A 37-base pair element in the far upstream spacer region can enhance transcription of rat rDNA in vitro and can bind to the core promoter-binding factor(s)

Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots

Transcription initiation, essential to gene expression regulation, involves recruitment of basal transcription factors to the core promoter elements (CPEs). The distribution of currently known CPEs across plant genomes is largely unknown. This is the first large scale genome-wide report on the computational prediction of CPEs across eight plant genomes to help better understand the transcription initiation complex assembly. The distribution of thirteen known CPEs across four monocots (Brachypodium distachyon, Oryza sativa ssp. japonica, Sorghum bicolor, Zea mays) and four dicots (Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera, Glycine max) reveals the structural organization of the core promoter in relation to the TATA-box as well as with respect to other CPEs. The distribution of known CPE motifs with respect to transcription start site (TSS) exhibited positional conservation within monocots and dicots with slight differences across all eight genomes. Further, a more refined subset of annotated genes based on orthologs of the model monocot (O. sativa ssp. japonica) and dicot (A. thaliana) genomes supported the positional distribution of these thirteen known CPEs. DNA free energy profiles provided evidence that the structural properties of promoter regions are distinctly different from that of the non-regulatory genome sequence. It also showed that monocot core promoters have lower DNA free energy than dicot core promoters. The comparison of monocot and dicot promoter sequences highlights both the similarities and differences in the core promoter architecture irrespective of the species-specific nucleotide bias. This study will be useful for future work related to genome annotation projects and can inspire research efforts aimed to better understand regulatory mechanisms of transcription.

The -148 to -124 region of c-jun interacts with a positive regulatory factor in rat liver and enhances transcription

The c-jun gene encodes the protein Jun, a component of the essential transcription factor, AP1. Jun/AP-1 occupies a central position in signal transduction pathways as it is responsible for the induction of a number of genes in response to growth promoters. However, the exact mechanisms leading to an enhanced expression of the c-jun gene itself during proliferation, differentiation, cell growth and development are not fully understood. Cell culture studies have given some insight in the mechanisms involved in the up-regulation of c-jun expression by UV irradiation and phorbol esters. However, it is well known that transformed cells do not accurately reflect the biology of a normal cell. We now report the identification of a positive regulatory factor from normal rat liver that activates transcription from the c-jun promoter by binding to the -148 to -124 region of c-jun. Preincubation of fractionated rat liver nuclear extract with an oligonucleotide encompassing this region of the gene significantly reduced transcription from cloned c-jun promoter. In vitro transfection studies using green fluorescent protein as a reporter gene under the control of the c-jun promoter with (-148 to +53) and without (-123 to +53) this region further confirmed its role in transcription. A DNA-binding protein factor, interacting with this region of c-jun was identified from rat liver by using electrophoretic mobility shift assays. This factor binds to its recognition sequence only in the phosphorylated form and exhibits high affinity and specificity. UV cross-linking studies, South-Western analysis and affinity purification collectively indicated the factor to be approximately 40 kDa and to bind to its recognition sequence as a dimer.

Regulation of rDNA transcription during endothelin-1-induced hypertrophy of neonatal cardiomyocytes. Hyperphosphorylation of upstream binding factor, an rDNA transcription factor

Treatment of cultured neonatal cardiomyocytes with endothelin-1 and phorbol 12-myristate 13-acetate (PMA) results in cardiomyocyte hypertrophy. However, the signal transduction pathways involved in this process are poorly understood. Because increased ribosome biogenesis is a requisite for hypertrophy, we sought to (1) confirm the hypothesis that these two hypertrophic agents did indeed induce rRNA synthesis and (2) examine the mechanism through which this induction was accomplished. In this study, hypertrophy of contraction-arrested neonatal cardiomyocytes induced by treatment with either endothelin-1 or PMA was associated with increased rDNA transcription. Western blots demonstrated that the enhanced rates of rDNA transcription were not mediated by increased amounts of either RNA polymerase I or upstream binding factor (UBF), an rDNA transcription factor. However, immunoprecipitation of [32P] orthophosphate-labeled UBF from hypertrophying neonatal cardiomyocytes suggested that the increased rate of rDNA transcription may be due to the hyperphosphorylation of UBF, which would increase the activity of UBF. The increase in UBF phosphorylation occurred within 3 to 6 hours after exposure to either agent, was maximal at 12 hours, and was sustained for at least the first 24 hours of exposure. Phosphoamino acid analysis of UBF immunoprecipitated from control and treated cardiomyocytes demonstrated that UBF was phosphorylated exclusively on serine residues. Our previous studies have shown that the cellular UBF content increased in adrenergic- and contraction-induced models of cardiac hypertrophy. This study with endothelin-1 and PMA demonstrates that the modulation of UBF phosphorylation is an additional pathway by which ribosome biogenesis may be regulated in neonatal cardiomyocytes. These results support the hypothesis that UBF is an important regulatory factor during the initiation and maintenance of the accelerated rate of rDNA transcription observed during neonatal cardiomyocyte hypertrophy mediated by both phorbol esters and endothelin-1.

Effects of repetitive and non-repetitive rat rDNA enhancer elements on in vivo transcription by RNA polymerases I and II

Previous study has demonstrated that a far upstream 174-bp spacer sequence of the rat rRNA-encoding (rDNA) gene can function as an enhancer in vitro in an orientation- and distance-independent manner [Dixit et al., J. Biol. Chem. 262 (1987) 11616-11622]. To demonstrate that this element can also function in vivo, two rat rDNA-cat plasmids, one with the 174-bp element and the other without this sequence, were constructed and transfected into CHO cells. Primer extension analysis of the transcripts produced after transfection showed that transcription initiation occurred at the +1 site of the rDNA. The 174-bp sequence stimulated the rat polI promoter activity in cis 4-5-fold over the control (with the promoter alone). This RNA polymerase (polI) enhancer also stimulated the mouse metallothionein-I (MT-I) and SV40 promoter activities in vivo, irrespective of its distance and orientation. Further dissection of the 174-bp element revealed that the stimulatory activity on the RNA polymerase II (polII) promoter resides within the 37-bp and 43-bp domains at the 3' end of the 174-bp element. Unlike this spacer enhancer, the 130-bp repeat element (RE) proximal to the rat promoter [Ghosh et al., Gene 125 (1993) 217-222] was unable to modulate the polII promoter activity in vivo. These data show that while the non-repetitive enhancer sequence of rat rDNA is interchangeable for the polI and polII promoters, the RE is polI-specific.

Characterization of the 130-bp repeat enhancer element of the rat ribosomal gene: functional interaction with transcription factor E1BF

The 130-bp repetitive element (RE) of the rat rDNA (ribosomal RNA-encoding gene) intergenic spacer stimulated the synthesis of rRNA four- to sixfold, in comparison with that of the promoter alone, both in vivo and in vitro, when ligated to the rat rDNA promoter. The addition of increasing amounts of highly purified E1BF (enhancer-1 binding factor), which binds to the rat rDNA promoter and an upstream nonrepetitive enhancer element [Zhang and Jacob, Mol. Cell. Biol. 10 (1990) 5177-5186], to an in vitro transcription system resulted in enhancement of rDNA transcription from the recombinant plasmids containing the promoter or promoter-RE. However, E1BF-mediated stimulation of transcription under the influence of the RE continued at higher concentrations of E1BF than did the control transcription from the promoter alone. The binding affinity of E1BF for the RE was comparable to its affinity for the nonrepetitive far upstream enhancer element previously characterized in our laboratory. The sequences protected by E1BF in the RE differed from those protected by UBF (upstream control element-binding factor), a well characterized pol I transcription factor. These data suggest that E1BF belongs to a class of transcription factors which interact with the promoter and spacer cis-acting RE to modulate rDNA transcription.

Common RNA polymerase I, II, and III upstream elements in mouse 7SK gene locus revealed by the inverse polymerase chain reaction

7SK RNA in mammalian cells is derived from a gene or genes belonging to a middle-repetitive family in the genome. Standard library search techniques applied to isolating such genes are complicated by the finding of multiple truncated or otherwise modified versions of the sequence, whereas the true gene loci can sometimes be eliminated from amplified libraries. After an unsuccessful search for the 7SK RNA gene in four mouse genomic libraries, we used the inverse polymerase chain reaction (IPCR) on fractionated genomic DNA to characterize sequences containing complete copies of 7SK plus flanking regions for analysis of putative transcription regulatory sequences. Direct sequence of IPCR-amplified material allowed for selection of upstream and downstream primers which could then be used for direct PCR, sequencing, and characterization of the mouse 7SK gene locus. So far, we found only one complete copy of the canonical 7SK gene that differed from the human sequence in only 4 bases. The gene is flanked by a very well-conserved upstream control region that includes a TATA motif, two direct repeats, and a proximal sequence element common to mammalian genes transcribed by all three RNA polymerases. The 3' region contains multiple stretches of T residues, typical of class III terminators.

A cis-acting sequence within the rat ribosomal DNA enhancer region can modulate RNA polymerase II-directed transcription of the metallothionein I gene in vitro

Plasmids were constructed by inserting a 557-bp or 174-bp spacer fragment of rat ribosomal (r)DNA containing an enhancer element(s) at -148 bp upstream from a cloned mouse metallothionein gene (pMT-I). Transcription of these plasmids in a fractionated nuclear extract from a rat hepatoma resulted in 5 to 20-fold stimulation of MT-I gene transcription. This enhancement occurred independent of orientation of the enhancer or its distance from the metallothionein gene promoter or in the presence of the MT-I gene enhancer, and was sensitive to low levels of alpha-amanitin. Stimulation of MT-I gene transcription under the direction of the rDNA spacer element also occurred in HeLa nuclear extract, albeit to a smaller extent. Prior incubation of the nuclear extract with the 557-bp or 174-bp fragment resulted in as much as 5- to 10-fold stimulation of MT-I gene transcription. No significant effect on MT-I gene transcription was observed following preincubation with other DNAs. Preincubation of the extract with three subfragments of the 174-bp spacer inhibited MT-I gene transcription, which suggests that the majority of the 174-bp domain is required for binding to the negative regulatory factor(s) for MT-I gene transcription and that the subfragments can only interact with the positive core promoter-binding factor. The 37-bp subfragment, which has been shown to interact with a positive rDNA trans-acting factor, could also interact with a positive polymerase II (pol II) trans-acting factor. These studies have demonstrated that the 174-bp rat rDNA spacer element containing the pol I enhancer can also modulate pol II-directed transcription.