The effect of changing the distance between the TATA-box and cap site by up to three base pairs on the selection of the transcriptional start site of a cloned eukaryotic gene in vitro and in vivo

A code for transcription initiation in mammalian genomes

Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian genomes. Most core promoters do not have a single TSS, but an array of closely located TSSs with different rates of initiation. As a rule, genes have more than one such core promoter; however, defining the boundaries between core promoters is not trivial. These discoveries prompt a re-evaluation of our models for transcription initiation. We describe a new framework for understanding the organization of transcription initiation. We show that initiation events are clustered on the chromosomes at multiple scales-clusters within clusters-indicating multiple regulatory processes. Within the smallest of such clusters, which can be interpreted as core promoters, the local DNA sequence predicts the relative transcription start usage of each nucleotide with a remarkable 91% accuracy, implying the existence of a DNA code that determines TSS selection. Conversely, the total expression strength of such clusters is only partially determined by the local DNA sequence. Thus, the overall control of transcription can be understood as a combination of large- and small-scale effects; the selection of transcription start sites is largely governed by the local DNA sequence, whereas the transcriptional activity of a locus is regulated at a different level; it is affected by distal features or events such as enhancers and chromatin remodeling.

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters

BACKGROUND

The TATA box, one of the most well studied core promoter elements, is associated with induced, context-specific expression. The lack of precise transcription start site (TSS) locations linked with expression information has impeded genome-wide characterization of the interaction between TATA and the pre-initiation complex.

RESULTS

Using a comprehensive set of 5.66 x 10(6) sequenced 5' cDNA ends from diverse tissues mapped to the mouse genome, we found that the TATA-TSS distance is correlated with the tissue specificity of the downstream transcript. To achieve tissue-specific regulation, the TATA box position relative to the TSS is constrained to a narrow window (-32 to -29), where positions -31 and -30 are the optimal positions for achieving high tissue specificity. Slightly larger spacings can be accommodated only when there is no optimally spaced initiation signal; in contrast, the TATA box like motifs found downstream of position -28 are generally nonfunctional. The strength of the TATA binding protein-DNA interaction plays a subordinate role to spacing in terms of tissue specificity. Furthermore, promoters with different TATA-TSS spacings have distinct features in terms of consensus sequence around the initiation site and distribution of alternative TSSs. Unexpectedly, promoters that have two dominant, consecutive TSSs are TATA depleted and have a novel GGG initiation site consensus.

CONCLUSION

In this report we present the most comprehensive characterization of TATA-TSS spacing and functionality to date. The coupling of spacing to tissue specificity at the transcriptome level provides important clues as to the function of core promoters and the choice of TSS by the pre-initiation complex.

Spacing requirements for simultaneous recognition of the adenovirus major late promoter TATAAAAG box and initiator element

The distance between the TATAAAAG box and initiator element of the strong adenovirus major late promoter was systematically altered to determine the optimal spacing for simultaneous recognition of both elements. We find that the TATAAAAG element is strongly dominant over the initiator for specification of the start site. The wild type spacing of 23 base pairs between TATAAAAG and +1A is optimal for promoter strength and selective recognition of the A-start. Initiation is constrained to a window spaced 19-26 base pairs downstream of (-31)-TATAAAAG-(-24), and A-starts are favored over alternate starts only when spaced between 21 and 25 base pairs downstream of TATAAAAG. We report an expanded TATAAAAG and initiator promoter consensus for vertebrates and plants. Plant promoters of this class are (A-T)-rich and have an A-rich (non-template strand) core promoter sequence element downstream of +1A.

The bovine alpha-lactalbumin promoter directs expression of ovine trophoblast interferon in the mammary gland of transgenic mice

A hybrid construct derived from ovine trophoblastin cDNA and bovine alpha-lactalbumin-encoding gene, was injected into the pronuclei of mouse eggs. In one of the resulting transgenic mouse lines, expression of the hybrid construct was detected and found to be limited to the mammary gland of lactating females which secreted active ovine trophoblastin. This strongly suggests that important cis-acting DNA sequences involved in tissue-specific expression of the bovine gene are located within the second half of the 3' untranslated region, or/and the proximal 5' and 3' regions flanking the transcriptional unit.

Functional significance of sequences following the TATA box of an immunoglobulin promoter studied by random mutagenesis

We have investigated the importance of sequences downstream to the TATA box of an immunoglobulin promoter by transfection and in vitro transcription assays. A sequence from -11 to +10 with respect to the transcriptional start site was synthesised by a procedure allowing for random misincorporation of nucleotides. The pool of mutant oligonucleotides was cloned into the respective position of a vector carrying a fusion of a synthetic immunoglobulin heavy chain promoter with the human growth hormone gene. From 200 clones sequenced, 115 were mutants with at least one nucleotide exchange in every position. Whereas most mutations are of minor functional importance, changes at or near the transcriptional start site reduce the promoter activity considerably.

Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin

Genes encoding high molecular weight (HMW) glutenin, a wheat seed storage protein, are expressed only in the developing endosperm. It was previously demonstrated that sequences essential for endosperm-specific transcription reside within 436 base pairs upstream of the initiation codon for HMW glutenin translation. We have further analyzed this region by testing the ability of a series of truncated HMW glutenin promoter fragments to enhance transcription from an adjacent heterologous promoter. The activity of these hybrid promoters was determined by measuring the expression of a linked beta-glucuronidase (GUS) reporter gene in transgenic tobacco plants. An HMW glutenin promoter fragment spanning nucleotides -375 to -45 relative to the transcription start site was found to stimulate GUS expression in tobacco seeds when inserted in either orientation upstream of the heterologous promoter. Furthermore, this fragment could also potentiate transcription when located 3' to the GUS reporter gene. Stimulation of GUS gene expression in transgenic tobacco seeds did not occur until 9 days to 12 days after anthesis, coincident with the onset of storage protein synthesis in the developing tobacco and wheat seed, and was confined to the endosperm tissue. By testing progressively shorter promoter fragments, the enhancer element responsible for this pattern of expression was localized to a 40-base pair region some 170 base pairs upstream of the start site for HMW glutenin transcription.

Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin

Genes encoding high molecular weight (HMW) glutenin, a wheat seed storage protein, are expressed only in the developing endosperm. It was previously demonstrated that sequences essential for endosperm-specific transcription reside within 436 base pairs upstream of the initiation codon for HMW glutenin translation. We have further analyzed this region by testing the ability of a series of truncated HMW glutenin promoter fragments to enhance transcription from an adjacent heterologous promoter. The activity of these hybrid promoters was determined by measuring the expression of a linked beta-glucuronidase (GUS) reporter gene in transgenic tobacco plants. An HMW glutenin promoter fragment spanning nucleotides -375 to -45 relative to the transcription start site was found to stimulate GUS expression in tobacco seeds when inserted in either orientation upstream of the heterologous promoter. Furthermore, this fragment could also potentiate transcription when located 3' to the GUS reporter gene. Stimulation of GUS gene expression in transgenic tobacco seeds did not occur until 9 days to 12 days after anthesis, coincident with the onset of storage protein synthesis in the developing tobacco and wheat seed, and was confined to the endosperm tissue. By testing progressively shorter promoter fragments, the enhancer element responsible for this pattern of expression was localized to a 40-base pair region some 170 base pairs upstream of the start site for HMW glutenin transcription.

Molecular characterization of an active wheat LMW glutenin gene and its relation to other wheat and barley prolamin genes

The isolation and characterisation by DNA sequencing of a low molecular weight (LMW) glutenin gene from wheat is described. The deduced protein contains a signal peptide, a central repetitive region rich in proline and glutamine and N and C terminal non-repetitive domains, similar to other prolamins. A detailed comparison of the C terminal domain of 20 prolamin genes enabled us to divide them into 4 families. The LMW glutenin family is distinct from the alpha, beta- and gamma-gliadin families of wheat and is closest to the B hordein genes of barley. This and other comparisons were also used to assess the pattern of genetic variation among prolamin sequences and to provide a molecular basis for the interpretation of prolamin size polymorphism. The 5' flanking fragment of the isolated gene was previously shown to direct endosperm-specific expression of a reporter gene in transgenic tobacco. Evidence is provided that the isolated gene is also active in wheat and its transcription initiation site was determined. Features of the gene which may be relevant to its activity are discussed.

Transcription elements and factors of RNA polymerase B promoters of higher eukaryotes

The promoter for eukaryotic genes transcribed by RNA polymerase B can be divided into the TATA box (located at -30) and startsite (+1), the upstream element (situated between -40 and about -110), and the enhancer (no fixed position relative to the startsite). Trans-acting factors, which bind to these elements, have been identified and at least partially purified. The role of the TATA box is to bind factors which focus the transcription machinery to initiate at the startsite. The upstream element and the enhancer somehow modulate this interaction, possibly through direct protein-protein interactions. Another class of transcription factors, typified by viral proteins such as the adenovirus EIA products, do not appear to require binding to a particular DNA sequence to regulate transcription. The latest findings in these various subjects are discussed.

Effects of mutations in the TATA box region of the Agrobacterium T-cyt gene on its transcription in plant tissues

We have generated mutations in the promoter region of the octopine type cytokinin gene of Agrobacterium tumefaciens, and studied their effects on mRNA formation in different plant species. The promoter region of this gene contains several putative TATA boxes. Phenotypic expression and Northern blot hybridization showed that TATA boxes are essential for expression, but that one TATA box leads to wild-type transcript levels. Analysis of the 5' ends of T-cyt transcripts by primer extension using RNA from T-cyt gene transformed tobacco shoots revealed two major cap site clusters and one minor cap site. TATA box consensus sequences can be found approximately 30 bp upstream from each cap site cluster. Deletion of a TATA box results in loss of the corresponding cap sites. An insertion of 7 bp between the right TATA box and corresponding cap sites results in a shift of the position of the cap sites, so that the original distance of TATA box to cap sites is conserved as much as possible.

Functional domains of a T-DNA promoter active in crown gall tumors

Promoter domains required for transcriptional expression of the 780 gene of T-right (pTi15955) were identified by deletion mutagenesis. Accurate quantitation of transcriptional activity of a series of 5' and internal deletion mutants was achieved by using a double gene vector containing a reference 780 gene as an internal standard. Results of the 5' deletions delineated an activator element located between -440 and -229 base pairs (bp) from the start of transcription. Removal of this region resulted in a 100-fold decrease in promoter activity. Two relatively small internal deletion/substitution mutations at positions -74 to -76 and -98 to -112 reduced promoter activity to 38 and 42%, respectively. In most cases large-scale internal deletions (38 to 151 bp) occurring in various locations from positions -12 to -348 bp caused a significant loss in major promoter activity. However, three internal deletions starting at position -37 and extending upstream as far as -153 bp either had little effect on transcriptional activity or resulted in increased activity. Removal of the TATA motif drastically reduced promoter activity to less than 0.1% of the wild type. A minor start of transcription was detected 60 bases upstream from the major transcriptional start site. This minor promoter shares the same activator element as the major promoter for full activity. Deletion and insertion mutations downstream of the minor promoter TATA demonstrated the role of the TATA box in positioning the start of transcription.

Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants

To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.

Functional domains of a T-DNA promoter active in crown gall tumors

Promoter domains required for transcriptional expression of the 780 gene of T-right (pTi15955) were identified by deletion mutagenesis. Accurate quantitation of transcriptional activity of a series of 5' and internal deletion mutants was achieved by using a double gene vector containing a reference 780 gene as an internal standard. Results of the 5' deletions delineated an activator element located between -440 and -229 base pairs (bp) from the start of transcription. Removal of this region resulted in a 100-fold decrease in promoter activity. Two relatively small internal deletion/substitution mutations at positions -74 to -76 and -98 to -112 reduced promoter activity to 38 and 42%, respectively. In most cases large-scale internal deletions (38 to 151 bp) occurring in various locations from positions -12 to -348 bp caused a significant loss in major promoter activity. However, three internal deletions starting at position -37 and extending upstream as far as -153 bp either had little effect on transcriptional activity or resulted in increased activity. Removal of the TATA motif drastically reduced promoter activity to less than 0.1% of the wild type. A minor start of transcription was detected 60 bases upstream from the major transcriptional start site. This minor promoter shares the same activator element as the major promoter for full activity. Deletion and insertion mutations downstream of the minor promoter TATA demonstrated the role of the TATA box in positioning the start of transcription.

Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants

To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.

DNA sequences which influence the selection and efficient utilisation of transcriptional start sites of a eukaryotic gene by RNA polymerase II in vitro and in vivo

Experiments are described which probe the relationship between three sequence elements which make up the eukaryotic RNA polymerase II promoter. A cloned eukaryotic gene, from which the TATA-box and 400 base pairs of 5'-flanking sequence has been deleted, is still transcriptionally active in vivo (following its transfection into cultured mammalian cells) and in vitro. Deletion has appropriately positioned a cluster of five TATA box-like sequences upstream from multiple potential cap sites. Which cap sites are actually used can be predicted from the DNA sequence of TATA box-like sequences and their spatial relationship with respect to possible transcriptional start sites, although there appears to be some difference in cap site utilisation in vitro and in vivo. Data suggest that deletion has also removed "upstream" sequences which affect promoter function.