Delineation of DNA sequences that are important for in vitro transcription from the adenovirus EIIa late promoter

The promoter region of the carbamoyl-phosphate synthetase III gene of Squalus acanthias

Carbamoyl-phosphate synthetase III (CPSase III) of Squalus acanthias (spiny dogfish) is a nuclear-encoded mitochondrial enzyme that catalyzes glutamine-dependent formation of carbamoyl phosphate for urea synthesis. In this paper we report the results of cloning a 10-kb segment of genomic DNA which includes the region flanking the 5' end of the spiny dogfish CPSase III gene. A total of 1,295 base pairs of sequence straddling the start codon was obtained. Primer extension experiments revealed that the transcription start site is the G located 114 residues upstream of the translation start codon ATG. The first exon has 240 base pairs, including the 5' untranslated region, the coding sequence for the signal peptide (38 amino acids), and the four N-terminal amino acids of the mature enzyme. The boundary of the first exon and the first intron of the CPSase III gene is concordant with that of rat and frog (Rana catesbeiana) CPSase I, which have been suggested to have evolved from CPSase III. The putative TATA box sequence, TACAAA, is located at position -31 with an uncommonly found C at the third position. Two C/EBP binding site sequences, ATTCTGCAAG (-405 to -397) and GTGCAGTAAG (-168 to -160), were identified in the promoter region, which suggests that spiny dogfish CPSase III might be subjected to transactivation of transcription by C/EBP-related proteins, as has been reported for rat CPSase I. The preparation and binding of a recombinant RcC/EBP-1 protein (the R. catesbeiana homolog of the mammalian C/EBP alpha) to the two spiny dogfish C/EBP binding sequences are described. Two putative heat-shock binding elements were also identified in the promoter region.

Functional analysis of cis-linked regulatory sequences in the HLA DRA promoter by transcription in vitro

Two consensus sequences, called X and Y boxes, capable of binding nuclear proteins and regulating expression in B cells have been defined within the immediate upstream region of major histocompatibility complex (MHC) class II promoters. Unlike other class II promoters, the HLA-DR alpha (DRA) promoter also contains one element identical to the "octamer" motif of immunoglobulin variable region promoters that is responsible for B cell-specific transcription. This "octamer" in the context of DRA appears capable of binding both the ubiquitous (OTF-1) and lymphoid-specific (OTF-2) "octamer" binding proteins, but at least one other distinct "octamer" complex was found. In order to characterize the function of cis-acting elements, we have developed an in vitro system in which a DRA promoter construct is transcribed more efficiently in extracts from B cells than in extracts from class II-negative HeLa cells. 5' deletion constructs which lacked the Y box, but retained the "octamer" motif and TATA box were completely inactive, and internal deletion of the Y box reduced transcription by 95%. Using supercoiled, but not linear templates, we observed differences in transcription efficiencies from templates lacking or disrupting the X consensus element that reflect effects of random replacement of X box sequences in transient expression assays. Demonstration of the complete dependence on the Y box in this system suggests that, despite its demonstrated importance in the DRA promoter, the DRA "octamer" does not utilize OTF-2 in a manner analogous to immunoglobulin promoters in B cells.

Establishment of de novo DNA methylation patterns. Transcription factor binding and deoxycytidine methylation at CpG and non-CpG sequences in an integrated adenovirus promoter

The establishment of de novo patterns of DNA methylation in mammalian genomes is characterized by the gradual spreading of methylation, which has been documented to occur across an entire integrated adenovirus genome as well as at the nucleotide level in the integrated late E2A promoter of adenovirus type 2. By applying the techniques of genomic sequencing and dimethylsulfate or DNase I genomic footprinting in vivo, we have now demonstrated that the spreading of methylation in cell lines that carry the late E2A promoter with three in vitro pre-methylated 5'-CCGG-3' sequences initially involves a DNA domain of this promoter that is devoid of bound proteins. Subsequently, methylation further spreads to neighboring regions, and the patterns of complexed transcription factors are altered. Evidence has been adduced that DNA methylation at sequences homologous to the AP-1 and octamer binding factor sites interferes with protein binding. In contrast, the methylation of sequences in the vicinity of but not involving sequences homologous to an AP-2 site still permits the binding of proteins to these sites. It is significant that during the spreading of methylation a few 5'-CG-3' sequences can remain hemimethylated for several cell generations, before they also become methylated in both complements. Moreover, in cell line HE2, the integrated, heavily methylated late E2A promoter has been shown by the genomic sequencing technique to contain 5-methyldeoxycytidine residues, not only in all 5'-CG-3' dinucleotides but also in a 5'CA-3' and a 5'-CT-3' dinucleotide sequence. Hence, 5-methyldeoxycytidine occurs in a silenced mammalian DNA sequence also in dinucleotides other than 5'-CG-3'. This finding raises the question of whether 5-methyldeoxycytidine in non-5'-CG-3' dinucleotides can be maintained in the methylated state during continuous cell propagation.

cis-acting enhancement of RNA polymerase III gene expression in vitro

The Xenopus laevis S-150 cell-free extract catalyzes in vitro transcription of several RNA polymerase III genes. Among these are the Xenopus 5S RNA gene (somatic type) and the Xenopus methionine tRNA gene. In this report we present an analysis of the transcriptional activity of these two genes either in trans-competition experiments or when the genes are co-localized in the same circular plasmid. In the "cis" arrangement, elevated levels of 5S and tRNA gene expression are observed, which are dependent on the relative orientation of the two genes (convergent or in tandem) and the distance between them. The results of these analyses reveal important parameters affecting the expression of juxtaposed genes.

DNA superhelicity enhances the assembly of transcriptionally active chromatin in vitro

Using an in vitro chromatin assembly system, we analyzed the influence of DNA superhelicity on the development of transcriptionally active minichromosomes. Plasmid DNA molecules containing either a Xenopus borealis 5S RNA gene or an X. laevis methionine tRNA gene were utilized as templates for the assembly of chromatin. Both plasmids were processed into active minichromosomes if introduced as supercoiled molecules into the extract (S-150). The degree of superhelicity is a determining factor in the assembly of active chromatin. Molecules containing varying superhelical densities were processed into minichromosomes with different transcriptional activities. The absence of supercoils leads to the assembly of chromatin with substantially lower transcriptional activity. Assembled minichromosomes are stable enough to be isolated by sucrose gradient centrifugation while retaining their transcriptional phenotype. The formation of nucleosomes with a periodic spacing occurred with the same efficiency and to the same degree regardless of the initial DNA topology. Hence, a determining factor in the development of transcriptionally active chromatin may be the initial superhelicity of the DNA molecule to which activator (trans-acting factors) or repressor (histones) proteins bind. Once the chromatin assembly process has begun, the transcriptional activity of the resulting minichromosome may already have been determined.