In vitro transcription of normal, mutant, and truncated mouse alpha-globin genes

Transcription from the SV40 early-early and late-early overlapping promoters in the absence of DNA replication

Transcription for a hybrid SV40 promoter-beta globin coding sequence recombinant initiates from both early-early (EE) and late-early (LE) SV40 start sites (EES and LES) in the absence of DNA replication. The 72-bp repeat is essential to potentiate the elements of the two overlapping EE and LE promoters (EEP and LEP). Two current models, which can account for the EE to LE shift in RNA chain initiation during the SV40 replication cycle, are that LE transcription is linked to replication and occurs on newly replicated DNA molecules or that there are two promoter elements, a stronger EEP and a weaker LEP, T antigen repressing the EEP late in infection. Our results support the second model. A 5'-TATTTAT-3' to 5'-TATCGAT-3' mutation in the putative SV40 TATA box decreases transcription from EES, increases transcription from LES, and inhibits DNA replication. Therefore, this element acts as a classical TATA box for transcription, and yet is also important for DNA replication.

Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs

We have characterized a family of tRNA-derived short interspersed repetitive elements (SINEs) in the tobacco genome. Members of this family of SINEs, designated TS, have a composite structure and include a region structurally similar to a rabbit tRNA(Lys), a tRNA-unrelated region, and a TTG repeat of variable length at the 3' end. Southern blot hybridization, together with a search of the GenBank data base, showed that various plants belonging to the families Solanaceae and Convolvulaceae contain sequences homologous to the TS family in the introns and flanking regions of many genes, whereas Arabidopsis in the family Cruciferae and several species of monocoytledonous plants do not. The TS family is widely involved in structural and genetic variations in the genomes of many plants that belong to the order Tubiflorae. All of nine sequences identified in a data base search are truncated at their 5' regions and lack the tRNA-related region of the TS family. We characterized the entire sequence of the members of the TS family and found that this family can be categorized as a member of a group of SINEs with a tRNA(Lys)-like structure, as can several animal SINEs. The TS family can be divided into two major subfamilies by analysis of diagnostic positions, and one of the subfamilies is clearly younger than the other. Amplification of many copies of the full sequence of the younger subfamily occurred during the recent evolution of the tobacco lineage. We also discuss mechanisms that could be involved in the generation of SINEs in animals and also in plants.

Autoantibody reactive with three classes of RNA polymerases in sera from patients with systemic sclerosis

We have identified a novel autoantibody reactive with all three classes of RNA polymerases, well-characterized nuclear enzymes, in sera from patients with systemic sclerosis (SSc). After incubation with [35S]methionine-labeled HeLa cell extracts, 14 of 275 SSc sera immunoprecipitated 12 or 14 proteins with similar molecular weights as those of several subunit proteins of eukaryotic RNA polymerases I, II, and III. Purified IgG from these two types of sera inhibited RNA transcription catalyzed by RNA polymerases I, II, and III in vitro. Immunoblot analysis using RNA polymerase-enriched fraction showed that the majority of these sera reacted with 42- or 25-kD protein. Anti-RNA polymerase antibody was highly specific to SSc, especially to diffuse cutaneous SSc. Clinical features associated with this antibody included a high frequency of heart and kidney involvement and a poor survival rate at 5 yr after first visit. These findings indicate that the autoantibody to three classes of RNA polymerases is a new marker for a unique subset of diffuse cutaneous SSc.

An additional promoter functions in the human aldolase A gene, but not in rat

The aldolase A gene was isolated from a human DNA library, mapped and sequenced. This gene comprises 12 exons and spans 6.5 kb. From the genomic DNA sequence and from the previous sequence analysis of the cDNA, it was revealed that the first exon L1 and the second exon encode the 5' non-coding sequence of mRNA L1, while the third and forth exons (corresponding to exons M and L2) encode different mRNA, mRNA M and L2, respectively; the following eight exons (exons 5-12) are shared commonly by all the mRNA species. These results indicate that the mRNA species are generated from a single aldolase A gene from one of exons L1, M or L2, in addition to exons 5-12, and also that the usage of a leader exon is similar but clearly distinct from that of rat aldolase A gene which we analyzed [Joh, K., Arai, Y., Mukai, T. & Hori, K. (1986) J. Mol. Biol. 190, 401-410]. By comparing the promoter regions in the human and rat aldolase A genes, we found similar sequences in the rat genome corresponding to those of the human L1, M and L2 promoter. We could not, however, detect any transcripts starting from sequences corresponding to the human L1 promoter in the rat genome, although the products corresponding to human M and L2 were detected. Thus, we conclude that the L1 promoter was either acquired by the human genome or deleted from the rat genome after human and rat diverged during evolution.

Distribution of the salmonid Hpa 1 family in the salmonid species demonstrated by in vitro runoff transcription assay of total genomic DNA: a procedure to estimate repetitive frequency and sequence divergence of a certain repetitive family with a few known sequences

An in vitro runoff transcription assay of total genomic DNA was developed. As an example of use of this assay, analysis of a highly repetitive sequence in the cherry salmon (Oncorhynchus masou) is described. Total genomic DNA of the cherry salmon was completely digested with Hpa 1, whose site is known to be in the tRNA-unrelated region of the cherry salmon Hpa 1 family. On transcription of the digested DNA in a HeLa cell extract, a discrete-sized RNA of about 100 nucleotides, constituting 70% of the transcripts, was produced, whereas on transcription of the undigested total DNA, only smeared RNA was obtained. In a fingerprint, the oligonucleotides of the discrete transcript from the digested total DNA were very distinct and exactly corresponded to those of a transcript from an Hpa 1 digest of a cloned DNA, but with few extra oligonucleotides. These results showed that the cherry salmon Hpa 1 family constitutes a major repetitive family in the genome of the cherry salmon. For determination of the distribution of the salmonid Hpa 1 family in other salmonid species, the same analysis was applied to DNAs from the chum salmon (Onchorhynchus keta), brown trout (Salmo trutta), Japanese common charr (Salvelinus leucomaenis pluvius), and Japanese huchen (Hucho perryi). The results showed that the salmonid Hpa 1 family is widespread in the genomes of salmonid species. A method and equations are also presented for estimating the relationship between the ratio of a given repetitive family to all the Pol III genes and its average sequence divergence by calculating the molar ratio of the runoff transcript to all the in vitro Pol III transcripts.

A highly repetitive and transcribable sequence in the tortoise genome is probably a retroposon

On in vitro transcription of total genomic DNA of the tortoise (Geoclemys reevessi), a discrete-sized RNA of 6.5S was obtained that represented a highly repetitive and transcribable sequence in the tortoise genome. Three sequences of the 6.5S RNA gene were sequenced, and a consensus sequence was deduced from these three sequences and one reported previously [Endoh, H & Okada, N. (1986) Proc. Natl Acad. Sci. USA 83, 251-255]. The 5' part of the gene showed close similaries to lysine (rabbit) and threonine (mouse) tRNAs (overall similarity 68-70%), so this tortoise sequence may have evolved from one of these tRNAs. The consensus sequence retained the expected CCA triplet at the 3' end of tRNA, but not at the 3' end of tDNA, supporting the idea that the tRNA-related region of the gene was generated via an RNA intermediate. The 5' and 3' flanking sequences of the four genes were found to be completely different from each other. Fingerprint analysis and S1 nuclease mapping analysis also showed that sequence boundaries of tortoise repetitive units exactly corresponded to RNA species. These results, together with data obtained by Southern blot hybridization, indicated that the 6.5S RNA genes are dispersed in the tortoise genome. Therefore, generation of the tRNA-related region of the gene and amplification of the whole unit of the gene are both RNA-mediated events. The existence of this tortoise sequence suggests that short interspersed sequences are more common in eukaryotic genomes than had previously been thought.

Tse-2: a trans-dominant extinguisher of albumin gene expression in hepatoma hybrid cells

Serum albumin gene expression is generally extinguished in hepatoma x fibroblast hybrids. To define the genetic basis of this phenomenon, we screened a panel of hepatoma hybrids retaining different fibroblast chromosomes for albumin production by immunofluorescence. We report that albumin extinction in these clones was strictly correlated with the retention of mouse chromosome 1. Furthermore, albumin was systematically reexpressed in chromosome 1 segregants. These data define a tissue-specific extinguisher locus (Tse-2) that affects albumin gene expression in trans. Two other liver genes, those encoding liver alcohol dehydrogenase and liv-10, were coordinately extinguished with albumin in monochromosomal hybrids that specifically retained mouse chromosome 1.

Tse-2: a trans-dominant extinguisher of albumin gene expression in hepatoma hybrid cells

Serum albumin gene expression is generally extinguished in hepatoma x fibroblast hybrids. To define the genetic basis of this phenomenon, we screened a panel of hepatoma hybrids retaining different fibroblast chromosomes for albumin production by immunofluorescence. We report that albumin extinction in these clones was strictly correlated with the retention of mouse chromosome 1. Furthermore, albumin was systematically reexpressed in chromosome 1 segregants. These data define a tissue-specific extinguisher locus (Tse-2) that affects albumin gene expression in trans. Two other liver genes, those encoding liver alcohol dehydrogenase and liv-10, were coordinately extinguished with albumin in monochromosomal hybrids that specifically retained mouse chromosome 1.

Differential activity of a tissue-specific extinguisher locus in hepatic and nonhepatic cells

Tissue-specific extinguisher 1 (Tse-1) is a genetic locus on mouse chromosome 11 that can repress expression of several liver genes in trans. This locus is clearly active in fibroblasts, as hepatoma cells retaining fibroblast chromosome 11 are extinguished for both tyrosine aminotransferase and phosphoenolpyruvate carboxykinase gene expression. To assess the activity of Tse-1 in other tissues, we transferred mouse chromosome 11 from several different cell types into rat hepatoma recipients. Tse-1 was active in nonhepatic cell lines derived from each primary germ layer, but Tse-1 activity was not apparent in hybrids between hepatoma cells and primary mouse hepatocytes. These differences in the genetic activity of murine Tse-1 were apparently heritable in cis.

Differential activity of a tissue-specific extinguisher locus in hepatic and nonhepatic cells

Tissue-specific extinguisher 1 (Tse-1) is a genetic locus on mouse chromosome 11 that can repress expression of several liver genes in trans. This locus is clearly active in fibroblasts, as hepatoma cells retaining fibroblast chromosome 11 are extinguished for both tyrosine aminotransferase and phosphoenolpyruvate carboxykinase gene expression. To assess the activity of Tse-1 in other tissues, we transferred mouse chromosome 11 from several different cell types into rat hepatoma recipients. Tse-1 was active in nonhepatic cell lines derived from each primary germ layer, but Tse-1 activity was not apparent in hybrids between hepatoma cells and primary mouse hepatocytes. These differences in the genetic activity of murine Tse-1 were apparently heritable in cis.

Multiple 5'-flanking regions of the human alpha-skeletal actin gene synergistically modulate muscle-specific expression

Transfection into myogenic and nonmyogenic cell lines was used to investigate the transcriptional regulation of the human alpha-skeletal actin gene. We demonstrated that 1,300 base pairs of the 5'-flanking region directed high-level transient expression of the bacterial chloramphenicol acetyltransferase gene in differentiated mouse C2C12 and rat L8 myotubes but not in mouse nonmuscle L.TK- and HuT-12 cells. Unidirectional 5' deletion analysis and heterologous promoter stimulation experiments demonstrated that at least three transcription-regulating subdomains lie in this 1,300-base-pair region. A proximal cis-acting transcriptional element located between positions -153 and -87 relative to the start of transcription at +1 was both sufficient and necessary for muscle-specific expression and developmental regulation during myogenesis in the two myogenic cell systems. The region 3' of position -87 interacted with factors present in both myogenic and fibroblastic cells and appeared to define, or to be a major component of, the basal promoter. In C2C12 myotubes, but not in L8 myotubes, a distal sequence domain between positions -1300 and -626 and the proximal sequence domain between positions -153 and -87 each induced transcription about 10-fold and synergistically increased CAT expression 100-fold over levels achieved by the sequences 3' of position -87. Furthermore, these cis-acting elements independently and synergistically modulated an enhancerless, heterologous simian virus 40 promoter in a tissue-specific manner. DNA fragments which included the proximal domain displayed classical enhancerlike properties. The central region between positions -626 and -153, although required in neither cell line, had a positive, two- to threefold, additive role in augmenting expression in L8 cells but not in C2C12 cells. This suggests that certain elements between positions -1300 and -153 appear to be differentially utilized for maximal expression in different myogenic cells and that the particular combination of domains used is dependent on the availability, in kind or amount, of trans-acting, transcription-modulating factors present in each cell type. Thus, multiple myogenic factors that vary qualitatively and quantitatively may be responsible for the different and complex modulatory programs of actin gene expression observed during in vivo muscle differentiation.

Multiple 5'-flanking regions of the human alpha-skeletal actin gene synergistically modulate muscle-specific expression

Transfection into myogenic and nonmyogenic cell lines was used to investigate the transcriptional regulation of the human alpha-skeletal actin gene. We demonstrated that 1,300 base pairs of the 5'-flanking region directed high-level transient expression of the bacterial chloramphenicol acetyltransferase gene in differentiated mouse C2C12 and rat L8 myotubes but not in mouse nonmuscle L.TK- and HuT-12 cells. Unidirectional 5' deletion analysis and heterologous promoter stimulation experiments demonstrated that at least three transcription-regulating subdomains lie in this 1,300-base-pair region. A proximal cis-acting transcriptional element located between positions -153 and -87 relative to the start of transcription at +1 was both sufficient and necessary for muscle-specific expression and developmental regulation during myogenesis in the two myogenic cell systems. The region 3' of position -87 interacted with factors present in both myogenic and fibroblastic cells and appeared to define, or to be a major component of, the basal promoter. In C2C12 myotubes, but not in L8 myotubes, a distal sequence domain between positions -1300 and -626 and the proximal sequence domain between positions -153 and -87 each induced transcription about 10-fold and synergistically increased CAT expression 100-fold over levels achieved by the sequences 3' of position -87. Furthermore, these cis-acting elements independently and synergistically modulated an enhancerless, heterologous simian virus 40 promoter in a tissue-specific manner. DNA fragments which included the proximal domain displayed classical enhancerlike properties. The central region between positions -626 and -153, although required in neither cell line, had a positive, two- to threefold, additive role in augmenting expression in L8 cells but not in C2C12 cells. This suggests that certain elements between positions -1300 and -153 appear to be differentially utilized for maximal expression in different myogenic cells and that the particular combination of domains used is dependent on the availability, in kind or amount, of trans-acting, transcription-modulating factors present in each cell type. Thus, multiple myogenic factors that vary qualitatively and quantitatively may be responsible for the different and complex modulatory programs of actin gene expression observed during in vivo muscle differentiation.

DNA sequences required for specific and efficient initiation of transcription at the polyoma virus early promoter

The 5'-flanking DNA sequences involved in the specific and efficient transcription of the polyoma virus early region have been investigated. Sequence requirements for efficient in vivo expression differed from those in vitro. Deletion of DNA located between 200 and 400 base pairs before the principal cap sites severely inhibited in vivo expression as measured by transformation ability, but did not affect in vitro transcription. Viable deletion mutants which lack the principal cap sites and the "TATA" box were very poor templates for in vitro transcription. Analysis of other deletion mutants in vitro demonstrated that no specific sequences more than 46 base pairs before the cap sites were important. Removal of the TATA box reduced in vitro transcriptional efficiency but did not alter the initiation sites. The synthesis of transcripts with abnormal 5' termini did not occur in vitro until sequence between the TATA box and the normal cap sites was also deleted. We further observed a nonspecific requirement for 90 to 100 base pairs of DNA 5' to the cap site for optimal transcription of DNA fragments in vitro.

Formation of the transcription initiation complex on mammalian rDNA

Steps for the formation of transcription initiation complex on the human rRNA gene (rDNA) in vitro were analyzed with partially purified transcription factors and RNA polymerase I. The reaction requires at least two factors besides RNA polymerase I for maximal efficiency. Preincubation and short-pulse analyses of the accurate transcripts revealed the following steps. First, the species-dependent factor, designated TFID, bound to the rDNA template, forming a preinitiation complex (PIC-1) which was resistant to a moderate concentration (0.015 to 0.02%) of Sarkosyl. Other factors, designated TFIA and RNA polymerase I, were then added to convert it to the final preinitiation complex PIC-3. This complex incorporated the first two nucleoside triphosphates of the starting site to complete the initiation complex (IC), which was resistant to a high concentration (0.2%) of Sarkosyl. Binding of TFID was rate limiting in the overall initiation reaction in vitro. Together with the kinetics of incorporation, the results are interpreted to mean that TFID, one bound, remains complexed with rDNA together with TFIA as the PIC-2 for many rounds of transcription by RNA polymerase I. Thus, the formation of PIC-2 may be a prerequisite for the stable opening of rDNA for transcription in vivo.

Formation of the transcription initiation complex on mammalian rDNA

Steps for the formation of transcription initiation complex on the human rRNA gene (rDNA) in vitro were analyzed with partially purified transcription factors and RNA polymerase I. The reaction requires at least two factors besides RNA polymerase I for maximal efficiency. Preincubation and short-pulse analyses of the accurate transcripts revealed the following steps. First, the species-dependent factor, designated TFID, bound to the rDNA template, forming a preinitiation complex (PIC-1) which was resistant to a moderate concentration (0.015 to 0.02%) of Sarkosyl. Other factors, designated TFIA and RNA polymerase I, were then added to convert it to the final preinitiation complex PIC-3. This complex incorporated the first two nucleoside triphosphates of the starting site to complete the initiation complex (IC), which was resistant to a high concentration (0.2%) of Sarkosyl. Binding of TFID was rate limiting in the overall initiation reaction in vitro. Together with the kinetics of incorporation, the results are interpreted to mean that TFID, one bound, remains complexed with rDNA together with TFIA as the PIC-2 for many rounds of transcription by RNA polymerase I. Thus, the formation of PIC-2 may be a prerequisite for the stable opening of rDNA for transcription in vivo.

Processing of mammalian tRNA transcripts in vitro: different pre-tRNAs are processed along alternative pathways that contain a common rate-limiting step

We have analyzed the pathways and kinetics of processing of mouse tRNA gene transcripts in vitro. Different transcripts are processed along two alternative pathways. The 3' trailer sequence of the tRNA His primary transcript is excised before the 5' leader sequence. In contrast, for the tRNA Gly primary transcript, the 5' leader sequence is excised before the 3' trailer sequence, as has been found for other monomeric eukaryotic tRNA gene transcripts. Computerized analysis of the kinetics of processing indicates that tRNA Asp, tRNA Gly, tRNA Glu and tRNA His transcripts are processed in a substrate concentration-dependent manner and also reveals the existence of a common rate-limiting step, the rate constant of which is equivalent for three of the four transcripts tested. The processing of one pre-tRNA transcript can be competitively inhibited by addition of another pre-tRNA transcript to the processing reaction. The common rate-limiting step is associated with the conversion of the primary transcript to an intermediate and is independent of sequence and the particular processing pathway of the transcript.

Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures

Total DNAs from various animals were transcribed in vitro in a HeLa cell extract, and it was found that one to several discrete RNAs were transcribed by RNA polymerase III. With tortoise (Geoclemys reevessi) and newt (Cynops pyrrhogaster), distinct 6.5S and 8S RNAs were transcribed from these respective DNAs. Representative phage clones carrying the 6.5S and 8S RNA genes were isolated from genomic libraries of these animals, and the sequences of these genes were determined. The 5' parts of highly repetitive and transcribable sequences of tortoise and newt were found to have close resemblance to tRNALys1 (rabbit) gene (78% homology) and a tRNAGlu (Drosophila) gene (74% homology, not counting the aminoacyl stem region), respectively. The homologies extended to secondary structures, homologous nucleotides being located on similar secondary structures. It is proposed that many, if not all, highly repetitive and transcribable sequences detected by total DNA transcription have specific tRNA genes as their progenitors.

5-Methylcytidylic modification of in vitro transcript from the rat identifier sequence; evidence that the transcript forms a tRNA-like structure

Previous studies showed that the rat identifier sequence, the rodent type 2 Alu family, the rabbit C family and the bovine or goat 73 bp repeat show remarkable resemblance with a few specific tRNA molecules (Sakamoto and Okada, J. Mol. Evol. in press). This paper reports 5-methylcytidylic modification of the in vitro transcript from the ID sequence, and provides further evidence that the transcript forms a tRNA-like structure in vitro. Fingerprint analysis and oligonucleotide mapping suggested that the sequence of the oligonucleotide containing 5-methylcytidine is CpCpm5CpUpGp, which corresponds to the extra and T psi stem regions in the secondary structure of phenylalanine tRNA. Since the sequence of the corresponding oligonucleotide in the phenylalanine tRNA is Cpm5CpCpUpGp, these results suggests that a tRNA (cytosine-5) methyl transferase recognizes the secondary structure of the transcript from the ID sequence rather than the primary sequence. The significance of this modification in relation to the functional role of the ID sequence is discussed.

Specific transcription of preformed nucleoprotein complexes, containing the adenovirus major late promoter, with a chromatographic fraction containing RNA polymerase II

Incubation in a HeLa whole-cell extract converted a plasmid DNA containing the adenovirus type 2 major late promoter into ordered nucleoprotein complexes similar to those described for simian virus DNA [Sinha, S. N., Hellwig, R. J., Allison, D. P. & Niyogi, S. K. (1982) Nucleic Acids Res. 10, 5533-5552]. Purified nucleoprotein complexes containing the plasmid DNA were able to serve as template for accurate transcription in vitro. Use of such nucleoprotein complexes eliminated the need for addition of nontemplate DNA (poly[d(I-C)]) to transcription reaction mixtures with template concentrations too low to yield a detectable specific-transcription signal from "naked" DNA. Of the four fractions resulting from phosphocellulose column chromatography of the whole cell extract, only the fraction that contained the RNA polymerase II activity was needed to accurately transcribe these nucleoprotein complexes in the presence of human placental ribonuclease inhibitor. In contrast, specific transcription of naked template DNA under these conditions required at least one additional fraction containing specificity factors. These results show that the nucleoprotein complexes contain factor(s) needed for specific initiation of transcription and that these complexes may be useful in the purification and analysis of these factors.

Transcription control region within the protein-coding portion of adenovirus E1A genes

A single-base deletion within the protein-coding region of the adenovirus type 5 early region 1A (E1A) genes, 399 bases downstream from the transcription start site, depresses transcription to 2% of the wild-type rate. Complementation studies demonstrated that this was due to two effects of the mutation: first, inactivation of an E1A protein, causing a reduction by a factor of 5; second, a defect which acts in cis to depress E1A mRNA and nuclear RNA concentrations by a factor of 10. A larger deletion within the protein-coding region of E1A which overlaps the single-base deletion produces the same phenotype. In contrast, a linker insertion which results in a similar truncated E1A protein does not produce the cis-acting defect in E1A transcription. These results demonstrate that a critical cis-acting transcription control region occurs within the protein coding sequence in adenovirus type 5 E1A. The single-base deletion occurs in a sequence which shows extensive homology with a sequence from the enhancer regions of simian virus 40 and polyomavirus. This region is not required for E1A transcription during the late phase of infection.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Transcription control region within the protein-coding portion of adenovirus E1A genes

A single-base deletion within the protein-coding region of the adenovirus type 5 early region 1A (E1A) genes, 399 bases downstream from the transcription start site, depresses transcription to 2% of the wild-type rate. Complementation studies demonstrated that this was due to two effects of the mutation: first, inactivation of an E1A protein, causing a reduction by a factor of 5; second, a defect which acts in cis to depress E1A mRNA and nuclear RNA concentrations by a factor of 10. A larger deletion within the protein-coding region of E1A which overlaps the single-base deletion produces the same phenotype. In contrast, a linker insertion which results in a similar truncated E1A protein does not produce the cis-acting defect in E1A transcription. These results demonstrate that a critical cis-acting transcription control region occurs within the protein coding sequence in adenovirus type 5 E1A. The single-base deletion occurs in a sequence which shows extensive homology with a sequence from the enhancer regions of simian virus 40 and polyomavirus. This region is not required for E1A transcription during the late phase of infection.

The 6S RNA transcribed from rodent total DNA in vitro is the transcript of the type 2 Alu family

We have performed in vitro transcription, using total DNA isolated from mouse and a cloned mouse DNA fragment containing a representative type 2 Alu sequence characterized by Kominami et al. (1983) as templates. From each template, 6S RNA was transcribed. The fingerprint of the 6S RNA produced from in vitro transcription of total DNA showed a very clear pattern of oligonucleotides. By comparing the oligonucleotides of the 6S RNA produced from each template, we demonstrated that the 6S RNA transcribed from mouse total DNA is the in fact the transcript of type 2 Alu sequences. The composition of the oligonucleotides of the 6S RNA transcribed from mouse total DNA seems to reflect well that of the consensus sequence of the type 2 Alu family proposed by Krayev et al. (1982). In vitro transcripts of rat or hamster total DNA showed fingerprint patterns nearly identical to that of mouse DNA, confirming that rodents have equivalent type 2 Alu sequences whose transcripts have the same length and similar compositions of oligonucleotides. Thus total DNA transcription provides a novel approach to the detection and analysis of type 2 Alu sequences transcribed in vitro.

Simian virus 40 major late promoter: an upstream DNA sequence required for efficient in vitro transcription

We have previously identified an 11-base DNA sequence, 5'-G-G-T-A-C-C-T-A-A-C-C-3' (simian virus 40 [SV40] map position 294 to 304), which is important in the control of SV40 late RNA expression in vitro and in vivo (Brady et al., Cell 31:625-633, 1982). We report here the identification of another domain of the SV40 late promoter. A series of mutants with deletions extending from SV40 map position 0 to 300 was prepared by nuclease BAL 31 treatment. The cloned templates were then analyzed for efficiency and accuracy of late SV40 RNA expression in the Manley in vitro transcription system. Our studies showed that, in addition to the promoter domain near map position 300, there are essential DNA sequences between nucleotide positions 74 and 95 that are required for efficient expression of late SV40 RNA. Included in this SV40 DNA sequence were two of the six GGGCGG SV40 repeat sequences and an 11-nucleotide segment which showed strong homology with the upstream sequences required for the efficient in vitro and in vivo expression of the histone H2A gene. This upstream promoter sequence supported transcription with the same efficiency even when it was moved 72 nucleotides closer to the major late cap site. In vitro promoter competition analysis demonstrated that the upstream promoter sequence, independent of the 294 to 304 promoter element, is capable of binding polymerase-transcription factors required for SV40 late gene transcription. Finally, we show that DNA sequences which control the specificity of RNA initiation at nucleotide 325 lie downstream of map position 294.

Simian virus 40 major late promoter: an upstream DNA sequence required for efficient in vitro transcription

We have previously identified an 11-base DNA sequence, 5'-G-G-T-A-C-C-T-A-A-C-C-3' (simian virus 40 [SV40] map position 294 to 304), which is important in the control of SV40 late RNA expression in vitro and in vivo (Brady et al., Cell 31:625-633, 1982). We report here the identification of another domain of the SV40 late promoter. A series of mutants with deletions extending from SV40 map position 0 to 300 was prepared by nuclease BAL 31 treatment. The cloned templates were then analyzed for efficiency and accuracy of late SV40 RNA expression in the Manley in vitro transcription system. Our studies showed that, in addition to the promoter domain near map position 300, there are essential DNA sequences between nucleotide positions 74 and 95 that are required for efficient expression of late SV40 RNA. Included in this SV40 DNA sequence were two of the six GGGCGG SV40 repeat sequences and an 11-nucleotide segment which showed strong homology with the upstream sequences required for the efficient in vitro and in vivo expression of the histone H2A gene. This upstream promoter sequence supported transcription with the same efficiency even when it was moved 72 nucleotides closer to the major late cap site. In vitro promoter competition analysis demonstrated that the upstream promoter sequence, independent of the 294 to 304 promoter element, is capable of binding polymerase-transcription factors required for SV40 late gene transcription. Finally, we show that DNA sequences which control the specificity of RNA initiation at nucleotide 325 lie downstream of map position 294.

Definition of the ovalbumin gene promoter by transfer of an ovalglobin fusion gene into cultured cells

In order to study the initiation of transcription from the ovalbumin gene promoter, we constructed a hybrid gene (ovalglobin) in which 753 bps of ovalbumin gene 5'-flanking sequence were joined to the chicken adult beta-globin gene. When transfected into HeLa S3 cells, ovalglobin gene transcription initiated at the ovalbumin gene cap site, as measured by S1 nuclease and primer extension analysis. Deletion of 5'-flanking sequences to position -95 had little effect on transcription; deletion to -77 reduced transcription to about 20% of the wild type level and deletion to -48 reduced the level to about 2%. A deletion to -24, removing the sequence TATATAT, abolished transcription entirely. Hormonal regulation of the ovalglobin gene was observed when primary oviduct cells were used as recipients for DNA transfection. Under these conditions, addition of progesterone increased the level of ovalglobin transcripts to more than 10 times the uninduced level.

Accurate transcription of simian virus 40 chromatin in a HeLa cell extract

During simian virus 40 viral maturation, a series of modifications occur which alter the composition of viral nucleoprotein complexes. As a consequence, the chromatin that is extracted from extracellular simian virus 40 virions exhibits properties that are similar to those of transcriptionally active eucaryotic chromatin. The influence of this chromatin structure on specific RNA initiation by RNA polymerase II was examined by using the in vitro HeLa cell extract of Manley et al. (Proc. Natl. Acad. Sci. U.S.A. 77:3855-3859, 1980). The 5' ends of RNA transcripts were positioned by the "run-off" assay, in which transcripts extend from the initiation site to termination sites created by restriction cleavage and by S1 nuclease analysis, using DNA probes labeled at their 5' termini. Two major early RNA transcripts, which originated at map positions 5,240 +/- 10 and 5,145 +/- 10, and two major late RNA transcripts, which originated at map positions 325 +/- 10 and 185 +/- 10, were identified. Transcripts were initiated with comparable relative efficiencies at the same 5' site when either purified DNA or chromatin was used as the template. Our results suggest that extracellular simian virus 40 virion chromatin modifications do not regulate simian virus 40 promoter selection but function to increase the accessibility of RNA promoter sequences to RNA polymerase II and allow efficient elongation of the RNA chain after the initiation event.

Deletions at intervening sequence splice sites in the alcohol dehydrogenase gene of Drosophila

Two formaldehyde-induced, homozygous viable ADH-negative mutants, Adhfn4 and Adhfn6, possess no material that cross-reacts with antibody directed against ADH, no mature mRNA of wild-type size, and greatly reduced amounts of RNA that hybridizes with an Adh probe. We have cloned the genomic DNA sequences from these mutants in bacteriophage lambda Charon 4 and subcloned the Adh region into plasmid vector pBR327. Restriction analyses revealed one small deletion in each of these mutants and DNA sequencing showed that the splice junctions of the 65-base pair (bp) intervening sequence (IVS) were altered. Both cloned mutant Adh genes, as well as the wild-type gene, are capable of promoting correct specific transcription initiation in HeLa cell nuclear extracts in vitro. We conclude that Adhfn4 and Adhfn6 are defective in RNA processing. Our results provide evidence for the importance of the splice junction sequences in normal ADH RNA processing and stabilization in Drosophila. We also speculate that splicing of ADH RNA proceeds in a nonrandom manner: mutations in one of the intervening sequences appear to cause accumulation of a large ADH RNA containing at least one other IVS.

Conversion of simian virus 40 DNA to ordered nucleoprotein structures by extracts that direct accurate initiation by eukaryotic RNA polymerase II

Interaction of SV40 DNA with three different HeLa cell extracts capable of directing correct initiation of transcription leads to the formation of ordered nucleoprotein complexes that are structurally similar to SV40 minichromosomes and eukaryotic chromatin. These nucleoprotein complexes can be conveniently purified by band sedimentation or gel filtration. Their sedimentation and elution properties resemble those of SV40 minichromosomes. Electron microscopy of purified complexes shows beaded structures that are sensitive to proteases, resulting in recovery of naked, largely undegraded DNA. Contour lengths and compaction ratios of these nucleoprotein complexes are similar to those of authentic SV40 minichromosomes. Their digestion patterns with micrococcal nuclease and pancreatic DNase I resemble those of SV40 minichromosomes. Such nucleosome-like structures can also be obtained with linear SV40 DNA. Unlike nucleosomes, no histones could be detected in the purified nucleoprotein complexes. Non-histone chromosomal protein fractions (high mol. wt. and free of high mobility group proteins) prepared from the HeLa cell extracts can also generate similar ordered structures. We conclude that ordered nucleoprotein structures with certain common characteristics can be formed by interaction of DNA with non-histone chromosomal proteins as well as with histones. Only the former structures are generated in currently used cell-free transcription systems. It appears that only those purified nucleoprotein complexes containing the promoter can be actively transcribed in the presence of additional cell-free extract, suggesting that such structures and their protein components may be important in transcription.

Identification of the in vivo and in vitro origin of transcription in human rDNA

A Hela cell /-100 extract primed with a purified human rDNA containing clone, has been shown to be capable of initiating specific alpha-amanitin-resistant RNA transcripts. By using a number of truncated templates, the site of RNA polymerase I initiation in vitro has been identified. The origin of transcription in vitro and in vivo was further defined by S1-mapping studies with total Hela cell RNA or RNA isolated from the in vitro transcription reaction. The initiation site was found to be the same. The nucleotide sequence of an 848 bp region around the initiation site, has also been determined. A perfect 15 bp homology has been found to exist between human and mouse rDNA very close to the origin of transcription, although little homology exists elsewhere. Sequences homologous to the origin of transcription region were not found repeated within a 12 kb non-transcribed spacer segment upstream from it.

DNA sequences required for specific and efficient initiation of transcription at the polyoma virus early promoter

The 5'-flanking DNA sequences involved in the specific and efficient transcription of the polyoma virus early region have been investigated. Sequence requirements for efficient in vivo expression differed from those in vitro. Deletion of DNA located between 200 and 400 base pairs before the principal cap sites severely inhibited in vivo expression as measured by transformation ability, but did not affect in vitro transcription. Viable deletion mutants which lack the principal cap sites and the "TATA" box were very poor templates for in vitro transcription. Analysis of other deletion mutants in vitro demonstrated that no specific sequences more than 46 base pairs before the cap sites were important. Removal of the TATA box reduced in vitro transcriptional efficiency but did not alter the initiation sites. The synthesis of transcripts with abnormal 5' termini did not occur in vitro until sequence between the TATA box and the normal cap sites was also deleted. We further observed a nonspecific requirement for 90 to 100 base pairs of DNA 5' to the cap site for optimal transcription of DNA fragments in vitro.

Comparison of the polyoma virus early and late promoters by transcription in vitro

Polyoma virus DNA was transcribed in the HeLa whole cell extract in vitro system (1). Early region transcripts with the same 5'-ends as in vivo mRNAs, located 31 +/- 2bp from 'TATA'-boxes, were synthesized by RNA polymerase II. Sequences sufficient for efficient expression of the early promoter were present in a substitution mutant lacking viral DNA from a position 55bp before the principal cap sites. Late region transcripts were synthesised inefficiently. Only one (at nt5129 +/- 2) of the many late mRNA cap sites functioned as an in vitro initiation point. This was the one 5'-end located 31 +/- 2bp from a sequence resembling the 'TATA' consensus. The proportion of late to early region RNA polymerase II transcripts decreased dramatically at suboptimal template concentrations. An hypothesis to explain the regulation of late gene expression in vivo based on these results is proposed. A linear templates were transcribed only by RNA polymerase II, transcripts with the same sense as late mRNAs and 5'-ends at nt5076 +/- 2 were produced from superhelical template by an alpha amanitin resistant enzyme.

In vitro transcription of a cloned mouse ribosomal RNA gene

An in vitro transcription system which utilizes cloned mouse ribosomal RNA gene (rDNA) fragments and a mouse cell extract has been developed. RNA polymerases I is apparently responsible for this transcription as evidenced by the complete resistance to a high concentration (200 micrograms/ml) of alpha-amanitin. Run-off products obtained with three different truncated rDNA fragments indicated that RNA was transcribed from a unique site of rDNA. The S1 nuclease protection mapping of the in vitro product and of in vivo 45S RNA confirmed this site, indicating that, in this in vitro system, transcription of rDNA started from the same site as in vivo. This site is located at several hundred nucleotides upstream from the putative initiation site reported by us (1) and by others (2). Some sequence homology surrounding this region was noted among mouse, Xenopus laevis and Drosophila melanogaster. The data also suggest that some processing of the primary transcript occurs in this in vitro system.

Complete nucleotide sequence of the chicken chromosomal ovalbumin gene and its biological significance

The nucleotide sequence of the entire chicken chromosomal ovalbumin gene has been determined. The gene is 7564 nucleotides in length to code for a mature messenger RNA of 1872 nucleotides. Comparison of the sequence at the 5'-terminal region of the gene with that reported by others has revealed multiple polymorphic nucleotides in the structural, intervening, and flanking DNA sequences. Some of the polymorphic sites occur at positions very close to splice junctions or the eucaryotic promoter sequence, yet apparently have little or no effect on the expression of this gene. The heptanucleotide promoter sequence TATATAT present in the 5'-flanking region of the ovalbumin gene does not occur within the confines of the gene. Nevertheless, multiple Hogness box sequences similar to those found in other eucaryotic genes were delineated within the boundaries of the gene. These internal Hogness box sequences are not used for transcription initiation. Similarly, the hexanucleotide sequence AATAAA common to all eucaryotic messenger RNAs at the 3'-untranslated region occurs seven additional times within the ovalbumin gene. These sites are not used for transcription termination or polyadenylation. Thus, although these sequences may play important roles in the initiation or termination of gene transcripts as well as polyadenylation of the transcripts, the specificity for such biological functions must not reside within these sequences alone. Furthermore, sequences complementary to the highly conserved rat U1 small nuclear RNA have been found throughout the gene. Many of these regions of complementarity occur in the structural sequences. If the small nuclear RNA does play a role in splicing, the specificity must be provided also by other as yet undefined components.

Transcription of the beta-like globin genes and pseudogenes of the goat in a cell-free system

We have examined the transcription in a cell-free system of all the members of a highly regulated gene family, the beta-like hemoglobin genes of the goat. These five genes, which code for embryonic, fetal, juvenile, and adult beta-globin proteins, are all transcribed to roughly the same extent in the in vitro system. In all cases initiation of transcription is accurate. However, two goat beta-globin pseudogenes, as well as several artificially constructed deletion mutants, are not transcribed in vitro. A common feature of the transcriptionally inactive genes is the lack of an AT-rich consensus sequence just upstream of the presumptive initiation site.

Promotion of specific in vitro transcription by excised "TATA" box sequences inserted in a foreign nucleotide environment

We have cloned into plasmid pBR322 a DNA fragment extending from position -32 to position -12 of the adenovirus type 2 major late promoter region (position +1 referring to the cap site). In vitro transcription experiments show that this 21 base pair sequence, which contains the Goldberg-Hogness or "TATA" box, is both necessary and sufficient for specific initiation of transcription by RNA polymerase B (or II). Furthermore, we show that similar sequences, randomly occurring in the bacterial plasmid pBR322, are also recognized by the RNA polymerase B transcription machinery and able to promote specific in vitro transcription. Finally, we discuss the possible importance of the nucleotide sequence of the start region in the actual efficiency of initiation of in vitro transcription.

Mutation in an intervening sequence splice junction in man

The alpha 2-globin gene of an individual with alpha-thalassemia associated with the absence of alpha 2 mRNA was cloned in bacteriophage. This mutant globin gene was normally active in transcription in vitro. The DNA sequence of the gene, however, revealed a pentanucleotide deletion within the 5' splice junction of the first intervening sequence. Following the G of the invariant G-T dinucleotide normally located within such junctions, a deletion of T-G-A-G-G was found. No other sequence abnormalities within the mutant gene were present. We speculate therefore that this deletion within the splice junction is the primary genetic defect in this individual with thalassemia and that loss of a functional splice junction results in failure of stable mRNA formation.

Mouse globin system: a functional and evolutionary analysis

Structural and functional analysis of the mouse alpha-globin and beta-globin genes reveals that the globin genes are encoded in discontinous bits of coding information and that each gene locus is much more complex than was originally supposed. Each seems to consist of an array of several authentic genes as well as several apparently inactive pseudogenes. Comparison of the sequences of some of these genes to one another indicates that chromosomal DNA is a dynamic structure. Flanking and intervening sequences change in two ways: quickly, by duplication and extensive insertions and deletions, and slowly, by point mutation. Active coding sequences are usually limited to the slower mode of evolution. In addition to identifying fast and slow modes of evolution, it has also been possible to test the function of several signals that surround these genes and to identify those that appear to play a role in gene expression.