The transcription factors Sp1 and Oct-1 interact physically to regulate human U2 snRNA gene expression

The expression of human small nuclear U2 RNA genes is controlled by the proximal sequence element (PSE), which determines the start site of transcription, and a distal sequence element (DSE). The DSE contains an octamer element and three Sp1 binding sites. The octamer, like the PSE, is essential for U2 transcription. The Sp1 sites contribute to full promoter activity by distance-dependent cooperative interactions with the transcription factors Sp1 and Oct-1. Here we show that purified recombinant Sp1 and Oct-1 bind cooperatively to the DSE and that they physically interact in vitro. Furthermore, we show that Sp1 and Oct-1 interact in vivo using a yeast two-hybrid system. The domain of Sp1 which interacts with Oct-1 is confined to the region necessary for transcriptional stimulation of U2 RNA transcription. This region contains the glutamine-rich activation domain B and a serine/threonine-rich part. The results demonstrate that Sp1, in addition to binding to a number of other factors, also interacts directly with transcription factor Oct-1.

Activation functions of transcription factor Sp1 at U2 snRNA and TATA box promoters

To localize regions in the human transcription factor Sp1, which are involved in activating transcription of the U2 snRNA gene promoter and of a TATA box gene promoter, the activation potentials of GAL4/Sp1 chimeras were analyzed in mammalian cells. In vitro mutagenesis analysis of Sp1 showed that mutation of a hydrophobic amino acid residue in glutamine-rich activation domain A impairs stimulation of transcription from the TATA box promoter, but not from the U2 promoter. Furthermore, we found that similar parts of Sp1 are involved in synergistic activation of transcription together with the SV40 enhancer and with an enhancer which binds a single type of transcription factor. This suggests that the activating mechanism of Sp1 is the same with both enhancers. Interestingly, we found that the glutamine-rich domains A and B, that stimulate transcription from the TATA box promoter were not sufficient for U2 gene activation. Stimulation of U2 transcription required amino acid residues 231-485 of Sp1, which contain the glutamine-rich domain B and a serine/threonine-rich part. Since overlapping, but non-identical parts of Sp1 are required for activation of the two promoter types, we conclude that Sp1 activates the U2 snRNA and TATA box promoters by different mechanisms.

Enhancer effect of bovine papillomavirus E2 protein in replication of polyomavirus DNA

In polyomavirus, both transcription from the early promoter and viral DNA replication initiated at the origin of DNA replication is controlled by binding of proteins to the enhancer region. We have developed a simple model system to study the role of an enhancer binding factor in the initiation of polyomavirus DNA replication. A reporter plasmid was constructed which has the enhancer region replaced by two binding sites for a transcription factor, the E2 protein encoded by bovine papillomavirus type 1. Co-transfection of COP 5 cells which express polyomavirus large T-antigen, with the reporter plasmid and an E2 expression plasmid, resulted in E2-dependent stimulation of replication of the reporter plasmid. The activity of several E2 mutants was also analysed. Mutant proteins with decreased activity in transcriptional trans-activation, resulting from impaired DNA binding or other defects, were found to have quantitatively similar reductions of activity in viral DNA replication. The results suggest that the E2 protein activates transcription and polyomavirus DNA replication by similar mechanism(s).

Enhancer activation by a single type of transcription factor shows cell type dependence

Promoter and enhancer elements contain multiple binding sites for ubiquitous and cell type-specific transcription factors which stimulate transcription synergistically. Here we show that cell type-dependent enhancer activity can be achieved by mechanisms other than interactions between cell type-specific transcription factors and DNA. The ability of the SV40 enhancer and the E2 transactivator from bovine papillomavirus (BPV-1) to stimulate transcription from a reporter gene with different minimal promoters was tested in four cell lines. In lymphoid BJA-B cells all minimal promoters that synergized with the SV40 enhancer did so also with the E2-dependent enhancer. In sharp contrast to these results, the E2 enhancer stimulated transcription only from a subset of promoters in fibroblasts and in epithelial cells. The results suggest that lymphoid cells, unlike fibroblasts and epithelial cells, contain auxiliary factor(s) which are necessary for the activation of certain promoters by the E2 enhancer and infer that the specificity of enhancers also is regulated at a co-activator level.

Both Oct-1 and Oct-2A contain domains which can activate the ubiquitously expressed U2 snRNA genes

The U2 snRNA genes, which are transcribed by RNA polymerase II at high levels in all tissues examined, require both a distal and a proximal sequence element for efficient expression. The distal sequence element which has many properties in common with transcriptional enhancers contains, in addition to Sp1 binding sites, an octamer binding site which mediates activation through interactions with the ubiquitous transcription factor Oct-1. In the present study we have attempted to answer the question whether Oct-1 contains a unique activating domain which is required for activation of snRNA genes or whether ubiquitously expressed and lymphoid specific octamer binding factors both have the capacity to activate snRNA transcription. Our results show that in the presence of Oct-1, overexpression of Oct-2A in HeLa or COS1 cells neither inhibits nor stimulates transcription of U2 constructions which contain octamer binding sites with or without an adjacent Sp1 binding site. Moreover, an Oct-2A--GAL4 fusion protein in which the DNA binding domain of Oct-2A was substituted for by the one of the yeast transcription activator GAL4 activates transcription of a human U2 snRNA gene in which the octamer binding site was replaced by a GAL4 binding site. From the results it is concluded that both Oct-1 and Oct-2A contain domains which can activate the ubiquitously expressed U2 snRNA genes.

A zinc-responsive factor interacts with a metal-regulated enhancer element (MRE) of the mouse metallothionein-I gene

Heavy metal ions are effective inducers of metallothionein gene transcription. The metal response is dependent on short DNA motifs, so-called MREs (metal responsive elements) that occur in multiple copies in the promoter region of these genes. We have analysed an MRE of the mouse metallothionein-I gene (MREd) and we demonstrate that this can function over long distances as a bona fide metal ion-inducible enhancer. The transcription factor Sp1 and a zinc-inducible factor, designated MTF-1, bind to the MREd enhancer in vitro. The combined use of MREd mutants in a transient assay in HeLa cells and a competition band shift assay show that the zinc-inducible formation of the MTF-1/DNA complex in vitro correlates with zinc-inducible transcription in vivo. A chemical methylation interference assay revealed remarkably similar but non-identical guanine interference patterns for the MTF-1 and Sp1 complexes, which may mean that MTF-1 is related to the Sp1 factor.

Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated

In vertebrates, a negative correlation between gene activity and CpG methylation of DNA, notably in the promoter region, is well established. Therefore, it is conceivable that differential binding of transcription factors to methylated versus unmethylated binding sites is crucial for gene activity. Since the consensus binding site of transcription factor Sp1 contains a central CpG, we have investigated the binding of Sp1 factor to unmethylated and synthetically CpG-methylated DNA. A strong Sp1 binding site was methylated on both strands at two CpG positions, located in the center and at the periphery of the recognition sequence. Our studies show that neither binding in vitro, nor transcription in vivo and in vitro are affected by methylation of the Sp1 binding site. We discuss the possibility that binding of Sp1 factor, which is often associated with promoters of housekeeping genes, prevents CpG methylation.

Heavy metal ions in transcription factors from HeLa cells: Sp1, but not octamer transcription factor requires zinc for DNA binding and for activator function

Zinc is an important cofactor for many enzymes involved in nucleic acid metabolism such as DNA and RNA polymerases, reverse transcriptase and tRNA synthetases. We have developed an inducible in vitro transcription system using metal-depleted nuclear extracts to reveal the presence and functional relevance of heavy metal ions in transcription factors. Using protein-DNA binding assays (band shift and DNAase I footprint) we show that Sp1, a promoter-specific vertebrate transcription factor that binds to the "GC box" (Sequence in text), is reversibly inactivated by metal-depletion. Zinc is required for specific DNA binding in vitro and is also essential for Sp1 factor-directed transcription. In contrast, another factor from HeLa cells, the so-called octamer transcription factor (OTF) that binds to the sequence 5'-ATGCAAATNA, is not affected by metal-depletion and thus seems not to be a zinc metalloprotein.

OVEC, a versatile system to study transcription in mammalian cells and cell-free extracts

We have developed a vector, OVEC ("oligonucleotide vector") to study DNA sequences involved in the regulation of transcription in mammalian cells. This vector is equally suitable for studying expression in vivo after transfection into cells, or for transcription studies in vitro with cell-free extracts. Putative cis-acting DNA segments from enhancers or promoters can be inserted at a position immediately upstream of the TATA box and coding sequence of the rabbit beta-globin gene. A regulatory DNA segment can be tested by itself or in conjunction with an enhancer located either in an adjacent upstream position, or downstream of the beta-globin gene. S1 nuclease mapping can be used to study transcription from circular and linear templates and run-off transcription in vitro is also feasible. Transcripts from a reference globin gene with a small deletion around the transcription initiation site can be measured with the same S1 nuclease probe and thus serve as an internal standard. We demonstrate the usefulness of OVEC by inserting either short oligonucleotides comprising a metal responsive enhancer element, or the SV40 enhancer, directly upstream of the TATA box. Both constructs yield high levels of correctly initiated transcripts in a transient expression assay in HeLa cells. In a HeLa cell nuclear extract the SV40 enhancer stimulates transcription 40-fold.

Properties of a distal regulatory element controlling transcription of the U2 small nuclear RNA

The upstream region of human U2 genes contains a distal transcriptional control element, previously mapped between nucleotide (nt) positions -198 and -258 (Westin et al., 1984b). In the present study we show that it resembles transcriptional enhancers in being active even from a distance of 1.4 kb. However, in contrast to most other enhancers it functions unidirectionally in Xenopus laevis oocytes. The distal control element was further mapped by construction of truncated templates for U2 RNA transcription. The results showed that templates, which extended to either of nt positions -214 and -218, were inactive. Templates comprising sequences to nt positions -225 or -226 displayed an intermediate level of activity whereas templates which extend to nt -258 were fully active. It has previously been shown that the human U2 enhancer contains binding sites for the so-called octamer binding protein and for transcription factor Sp1 [Janson et al., Nucl. Acids Res. 15 (1987) 4997-5016]. The partially active templates included one binding site for the octamer binding protein, whereas the fully active template included, in addition, two Sp1 binding sites, thus indicating that these transcription factors are of importance for U2 RNA transcription. The structure of the enhancer was also probed by inserting a pair of complementary synthetic oligodeoxynucleotides which represented the region between nt positions -235 and -215 into a truncated template which lacked the enhancer. The oligodeoxynucleotide enhanced transcription to approximately 50% of the level obtained with templates extending to position -258.

Highly reiterated non-coding sequence in the genome of Plasmodium falciparum is composed of 21 base-pair tandem repeats

Clones containing highly reiterated DNA sequences were isolated from a Plasmodium falciparum genomic library. One clone, Rep2, was selected for further characterization by nucleotide sequence analysis. The results revealed that the insert of this clone is composed of tandemly arranged 21 base-pair imperfect repeats. These repeats are estimated to comprise approximately 1% of the P. falciparum genome and there are 10(4) to 2 X 10(5) copies, depending on the genome size estimate used for calculation. Moreover, the repeats are organized in clusters and do not appear to be transcribed in non-synchronized P. falciparum cultures.

The gene cluster for human U2 RNA is located on chromosome 17q21

The gene cluster for human U2 RNA has been mapped to chromosome 17q21 by in situ hybridization and hybridization analysis of DNA from mouse/human somatic cell hybrids.

Nuclease S1-sensitive sites in multigene families: human U2 small nuclear RNA genes

We show here that human U2 small nuclear RNA genes contain a 'strong nuclease S1 cleavage site' (SNS1 site), a sequence that is very sensitive to digestion by nuclease S1. This site is located 0.50-0.65 kb downstream of the U2 RNA coding region. It comprises a 0.15-kb region in which (dC-dT)n:(dA-dG)n co-polymeric stretches represent greater than 90% of the sequence. Nuclease S1 is able to excise unit length repeats of the human U2 RNA genes both from cloned fragments and total human genomic DNA. The precise locations of the cleavage sites are dependent on the superhelicity of the substrate DNA. In negatively supercoiled substrates, cleavages are distributed over the entire 0.15-kb region, but in linearized substrates, they occur within a more limited region, mainly at the boundary of the SNS1 site closest to the human U2 RNA coding region. Nuclease S1 cleavage of negatively supercoiled substrates occurs at pHs as high as 7.0; in contrast, cleavage of linearized substrates requires a pH less than 5.0, indicating that supercoiling contributes to the sensitivity of this site. Mung bean nuclease gives results similar to that observed with nuclease S1.

Nonrandom integration of human U4 RNA pseudogenes

Four loci for human U4 RNA have been characterized by DNA sequence analysis. The results show that all four loci represent pseudogenes, which are flanked by direct repeats. Three of the pseudogenes, designated U4/5, U4/6, and U4/8, have very similar structures; they are all truncated and contain the first 67 to 68 nucleotides of the U4 RNA sequence. Their properties suggest that they were created by integration of truncated cDNA copies of the U4 RNA into new chromosomal sites. An interesting observation was that their flanking regions exhibit sequence homology. A purine-rich 5'-flanking sequence 12 to 13 nucleotides long is almost perfectly conserved in all three loci. Boxes of homology were also found on the 3' side when the U4/6 and U4/8 loci were compared. The U4/4 locus has a slightly different structure; the pseudogene matches the first 79 nucleotides of U4 RNA, but contains a greater number of mutations than the other pseudogenes. Taken together, the results suggest that a frequently occurring type of pseudogene for human U4 was created by a RNA-mediated mechanism and that the integration sites have features in common.

Human U2 and U1 RNA genes use similar transcription signals

We have analyzed the requirements for human U2 RNA transcription by injection of cloned U2/6 RNA genes into nuclei of Xenopus laevis oocytes. Two forms of human U2 RNAs accumulate, a major species corresponding to mature-sized U2 RNA and a minor species corresponding to a 3'-extended precursor. This RNA polymerase II transcription requires only 258 and 94 bp of 5'- and 3'-flanking region sequences, respectively. Efficient U2 RNA synthesis depends on a promoter element located between positions -258 and -198. This region contains a 12-bp direct repeat which strongly resembles a comparable upstream promoter element of the human U1 RNA genes. Sequences between -258 and -198 also confer on the U2 RNA template the ability to complete with co-injected U1 RNA templates for a snRNA gene-specific transcription factor(s). Transcription of U2 RNA is reduced off templates containing an active RNA polymerase III transcription unit, presumably because of relaxation or sequestration of the DNA. In vitro transcription of the U2 RNA gene, like that of the U1 RNA gene, is initiated upstream of the point corresponding to the 5' end of in vivo synthesized RNA.