Transcriptional activity and factor binding are stimulated by separate and distinct sequences in the 5' flanking region of a mouse tRNAAsp gene

Identification of the transcription start site for the spinach chloroplast serine tRNA gene

Deleting part of the 3' end of the spinach chloroplast serine tRNA coding region, which destroyed the proper folding of its RNA transcript and resulted in the inhibition of tRNA processing, allowed the detection of a serine tRNA primary transcript. The transcription start site for this primary transcript, synthesized from the internal promoter, was mapped to -12 upstream from the mature tRNA coding region. Transcription analysis with various 5' deletion mutants suggested that the AT-rich region between -31 and -11, immediately upstream of the serine tRNA transcription start site, affects the transcription efficiency, and possibly the selection of transcription start site. Identification of the transcription start site for the spinach chloroplast serine tRNA gene in this study represents the first example of 5' end mapping of a tRNA precursor transcribed from chloroplast tRNA genes containing an internal promoter.

Transcriptional silencing of a tRNA1Gly copy from within a multigene family is modulated by distal cis elements

Individual copies of tRNA1Gly from within the multigene family in Bombyx mori could be classified based on in vitro transcription in homologous nuclear extracts into three categories of highly, moderately, or weakly transcribed genes. Segregation of the poorly transcribed gene copies 6 and 7, which are clustered in tandem within 425 base pairs, resulted in enhancement of their individual transcription levels, but the linkage itself had little influence on the transcriptional status. For these gene copies, when fused together generating a single coding region, transcription was barely detectable, which suggested the presence of negatively regulating elements located in the far flanking sequences. They exerted the silencing effect on transcription overriding the activity of positive regulatory elements. Systematic analysis of deletion, chimeric, and mutant constructs revealed the presence of a sequence element TATATAA located beyond 800 nucleotides upstream to the coding region acting as negative modulator, which when mutated resulted in high level transcription. Conversely, a TATATAA motif reintroduced at either far upstream or far downstream flanking regions exerted a negative effect on transcription. The location of cis-regulatory sequences at such farther distances from the coding region and the behavior of TATATAA element as negative regulator reported here are novel. These element(s) could play significant roles in activation or silencing of genes from within a multigene family, by recruitment or sequestration of transcription factors.

Developmental stage-specific regulation of Xenopus tRNA genes by an upstream promoter element

Typically the internal promoter elements of tRNA genes are necessary and sufficient to support transcription. Here a sequence element preceding a Xenopus tRNA gene is shown to be required for transcription in late stage, but not early stage oocyte extracts. The constitutive tyrD gene is expressed in both early and late oocyte extracts, whereas the early oocyte-specific tyrCooc gene is only expressed in early extracts. An upstream promoter element (URR), between positions -42 and -14 of the tyrD gene, mediates this differential expression. The URR is required for tyrD transcription in late oocyte extracts. Placing the URR upstream of the tyrCooc gene allows this gene to be transcribed in late extracts. The URR is irrelevant to transcription in early extracts; transcription of tyrD or tyrCooc requires only the internal promoter sequences. This indicates the polymerase III transcriptional machinery changes during oogenesis, resulting in a stringent upstream sequence requirement. Mutations within the URR are shown to alter the preferred site of initiation by RNA polymerase III. Shifting the position of the URR upstream by one-half helical turn also repositioned the site of initiation, suggesting the URR directs the placement of the initiation factor complex or polymerase itself.

Silkworm TFIIIA requires additional class III factors for commitment to transcription complex assembly on a 5S RNA gene

We find striking similarities in promoter structure and requirements for template commitment on 5S RNA and tRNA genes from silkworms. The promoters are nearly the same size (approximately 160 bp) and include flanking as well as internal sequences. To analyze the factor requirements for 5S RNA transcription complex assembly in a completely homologous system, we have isolated a silkworm fraction that is highly enriched for the 5S RNA-specific transcription factor, TFIIIA. Using this fraction, together with the other silkworm fractions, TFIIIB, TFIIIC, TFIIID and RNA polymerase III, we demonstrate that the requirements for 5S RNA transcription complex assembly are very similar to those previously established for a tRNA(C)(Ala) gene. Specifically, no individual factor fraction is sufficient for commitment of silkworm 5S RNA genes to transcription complex assembly. Rather, combinations of at least three factor fractions are required. Our observation that more than one subset of factors is competent for commitment suggests that silkworm 5S RNA genes further resemble tRNA(C)(Ala) genes in their ability to use multiple pathways for transcription complex formation.

Silk gland-specific tRNA(Ala) genes interact more weakly than constitutive tRNA(Ala) genes with silkworm TFIIIB and polymerase III fractions

Constitutive and silk gland-specific tRNA(Ala) genes from silkworms have very different transcriptional properties in vitro. Typically, the constitutive type, which encodes tRNA(AlaC), directs transcription much more efficiently than does the silk gland-specific type, which encodes tRNA(AlaSG). We think that the inefficiency of the tRNA(AlaCG) gene underlies its capacity to be turned off in non-silk gland cells. An economical model is that the tRNA(AlaSG) promoter interacts poorly, relative to the tRNA(AlaC) promoter, with one or more components of the basal transcription machinery. As a consequence, the tRNA(AlaSG) gene directs the formation of fewer transcription complexes or of complexes with reduced cycling ability. Here we show that the difference in the number of active transcription complexes accounts for the difference in tRNA(AlaC) and tRNA(AlaSG) transcription rates. To determine whether a particular component of the silkworm transcription machinery is responsible for reduced complex formation on the tRNA(AlaSG) gene, we measured competition by templates for defined fractions of this machinery. We find that the tRNA(AlaSG) gene is greatly impaired, in comparison with the tRNA(AlaC) gene, in competition for either TFIIIB or RNA polymerase III. Competition for each of these fractions is also strongly influenced by the nature of the 5' flanking sequence, the promoter element responsible for the distinctive transcriptional properties of tRNA(AlaSG) and tRNA(AlaC) genes. These results suggest that differential interaction with TFIIIB or RNA polymerase III is a critical functional distinction between these genes.

Silk gland-specific tRNA(Ala) genes interact more weakly than constitutive tRNA(Ala) genes with silkworm TFIIIB and polymerase III fractions

Constitutive and silk gland-specific tRNA(Ala) genes from silkworms have very different transcriptional properties in vitro. Typically, the constitutive type, which encodes tRNA(AlaC), directs transcription much more efficiently than does the silk gland-specific type, which encodes tRNA(AlaSG). We think that the inefficiency of the tRNA(AlaCG) gene underlies its capacity to be turned off in non-silk gland cells. An economical model is that the tRNA(AlaSG) promoter interacts poorly, relative to the tRNA(AlaC) promoter, with one or more components of the basal transcription machinery. As a consequence, the tRNA(AlaSG) gene directs the formation of fewer transcription complexes or of complexes with reduced cycling ability. Here we show that the difference in the number of active transcription complexes accounts for the difference in tRNA(AlaC) and tRNA(AlaSG) transcription rates. To determine whether a particular component of the silkworm transcription machinery is responsible for reduced complex formation on the tRNA(AlaSG) gene, we measured competition by templates for defined fractions of this machinery. We find that the tRNA(AlaSG) gene is greatly impaired, in comparison with the tRNA(AlaC) gene, in competition for either TFIIIB or RNA polymerase III. Competition for each of these fractions is also strongly influenced by the nature of the 5' flanking sequence, the promoter element responsible for the distinctive transcriptional properties of tRNA(AlaSG) and tRNA(AlaC) genes. These results suggest that differential interaction with TFIIIB or RNA polymerase III is a critical functional distinction between these genes.

Transcription of a silkworm tRNA(cAla) gene is directed by two AT-rich upstream sequence elements

A region within 35 nucleotides upstream of the transcription initiation site of a variety of silkworm Class III templates is absolutely required for transcription in vitro. To determine whether the activity of this region can be attributed to a particular sequence element, we systematically replaced 4-5 bp segments of the region upstream of a silkworm tRNA(cAla) gene. We show that replacement of either of two AT-rich blocks markedly impairs promoter function, whereas replacement of other sequences has little or no effect. Additional mutants were constructed to test whether base composition or sequence is important for function of the AT blocks. We find that some sequences are more effective than others, but that various AT-rich sequences can direct transcription at a high level. Possible mechanisms by which such elements could act are discussed.

The 5' flanking sequence negatively modulates the in vivo expression and in vitro transcription of a human tRNA gene

The consequences of altering the 5' flanking region of a human amber suppressor tRNA(ser) gene on phenotypic expression in vivo and transcription in vitro was examined by constructing a series of upstream deletion and substitution mutants. The resulting tDNA variants were examined for functional tRNA expression in vivo, by measuring suppression of a nonsense mutation in the Escherichia coli chloramphenicol acetyltransferase (cat) gene in co-transfection assays, and for transcriptional activity in vitro using HeLa cell nuclear extracts. Mutant genes in which the 18 nucleotides 5' proximal to the coding region were deleted and replaced with heterologous sequences were 2 to 5 fold more active in vivo in comparison to the wild type gene. There was a strong, but not exclusive, correlation between the levels of nonsense suppression observed in vivo and transcriptional activity in vitro. In certain cases, introduction of an oligonucleotide encompassing this 18 nucleotide element upstream of more active tRNA genes reduced both the levels of suppression and template activity. These results indicate that the immediate 5' contiguous sequence of this tRNA gene negatively modulates expression both in vivo and in vitro.

The role of the 5'-flanking sequence of a human tRNA(Glu) gene in modulation of its transcriptional activity in vitro

The role of a tRNA-like structure within the 5'-flanking sequence of a human tRNA(Glu) gene in the modulation of its transcription in vitro by HeLa cell extracts has been investigated using several deletion mutants of a recombinant of the gene which lacked part or all of the tRNA-like structure. The transcriptional efficiency of four mutants was the same as that of the wild-type recombinant, two mutants had decreased transcriptional efficiency, one was more efficient, and one, lacking part of the 5' intragenic control region, was inactive. Correlation of the transcriptional efficiencies with the position and the size of the 5'-flanking sequence that was deleted indicated that the tRNA-like structure may be deleted without loss of transcriptional efficiency. Current models for the modulation of tRNA gene transcription by the 5'-flanking sequence are assessed in the light of the results obtained, and a potential model is presented.

Flanking sequences are required for efficient transcription and stable complex formation for the human tRNAiMet3-coding gene

An analysis of 5' and 3' deletions of the human tRNAiMet3 gene has revealed upstream regions required for efficient transcription and stable complex formation in vitro. The 5' boundary of this essential region lies between nucleotides -39 to -18 (start point = + 1), and it has been shown that 3'-flanking sequences near the first termination site are also important for stable complex formation. The transcriptional efficiency of two non-allelic loci (TMET3 and TMET2) has been compared and TMET2 is more active. An analysis of chimeric (hybrid) genes indicates that much of the difference seen is due to 5'-flanking sequences and that there may be complex interactions between 5' and 3' sequences.