, pet is required for transcription complexes to read through this region during the first pass through net.

Transcription and polyadenylation in a short human intergenic region

The poly(A) signal of the human Lamin B2 gene was previously shown to lie 600 bp upstream of the cap site of a gene of unknown function (ppv 1). However, using RNase protection analysis, we show that ppv 1 has two clusters of multiple initiation sites, so that the 5"cap site lies only approximately 280 nt downstream of the Lamin B2 poly(A) signal. We analysed nascent transcription across this unusually short intergenic region using nuclear run-on analysis of both the endogenous locus and of transiently transfected hybrid constructs. Surprisingly, transcription of the Lamin B2 gene does not appear to terminate prior to any of the mapped ppv 1 start sites, although pausing of the elongating polymerase complexes is observed downstream of the Lamin B2 poly(A) signal. We suggest that this pausing may be sufficient to protect the downstream gene from transcriptional interference. Finally, we have also investigated the sequences required for efficient recognition of the Lamin B2 poly(A) signal. We show that sequences upstream of the AAUAAA element are required for full activity, which is an unusual feature of mammalian poly(A) signals.

Sequence-mediated regulation of adenovirus gene expression by repression of mRNA accumulation

Gene expression in complex transcription units can be regulated at virtually every step in the production of mature cytoplasmic mRNA, including transcription initiation, elongation, termination, pre-mRNA processing, nucleus-to-cytoplasm mRNA transport, and alterations in mRNA stability. We have been characterizing alternative poly(A) site usage in the adenovirus major late transcription unit (MLTU) as a model for regulation at the level of pre-mRNA 3'-end processing. The MLTU contains five polyadenylation sites (L1 through L5). The promoter proximal site (L1) functions as the dominant poly(A) site during the early stage of adenovirus infection and in plasmid transfections when multiple poly(A) sites are present at the 3' end of a reporter plasmid. In contrast, stable mRNA processed at all five poly(A) sites is found during the late stage of adenovirus infection, after viral DNA replication has begun. Despite its dominance during early infection, L1 is a comparatively poor substrate for 3'-end RNA processing both in vivo and in vitro. In this study we have investigated the basis for the early L1 dominance. We have found that mRNA containing an unprocessed L1 poly(A) site is compromised in its ability to enter the steady-state pool of stable mRNA. This inhibition, which affects either the nuclear stability or nucleus-to-cytoplasm transport of the pre-mRNA, requires a cis-acting sequence located upstream of the L1 poly(A) site.

Construction and characterization of a one-plasmid system for the controlled expression of genes in mammalian cells by tetracycline

The two-plasmid system of Gossen and Bujard [Gossen and Bujard (1992) Proc. Natl. Acad. Sci. USA 89, 5547-5551] to express mammalian genes in a tetracycline-repressed fashion was combined into a single-plasmid system. Two variants of this single-plasmid system that differ in the multiple cloning site (MCS) region are described. These vectors were used to stably transfect raf kinase domain into the normal rat kidney epithelial cell line (NRKE) to obtain a conditionally transformed cell line. These vectors were also used to stably transfect wild-type and mutant human p53 into the human osteosarcoma cell line, SAOS-2. Tetracycline repressed gene expression in both cell lines; about 12-fold in NRKE and about 80-fold in SAOS-2 cell line.

3' Processing and termination of mouse histone transcripts synthesized in vitro by RNA polymerase II

The highly expressed mouse histone H2a-614 gene is located 800 nt 5' of the histone H3-614 gene. There is a 140 nt sequence located 500 nt from the end of the H2-614 mRNA which has been defined as a transcription termination site for RNA polymerase II. We established an in vitro transcription system in which both 3' end processing and transcription termination occur. A template containing the adenovirus major late promoter, a portion of the histone H2a-614 coding region, its 3' processing signal, followed by the transcription termination site was transcribed in a nuclear extract prepared from mouse myeloma cells. Some of the transcripts synthesized in the extract were cleaved at the histone processing site in a reaction which was dependent both on the hairpin binding factor and the U7 snRNP. The efficiency of histone 3' end formation was similar both on synthetic transcripts and transcripts synthesized by RNA polymerase II. Defined transcripts, which were not processed and which mapped to the transcription termination site, were released from the template, suggesting that they were formed by transcription termination. Termination in vitro was dependent on a functional histone processing signal.

The 3'-untranslated region of membrane exon 2 from the gamma 2a immunoglobulin gene contributes to efficient transcription termination

Elements of the mouse Immunoglobulin gamma 2a gene, near the membrane-specific poly(A) addition site, were inserted into a heterologous location in either a synthetic mouse gamma 2b gene or a gpt/SV40 chimeric gene and then assayed for their ability to terminate RNA polymerase II transcription in isolated nuclei of transfected myeloma cells. The intact gamma 2a membrane-specific 3'-untranslated region, with its potential stem loop forming sequences and poly(A) site, is able to efficiently terminate transcription in the absence of the downstream region in which transcription normally terminates (term). Termination efficiency in the presence of the termination fragment decreases either when sequences specifying a potential stem/loop, upstream of the poly(A) region, are interrupted or when the stronger membrane poly(A) site is substituted with a weaker, secretory-specific poly(A) site. We therefore conclude that the gamma 2a membrane-specific untranslated region plays a major role in specifying downstream termination. We further conclude that the immunoglobulin gamma 2a, membrane-specific, 3'-untranslated region can function in the context of the gpt gene, driven by an SV40 promoter, to terminate transcription in a poly(A) site dependent fashion.

Two tightly-linked Drosophila male accessory gland transcripts with the same developmental expression derive from independent transcription units

Acp26Aa and Acp26Ab are Drosophila male accessory gland transcripts that are tightly linked and transcribed from the same DNA strand. Despite their being separated by 20 base pairs, the transcripts show identical responses to several developmental signals. These observations make it important to determine whether the 26A region contains two separable genes with the same developmental expression or a single developmentally regulated transcription unit whose product is processed to yield Acp26Aa and Acp26Ab. We show that Acp26Aa and Acp26Ab are separate mRNAs using a reverse transcription-polymerase chain reaction assay and reporter gene fusions. We also show that the regulatory elements for Acp26Ab lie within a fragment containing the intergenic region and transcribed sequences of Acp26Aa and Acp26Ab.

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.

Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites

The adenovirus major late transcription unit is a well-characterized transcription unit which relies heavily on alternative pre-mRNA processing to generate distinct populations of mRNA during the early and late stages of viral infection. In the early stage of infection, two major late transcription unit mRNA transcripts are generated through use of the first (L1) of five available poly(A) sites (L1 through L5). This contrasts with the late stage of infection when as many as 45 distinct mRNAs are generated, with each of the five poly(A) sites being used. In previous work characterizing elements involved in alternative poly(A) site use, we showed that the L1 poly(A) site is processed less efficiently than the L3 poly(A) site both in vitro and in vivo. Because of the dramatic difference in processing efficiency and the role processing efficiency plays in production of steady-state levels of mRNA, we have identified the sequence elements that account for the differences in L1 and L3 poly(A) site processing efficiency. We have found that the element most likely to be responsible for poly(A) site strength, the GU/U-rich downstream element, plays a minor role in the different processing efficiencies observed for the L1 and L3 poly(A) sites. The sequence element most responsible for inefficient processing of the L1 poly(A) site includes the L1 AAUAAA consensus sequence and those sequences which immediately surround the consensus hexanucleotide. This region of the L1 poly(A) site contributes to an inability to form a stable processing complex with the downstream GU/U-rich element. In contrast to the L1 element, the L3 poly(A) site has a consensus hexanucleotide and surrounding sequences which can form a stable processing complex in cooperation with the downstream GU/U-rich element. The L3 poly(A) site is also aided by the presence of sequences upstream of the hexanucleotide which facilitate processing efficiency. The sequence UUCUUUUU, present in the L3 upstream region, is shown to enhance processing efficiency as well as stable complex formation (shown by increased binding of the 64-kDa cleavage stimulatory factor subunit) and acts as a binding site for heterogeneous nuclear ribonucleoprotein C proteins.

Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites

The adenovirus major late transcription unit is a well-characterized transcription unit which relies heavily on alternative pre-mRNA processing to generate distinct populations of mRNA during the early and late stages of viral infection. In the early stage of infection, two major late transcription unit mRNA transcripts are generated through use of the first (L1) of five available poly(A) sites (L1 through L5). This contrasts with the late stage of infection when as many as 45 distinct mRNAs are generated, with each of the five poly(A) sites being used. In previous work characterizing elements involved in alternative poly(A) site use, we showed that the L1 poly(A) site is processed less efficiently than the L3 poly(A) site both in vitro and in vivo. Because of the dramatic difference in processing efficiency and the role processing efficiency plays in production of steady-state levels of mRNA, we have identified the sequence elements that account for the differences in L1 and L3 poly(A) site processing efficiency. We have found that the element most likely to be responsible for poly(A) site strength, the GU/U-rich downstream element, plays a minor role in the different processing efficiencies observed for the L1 and L3 poly(A) sites. The sequence element most responsible for inefficient processing of the L1 poly(A) site includes the L1 AAUAAA consensus sequence and those sequences which immediately surround the consensus hexanucleotide. This region of the L1 poly(A) site contributes to an inability to form a stable processing complex with the downstream GU/U-rich element. In contrast to the L1 element, the L3 poly(A) site has a consensus hexanucleotide and surrounding sequences which can form a stable processing complex in cooperation with the downstream GU/U-rich element. The L3 poly(A) site is also aided by the presence of sequences upstream of the hexanucleotide which facilitate processing efficiency. The sequence UUCUUUUU, present in the L3 upstream region, is shown to enhance processing efficiency as well as stable complex formation (shown by increased binding of the 64-kDa cleavage stimulatory factor subunit) and acts as a binding site for heterogeneous nuclear ribonucleoprotein C proteins.

3' RNA processing efficiency plays a primary role in generating termination-competent RNA polymerase II elongation complexes

In several mammalian transcription units, a transcription termination mechanism in which efficient termination is dependent on the presence of an intact 3' RNA processing site has been identified. The mouse beta maj-globin transcription unit is one such example, in which an intact poly(A) site is required for efficient transcription termination. It is now evident that 3' mRNA processing sites are not always processed with the same efficiency. In this study, we characterized several pre-mRNAs as substrates for the 3' mRNA processing reaction of cleavage and polyadenylation. We then determined whether poly(A) sites which vary in processing efficiency support a poly(A) site-dependent termination event. The level of processing efficiency was determined in vitro by assays measuring the efficiency of the pre-mRNA cleavage event and in vivo by the level of poly(A) site-dependent mRNA and gene product expression generated in transient transfection assays. The beta maj globin pre-mRNA is very efficiently processed. This efficient processing correlates with its function in termination assays using recombinant adenovirus termination vectors in nuclear run-on assays. When the beta maj globin poly(A) site was replaced by the L1 poly(A) site of the adenovirus major late transcription unit (Ad-ml), which is a poor processing substrate, termination efficiency decreased dramatically. When the beta maj globin poly(A) site was replaced by the Ad-ml L3 poly(A) site, which is 10- to 20-fold more efficiently processed than the Ad-ml L1 poly(A) site, termination efficiency remained high. Termination is therefore dependent on the yield of the processing event. We then tested chimeric poly(A) sites containing the L3 core AAUAAA but varied downstream GU-rich elements. The change in downstream GU-rich elements affected processing efficiency in a manner which correlated with termination efficiency. These experiments provide evidence that the efficiency of 3' processing complex formation is directly correlated to the efficiency of RNA polymerase II termination at the 3' end of a mammalian transcription unit.

3' RNA processing efficiency plays a primary role in generating termination-competent RNA polymerase II elongation complexes

In several mammalian transcription units, a transcription termination mechanism in which efficient termination is dependent on the presence of an intact 3' RNA processing site has been identified. The mouse beta maj-globin transcription unit is one such example, in which an intact poly(A) site is required for efficient transcription termination. It is now evident that 3' mRNA processing sites are not always processed with the same efficiency. In this study, we characterized several pre-mRNAs as substrates for the 3' mRNA processing reaction of cleavage and polyadenylation. We then determined whether poly(A) sites which vary in processing efficiency support a poly(A) site-dependent termination event. The level of processing efficiency was determined in vitro by assays measuring the efficiency of the pre-mRNA cleavage event and in vivo by the level of poly(A) site-dependent mRNA and gene product expression generated in transient transfection assays. The beta maj globin pre-mRNA is very efficiently processed. This efficient processing correlates with its function in termination assays using recombinant adenovirus termination vectors in nuclear run-on assays. When the beta maj globin poly(A) site was replaced by the L1 poly(A) site of the adenovirus major late transcription unit (Ad-ml), which is a poor processing substrate, termination efficiency decreased dramatically. When the beta maj globin poly(A) site was replaced by the Ad-ml L3 poly(A) site, which is 10- to 20-fold more efficiently processed than the Ad-ml L1 poly(A) site, termination efficiency remained high. Termination is therefore dependent on the yield of the processing event. We then tested chimeric poly(A) sites containing the L3 core AAUAAA but varied downstream GU-rich elements. The change in downstream GU-rich elements affected processing efficiency in a manner which correlated with termination efficiency. These experiments provide evidence that the efficiency of 3' processing complex formation is directly correlated to the efficiency of RNA polymerase II termination at the 3' end of a mammalian transcription unit.

Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements

For the majority of mRNA encoding eukaryotic transcription units, there is little or no knowledge of the elements responsible for transcription termination or how they may interact with RNA polymerase. In this report, we have used recombinant adenovirus reporter vectors to characterize the mouse beta maj globin sequence elements that cause transcription termination. Within the globin 3' termination region, we have identified at least three sequence elements which induce significant levels of transcription termination (> 50%). The smallest functionally active element (64% termination) is 69 bp in length. The natural arrangement of these elements results in a cumulative termination which is greater than 90%. Recognition of the termination elements by RNA polymerase II depends on the presence of a functional poly(A) signal sequence. We demonstrate that efficient transcription termination depends on appropriate spacing between the poly(A) signal sequence and the termination element.

Characterization of the mouse beta maj globin transcription termination region: a spacing sequence is required between the poly(A) signal sequence and multiple downstream termination elements

For the majority of mRNA encoding eukaryotic transcription units, there is little or no knowledge of the elements responsible for transcription termination or how they may interact with RNA polymerase. In this report, we have used recombinant adenovirus reporter vectors to characterize the mouse beta maj globin sequence elements that cause transcription termination. Within the globin 3' termination region, we have identified at least three sequence elements which induce significant levels of transcription termination (> 50%). The smallest functionally active element (64% termination) is 69 bp in length. The natural arrangement of these elements results in a cumulative termination which is greater than 90%. Recognition of the termination elements by RNA polymerase II depends on the presence of a functional poly(A) signal sequence. We demonstrate that efficient transcription termination depends on appropriate spacing between the poly(A) signal sequence and the termination element.

Association of AUUUA-binding protein with A+U-rich mRNA during nucleo-cytoplasmic transport

Resealed nuclear envelope (NE) vesicles from rat liver containing entrapped exogenous RNA were used to study the effect of adenosine+uridine binding factor (AUBF), present in cytosolic cell extracts, on ATP-dependent transport of A+U-rich RNA (AU+RNA) and A+U-free RNA (AU-RNA) across the NE. This factor specifically binds to A+U-rich sequences present in the 3' untranslated regions of lymphokine and cytokine mRNAs, containing overlapping AUUUA boxes (granulocyte-macrophage colony stimulating factor, interleukin-3). Addition of AUBF to the extravesicular compartment markedly increased the efflux of the in vitro transcribed, capped and polyadenylated AU+ RNAs. Export of entrapped AU- control RNA, such as beta-globin RNA, was not affected by AUBF, in contrast to chimeric AU+ beta-globin RNA containing the A+U-rich sequence of human interferon-alpha mRNA (6 reiterated AUUUA motifs). Competition experiments revealed that AUBF enhances the affinity of poly(A)-containing AU+ RNAs to the NE poly(A)-binding component (poly(A)-recognizing mRNA carrier p106), and thereby accelerates nuclear export of these RNAs. We could demonstrate that AUBF added to the extravesicular space forms stable complexes with polyadenylated AU+ RNA with relative molecular masses of about 45,000, 62,000 and 70,000 inside the vesicles or during ATP-dependent export. In addition we determined that AUBF may affect mRNA stability by protecting A+U-rich RNA against degradation by trans-acting, nuclear matrix-associated and A+U-specific endoribonuclease V.

A protein-binding site in the c-myc promoter functions as a terminator of RNA polymerase II transcription

Termination of transcription not only allows polymerases that have completed RNA synthesis to recycle, but it also has important functions in transcriptional regulation and in preventing promoter interference. The molecular basis for termination by RNA polymerase II (pol II) is unclear, however. We have identified a termination site in the promoter region of the c-myc gene, whose function correlates with DNA binding by a nuclear factor. When the c-myc gene was transcribed in injected Xenopus oocytes or a HeLa nuclear extract, a fraction of RNA initiated at the first promoter, P1, terminated at two positions, T1A and T1B, which flank the TATA box of the second promoter, P2. T1B is a T-rich sequence that resembles previously identified attenuation sites, but T1A appears to represent a different class of termination site. T1A is situated approximately 10 bases upstream of an element that overlaps the P2 TATA box. Mutagenesis of this element affected both the efficiency and the position at which termination occurred. A 28-base sequence including this element caused a low level of termination when inserted into the alpha-globin gene in either orientation. This sequence bound a factor called TBF I (terminator-binding factor), whose binding specificity correlated with T1A terminator function. We suggest that TBF I may function as a pol II termination factor.

An apparent pause site in the transcription unit of the rabbit alpha-globin gene

Transcription of the rabbit alpha-globin gene begins primarily at the cap site, although some upstream start sites are also observed. Analysis by RNA polymerase run-on assays in nuclei shows that transcription continues at a high level past the polyadenylation site, after which the polymerase density actually increases in a region of about 400 nucleotides, followed by a gradual decline over the 700 nucleotides. These features are also observed in the transcription unit of the rabbit beta-globin gene. The region with the unexpectedly high nascent RNA hybridization signal in the 3' flank contains a conserved sequence, KGCAGCWGGR (K = G or T, W = A or T, R = A or G), followed by an inverted repeat. The inverted repeat (perhaps with the conserved sequence) may be a pause site for RNA polymerase II, thus accounting for the increase in polymerase density. This sequence and inverted repeat are found in the 3' flank of several globin genes and the simian virus 40 (SV40) early genes, as well as in the regions implicated in pausing or termination of transcription of eight different genes. Deletion of the conserved sequence and inverted repeat from the 3' flank of the SV40 early region causes a small increase in the levels of transcription downstream from this site. Replacement with the conserved sequence and inverted repeat from the rabbit alpha-globin gene causes an accumulation of polymerases, supporting the hypothesis that polymerases pause at this site. This proposed pause site may affect the efficiency of termination at some sites further downstream, perhaps by loss of a processivity factor.

Termination of transcription in an 'in vitro' system is dependent on a polyadenylation sequence

Using HeLa cell nuclear extract as a source of the different transcription and polyadenylation factors and reverse transcription to analyze the levels of RNA 5' and 3' to the cleavage-polyadenylation site, an in vitro assay has been established to study polyadenylation coupled to transcription directed by different adenovirus promoters. The levels of transcription 5' and 3' to the cleavage site in the L3 polyadenylation region are practically the same as described previously, however, the level of transcription 3' to the cleavage site in the SV40 early polyadenylation region decreases immediately after the cleavage site indicating a termination of the transcription.

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.

A transcriptional terminator between enhancer and promoter does not affect remote transcriptional control

Enhancers stimulate transcription of RNA polymerase II-transcribed genes in an orientation-independent manner and over long distances. This stimulation is known to be associated with an increased polymerase density over the linked gene. However, many aspects of the exact mechanism of remote gene control remain to be elucidated. Based on some reports on RNA polymerase I transcription, we wanted to test whether RNA polymerase II enters at the enhancer and from there proceeds towards the promoter while synthesizing unstable transcripts ("scanning/readthrough transcription" model). For this, we have inserted a complete terminator region from the mouse beta-globinmaj gene between the SV40 enhancer and the rabbit beta-globin promoter. In contrast to what the model predicts, insertion of the terminator had no affect on remote enhancer action. Furthermore, we have determined the RNA polymerase density over the spacer DNA between enhancer and promoter, and over the reporter gene, by means of the so-called run-on transcription assay. We find very low transcription of the spacer, but high transcription of the globin reporter gene. Thus, our data are not consistent with a scanning/readthrough transcription mechanism where RNA polymerase II would move from the enhancer to the promoter while transcribing the intervening spacer DNA. These and other findings are compatible with a model where enhancer and promoter are brought into close proximity, perhaps with concomitant looping out of the intervening DNA.

Immunosuppressive function of hepatitis B antigens in vitro: role of endoribonuclease V as one potential trans inactivator for cytokines in macrophages and human hepatoma cells

The mRNAs of transiently expressed cytokine genes contain AUUUA-rich sequences in the 3' untranslated regions. In order to examine whether the AU-specific endoribonuclease V (EC 3.1.27.8) described previously by us transinactivates those mRNA species, we introduced a 51-nucleotide ATTTA sequence from tumor necrosis factor into the 3' untranslated region of beta-globin gene. Transcripts of that construct, synthesized in vitro, were prone to endoribonuclease V digestion at those AU-rich sequences. Stimulation of human macrophages with lipopolysaccharide resulted in a shift of the association state of the enzyme from the nuclear matrix-associated to the free form. This shift was strongly prevented by the hepatitis B surface antigen (HBsAg) and more weakly by hepatitis B nucleocapsid antigen and hepatitis B antigen of the X region. HBsAg and, to a lesser extent, hepatitis B nucleocapsid antigen and hepatitis B antigen of the X region inhibited the release of alpha interferon, tumor necrosis factor alpha, and granulocyte-macrophage colony stimulating factor, while it had no effect on interleukin-1 production from stimulated macrophages. Using the human hepatoma cell line PLC/PRF/5, we provide further experimental evidence that endoribonuclease V acts in trans as a posttranscriptional inactivator for nuclear matrix-associated cytokine transcripts. These results suggest that those cytokine transcripts which contain reiterated (overlapping) AUUUA sequences are degraded by nuclear matrix-associated endoribonuclease V. This degradation was comparably high in cells incubated with HBsAg or cells which produced this antigen.

A point mutation uncouples RNA 3'-end formation and termination during ribosomal gene transcription in Xenopus laevis

Two sites, T2 and T3, in the ribosomal gene spacer of Xenopus laevis both direct RNA 3'-end formation 15 bp upstream of the conserved box sequence GACTTGC. Site T2, which defines the 3' end of the 40S precursor, does not terminate transcription whereas site T3 at the 3' end of the spacer does. Here we show that T2 can be converted into a T3-like site with termination activity by a single point mutation 2 bp downstream of the T2 box. RNA 3'-end formation at T2 is unchanged by this mutation. Conversely, a point mutation 2 bp downstream of the T3 box inhibits termination without affecting 3'-end formation. Our results identify two separable events occurring at the 3' end of the ribosomal genes: (1) RNA 3'-end formation by processing and (2) transcription termination. The two processes are directed by two distinct, but overlapping, signals in the DNA sequence. Site T2 in X. laevis is damaged in the second process by a natural mutation.

Transcriptional termination between bovine papillomavirus type 1 (BPV-1) early and late polyadenylation sites blocks late transcription in BPV-1-transformed cells

Bovine papillomavirus type 1 (BPV-1) is a small DNA tumor virus which induces fibropapillomas in cattle and transforms rodent cells in culture. Transcripts are derived from a single strand of the circular viral genome, which has multiple promoters and two polyadenylation sites. In the transformed cell, the first (early) polyadenylation site is utilized exclusively and, therefore, only the early region is expressed. Transcription of the late genes, which requires use of the second (late) polyadenylation site, is seen only in the fully differentiated keratinocytes of the fibropapilloma. In this study, nascent RNA chain analysis of BPV-1-transformed C127 cells was used to demonstrate that at least 90% of the RNA polymerases which transcribe past the early polyadenylation site terminate transcription within the late region before reaching the late polyadenylation site. Therefore, transcription termination is at least partially responsible for the absence of late transcription in the BPV-1-transformed cell and is likely to be an important mechanism for regulation of papillomavirus late transcription during keratinocyte differentiation.

Transcription termination at the chicken beta H-globin gene

We characterized the transcription termination region of the chicken beta H-globin gene. First we located the region by nuclear runon transcription in vitro. Then we sequenced and subcloned it into a chloramphenicol acetyltransferase (CAT) expression vector for assay in vivo. The region of beta H termination contains two interesting elements located about 1 kilobase downstream of the beta H gene poly(A) site. Either element alone can block CAT expression if inserted between the promoter and the poly(A) site of the cat gene in pRSVcat. The first element in the termination region is an unusually large inverted repeat in the DNA (delta G = -71 kcal). The second element, 200 base pairs further downstream, is an RNA polymerase II promoter which directs transcription back upstream on the complementary strand. This transcription converges on and collides with that from the beta H gene at or near the inverted repeat where transcription from both directions stops. We propose that the inverted repeat is a strong pause site which positions the converging polymerases for mutual site-specific termination.

How RNA polymerase II terminates transcription in higher eukaryotes

The termination of transcription of eukaryotic genes by RNA polymerase II, at first sight, appears to be a rather random process, with the heterogeneous transcripts produced being processed to generate their correct 3' ends. However, recent studies have revealed that specific termination or pause sites may influence the process. The mechanism of termination may even play a role in eukaryotic gene regulation.

Transcription termination at the chicken beta H-globin gene

We characterized the transcription termination region of the chicken beta H-globin gene. First we located the region by nuclear runon transcription in vitro. Then we sequenced and subcloned it into a chloramphenicol acetyltransferase (CAT) expression vector for assay in vivo. The region of beta H termination contains two interesting elements located about 1 kilobase downstream of the beta H gene poly(A) site. Either element alone can block CAT expression if inserted between the promoter and the poly(A) site of the cat gene in pRSVcat. The first element in the termination region is an unusually large inverted repeat in the DNA (delta G = -71 kcal). The second element, 200 base pairs further downstream, is an RNA polymerase II promoter which directs transcription back upstream on the complementary strand. This transcription converges on and collides with that from the beta H gene at or near the inverted repeat where transcription from both directions stops. We propose that the inverted repeat is a strong pause site which positions the converging polymerases for mutual site-specific termination.

Multiple transcription terminators in E1a and E1b genes of adenovirus type 5

We located and characterized transcription terminators in the E1a and E1b genes by transferring the 3' fragments of the genes into the vector pSCAT10 [Sato et al., Mol. Cell. Biol. 6 (1986) 1032-1043] at a site located immediately downstream from the cat gene (coding for chloramphenicol acetyltransferase; CAT) and upstream from the simian virus 40 polyadenylation region. Multiple terminators were located downstream from the E1b gene, but not in the 3' region of the E1a gene. Fine analysis of these terminators by the CAT assay method and S1 nuclease mapping of in vivo transcripts indicated possible involvement of a G-rich sequence in transcription termination of the E1 region. These terminators were repeated tandemly and used by both the E1a and the E1b genes in a orientation-dependent manner.

Sequence requirements for premature termination of transcription in the human c-myc gene

We have used the Xenopus oocyte injection system to investigate the sequence requirements of premature termination of transcription within the human c-myc gene. We show that in the oocyte, truncated RNAs are produced by RNA polymerase II with 5' ends at the P1 and P2 promoters and 3' ends at two T stretches (sites I and II) near the exon 1/intron 1 junction. The location of these 3' ends is consistent with the site of the block to c-myc transcription identified by nuclear runoff assays in human cells and confirmed in dissected nuclei of injected oocytes. Evidence is presented that transcriptional termination rather than RNA processing produces these short c-myc RNAs. Deletion analysis of site I reveals that sequences upstream of the T stretch determine the site of 3' end formation, and that the stretch of T's on the sense DNA strand is not required for termination. The sequences specifying termination reside within a 95 base region located -130 to -35 relative to the exon 1/intron 1 boundary. The termination activity of these sequences is orientation-dependent and functions downstream of the HSV-TK promoter.

A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II

Polyadenylation of pre-mRNAs requires the conserved hexanucleotide AAUAAA, as well as sequences located downstream from the poly(A) addition site. The role of these sequences in the production of functional mRNAs was studied by analyzing a series of mutants containing deletions or substitutions in the SV40 early region poly(A) site. As expected, both a previously defined GU-rich downstream element and an AAUAAA sequence were required for efficient usage of the wild-type poly(A) addition site. However, when either of these elements was deleted, greatly increased levels of SV40-specific RNA were detected in the nuclei of transfected cells. Evidence is presented that this accumulation of RNA resulted from a failure of transcription termination, leading to multiple rounds of transcription of the circular templates. We conclude that the sequences required for efficient cleavage/polyadenylation of the SV40 early pre-mRNA also constitute an important element of an RNA polymerase II termination signal. A model proposing a mechanism by which the act of pre-mRNA 3' end formation is signaled to the elongating RNA polymerase, resulting in termination, is presented.

RNA processing of beta-globin transcripts containing 5' flanking and structural gene sequences

RNA species have been identified in murine erythroid cells which contain both 5' flanking and structural gene sequences from the beta maj globin gene. Two nonpolyadenylated RNA transcripts, average 3700 and 1800-1900 nucleotides long, were identified by denaturing agarose gel electrophoresis and were found to hybridize to both 5' and 3' beta maj globin flanking sequences. This finding suggests that transcription initiated in the 5' flanking region does proceed past the polyadenylation site. The apparent higher concentration of the 5' flanking sequences in precursor RNA molecules, as compared to mature polyadenylated globin mRNA, suggests increased precursor stability of beta globin transcripts initiated in the 5' flanking region.

A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene

Sequence elements within the mouse beta maj-globin transcription unit required for efficient termination of transcription by RNA polymerase II have been delineated. To facilitate nascent-chain analysis of termination, the DNA segment in which transcription ceases was introduced into the adenovirus chromosome within its E1A transcription unit. Two beta-globin DNA elements were required to effect efficient termination: an upstream sequence that includes two poly(A) addition signals and a downstream region previously shown to be where RNA synthesis stops. The role of poly(A) addition in termination was established by introduction of several single base pair substitutions into the AATAAA polyadenylylation motifs. These mutations inhibited both polyadenylylation and termination within the beta-globin DNA segment. Therefore, poly(A) addition appears to be a prerequisite for efficient termination.

Protein-binding site at the immunoglobulin mu membrane polyadenylylation signal: possible role in transcription termination

mRNAs specifying immunoglobulin mu and delta heavy chains are encoded by a single large, complex transcription unit (mu + delta gene). The transcriptional activity of delta gene segments in terminally differentiated, IgM-secreting B lymphocytes is 10-20 times lower than in earlier B-lineage cells expressing delta mRNA. We find that transcription of the mu + delta gene in IgM-secreting murine myeloma cells terminates within a region of 500-1000 nucleotides immediately following the mu membrane (mu m) polyadenylylation site. Transcription decreases only minimally through this region in murine cell lines representative of earlier stages in B-cell development. A DNA fragment containing the mu m polyadenylylation signal gives protein-DNA complexes with different mobilities in gel retardation assays with nuclear extracts from myeloma cells than with nuclear extracts from earlier B-lineage cells. However, using a recently developed "footprinting" procedure in which protein-DNA complexes resolved in gel retardation assays are subjected to nucleolytic cleavage while still in the polyacrylamide gel, we find that the DNA sequences protected by factors from the two cell types are indistinguishable. The factor-binding site on the DNA is located 5' of the mu m polyadenylylation signal AATAAA and includes the 15-nucleotide-long A + T-rich palindrome CTGTAAACAAATGTC. This type of palindromic binding site exhibits orientation-dependent activity consistent with the reported properties of polymerase II termination signals. This binding site is followed by two sets of directly repeated DNA sequences with different helical conformation as revealed by their reactivity with the chemical nuclease 1,10-phenanthroline-copper. The close proximity of these features to the signals for mu m mRNA processing may reflect a linkage of the processes of developmentally regulated mu m polyadenylylation and transcription termination.

DNA sequences downstream of the adenovirus type 2 fiber polyadenylation site contain transcription termination signals

The major late transcription unit of adenovirus type 2 (Ad2) terminates in a region near the end of the linear DNA genome at map units 98.2 to 100. Specific 3' ends mapping in the transcription termination region were detected in nuclear but not cytoplasmic RNA isolated at 16 to 18 h postinfection. Using S1 nuclease protection analysis, a major nuclear RNA species with a 3' terminus at map unit 98.9 was detected. With the use of recombinant expression vectors and run-on transcription in isolated nuclei, we demonstrated that the Ad2 sequences from map units 97.1 to 100, inserted into either the 5' or 3' untranslated sequences of the chloramphenicol acetyltransferase gene (cat), terminated transcription in transfected cells. Termination occurred only when the 97.1- to 100-map-unit sequence was in the same direction of transcription as the major late transcript and was not observed with Ad2 sequences upstream of map unit 97.1.

Oligonucleotide sequence signaling transcriptional termination of vaccinia virus early genes

In an in vitro system containing enzymes extracted from vaccinia virions, transcription of the vaccinia growth factor gene terminated approximately 50 base pairs downstream of a thymidine-rich sequence. Deletion mutagenesis suggested the presence of two tandem termination signals. The signal was identified by replacing the 3' end of the gene with the oligonucleotide AATTTTTAT that induced downstream termination. Further analysis of the transcripts formed with a series of templates containing 16 related synthetic oligonucleotides established the minimum functional termination signal as TTTTTNT, in which N represents any nucleotide. Termination efficiency may be increased, however, by the presence of an adenosine preceding the thymidine cluster. The general use of this signal at early times in infection but not at late times is supported by a survey of vaccinia virus gene sequences.

Evolution of steroid-inducible RP2 mRNA expression in the mouse kidney

We have examined the structure and expression of mRNAs encoded by the androgen-inducible RP2 gene in the kidneys of nine mouse species within the genus Mus. There is considerable interspecies variation in the lengths of the major RP2 transcripts; some of this variation is due to the presence or absence of a B1 repetitive element in the 3'-untranslated region of the gene. In addition, the extent of RP2 mRNA induction by testosterone differs among the species. Two species show 10-20-fold induction, while others display a reduced response or none at all. Analysis of an interspecific hybrid indicates that the inducibility phenotype is inherited in an additive fashion. A correlation between RP2 inducibility and the time of formation of lineages within the Mus genus suggests that induction evolved in a stepwise fashion, with the acquisition of a modest hormonal response being followed by the appearance of a greater response. The interspecies variations in RP2 mRNA structure and regulation provide a useful model for the identification and study of genetic elements that elicit evolutionary alterations in steroid-modulated gene expression.

Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences

We have identified and mapped several DNA sequences within a human histone gene (H3.3) at which in-vitro transcription by highly purified RNA polymerase II is efficiently terminated. Since transcription in our system involves only RNA polymerase II acting on a linear DNA template, these sequences contain "intrinsic" termination signals recognized by the polymerase protein itself. The existence of such signals within a gene suggests that efficient antitermination systems probably exist for mammalian transcription units. Alternatively, there could be a high frequency of premature transcription termination, or "polarity" for genes such as H3.3. Intrinsic transcription termination sites in H3.3 are located in sequences of consecutive thymidylate residues (5 to 8 nucleotides) on the non-transcribed DNA strand (T-runs), from which it is likely that such T-runs are elements of the intrinsic termination signal for RNA polymerase II. However, transcription proceeds without significant termination through many similar T-runs, from which it follows that these intrinsic termination signals include other elements. Since transcription is also terminated efficiently at these sites when the transcript remains bound along its full length as a DNA-RNA hybrid, it is unlikely that formation of specific RNA secondary structures in the transcript is a general element of the intrinsic termination signal. Although DNA sequences downstream from the coding portion of the mouse beta-globin gene have been implicated as sites of transcription termination in vivo, these regions do not contain strong intrinsic termination signals, and transcription in vitro proceeds through these regions almost undiminished. Transcriptional termination in this region in vivo may depend on the presence of termination factors or other intracellular elements, and there may be multiple classes of DNA signals that control eukaryotic termination.

Characterization of cDNA sequences corresponding to three distinct HMG-1 mRNA species in line CHO Chinese hamster cells and cell cycle expression of the HMG-1 gene

We have isolated cDNA clones encoding the high mobility group (HMG) protein HMG-1 in line CHO Chinese hamster cells. The cDNA clones correspond to the three HMG-1 mRNA species detected on Northern blots. Three different polyadenylation sites are found to be used. The three mRNA species of sizes 1.05, 1.45 and 2.45 kb are generated by differential polyadenylation at sites 115 nucleotides, 513 nucleotides and 1515 nucleotides downstream from the stop codon. A perfectly conserved putative poly(A) signal AAUAAA is present upstream of only one of the three poly(A) sites. Two homologous but imperfect sequences exist upstream from the other two poly(A) sites. All three HMG-1 mRNA species maintain significant levels throughout the M, G1 and S phases of the cell cycle and the rate of large HMG protein (HMG-1 and HMG-2) synthesis increases approximately two-fold from G1 to S phase.

Structure of the rat L-type pyruvate kinase gene

The total sequence of a 13,021 base-pair (bp) genomic fragment containing the rat L-type pyruvate kinase (L-PK) gene was determined by "shot gun" sequencing. This fragment includes 8360 bp of the L-PK gene, plus 3193 bp of the 5'-flanking and 1468 bp of the 3'-flanking regions. Like the chicken PK-M1 gene, the rat L-PK gene exhibits a fully conserved exon-intron structure, with 11 exons and 10 introns. In the chicken M1 gene, the coding sequences are well conserved (about 70%), in particular at the level of the exons implicated in the formation of PK active sites, exons that are also partially homologous to the corresponding sequences of the yeast gene. Various types of repetitive sequences exist in the L-PK gene, especially two ID (identifier) sequences located in the second intron and the 11th exon. Elements very similar to the "cyclic AMP-dependent regulatory element" recently described in the phosphoenolpyruvate carboxykinase and somatostatin genes are found in the sequenced fragment, but far upstream (-2338) and downstream (+5788) from the cap site. Various sequences homologous to described regulatory elements (glucocorticoid regulatory elements, enhancers, potential Z-DNA) are also observed 5' and 3' of the cap site. A comparison of the 5'-flanking region of the L-PK gene with the same regions of liver-specific or non-specific, cyclic-AMP-responsive or non-responsive genes was also made. It revealed various potentially interesting features that will be used to guide a further functional study. The cap site was determined by primer extension and nuclease S1 mapping using either mature mRNA or precursor RNA as templates. With both templates the start site of transcription appeared to be microheterogeneous, 19 to 14 bp before the ATG translation initiation codon.

Tripartite sequences within and 3' to the sea urchin H2A histone gene display properties associated with a transcriptional termination process

We have defined a DNA sequence that behaves as an RNA polymerase II termination signal by using the human HeLa cell transient expression system. Surprisingly, this sequence is tripartite, including part of the coding region of the sea urchin H2A histone gene together with two separate sequences in the 3' flanking region of the gene. We demonstrate that this signal functions both in its normal gene environment and also when placed within the human alpha-globin gene. However, we have failed to detect a discrete 3' terminus. Rather, our data indicate the presence of an extremely heterogeneous series of nonpolyadenylated RNAs. These heterogeneous nonpolyadenylated RNAs are stable when transcribed from the intact histone gene but are highly unstable within the human alpha-globin gene. This provides evidence for the role of poly(A) in the stability of mRNA.