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Transcriptional synergism between the vitamin D3 receptor and other nonreceptor transcription factors.

Small changes in the concentrations and/or combinations of trans-acting factors can result in profound alterations in gene expression. Synergistic interaction between different classes of transcription factors bound to distinct sites within a promoter/enhancer region is one mechanism by which this can occur. Reflecting this, hormone response elements, DNA recognition sites for steroid/nuclear receptors, are often found in promoter regions organized as multiple copies or are clustered among binding sites for other trans-acting factors. To systematically examine the potential interactions between one such receptor, the vitamin D3 receptor (VDR), and other nonreceptor transcription factors, we constructed a series of reporter plasmids containing one copy of the osteopontin (Spp1) vitamin D response element (VDRE), consisting of two direct repeats spaced by 3 base pairs, and one binding site for the transcription factors SP1, NF-1, Oct-1, or AP-1. We also generated reporters either under the control of two copies of Spp1 VDRE, or a distinct VDRE from the human osteocalcin gene promoter. The various reporters were used to transiently transfect HeLa or CV-1 cells in the presence and absence of 1,25-dihydroxyvitamin D3. Our results show that VDR transactivates 12-20 times more strongly from two Spp1-VDREs than from one, indicating that VDR synergizes with itself. VDR also synergizes with the other nonreceptor factors, since we observe a 6- to 12-fold degree of synergistic induction after ligand addition, depending on the particular factor. The functional basis for the transcriptional synergism appears to be at the level of cooperative DNA binding, at least for VDR alone and VDR-Oct-1, as demonstrated in vitro by gel mobility shift assays using purified factors. Consistent with this, we show that the minimal requirement for transcriptional synergism in vivo by VDR is its DNA-binding domain.

Base Sequence↗

Factors involved in specific transcription by mammalian RNA polymerase II. Transcription factor IIS stimulates elongation of RNA chains.

A factor that stimulates random transcription of purified DNAs by RNA polymerase II has been partially purified and analyzed with respect to its possible role in specific transcription from class II promoters. Studies of the effect of this factor (transcription factor IIS) on transcription from the adenovirus major late promoter in a system reconstituted with RNA polymerase II and purified factors (IIA, IIB, IIE, and IID) indicated that it acted subsequent to the initiation step and that it stimulated the rate of elongation. Kinetic experiments indicated that the factor affected the efficiency with which the RNA polymerase II passed through pausing sites. The relationship of transcription factor IIS to a protein previously purified from Erlich ascites tumor cells (Sekimizu, K., Nakanishi, Y., Mizuno, D., and Natori, S. (1979) Biochemistry 18, 1582-1588) was also studied.

Adenoviridae↗

Specific binding sites for a pol III transcriptional repressor and pol II transcription factor YY1 within the internucleosomal spacer region in primate Alu repetitive elements.

Alu interspersed repetitive elements possess internal RNA polymerase III promoters that are transcribed in vitro and in transfected mouse cells but are nearly silent in human HeLa cells. Transcriptional repression of these elements is to some extent reversible, as pol III-dependent Alu expression can be induced with herpes simplex or adenovirus. To assess whether sequence-specific DNA binding proteins might contribute to Alu transcriptional silencing, we examined the internucleosomal spacer region surrounding the B box of the Alu pol III promoter in HeLa cell nuclei for evidence of proteins bound at specific sites in vivo. We identified a DNase I-hypersensitive site 5' to the B box and a DNase I-resistant region 3' to the B box in nuclei. An Alu-specific repressor binds to a 5-bp inverted repeat motif overlapping the 5' end of the TFIIIC binding site and may inhibit pol III transcription through competitive displacement. The level of Alu-specific pol III repressor activity is significantly reduced in adenovirus-infected HeLa cells, suggesting that the repressor may contribute to Alu transcriptional silencing in vivo. The 3' DNase I-resistant region coincided with a binding site for the pol II transcription factor YY1 in vitro. YY1 is one of the major proteins in HeLa cells having binding specificity for Alu elements. YY1 bound to tandem arrays of genomic Alu elements may play a role in chromatin organization and silencing.

Adenoviridae↗

Transforming growth factor beta1 inhibits collagenase 3 expression by transcriptional and post-transcriptional mechanisms in osteoblast cultures.

Transforming growth factor (TGF) beta1 is an autocrine regulator of bone cell function. We demonstrated that TGF beta1 enhances bone collagen synthesis, but its effects on collagen degradation are not well characterized. We tested the effects of TGF beta1 on rat collagenase 3 expression in cultures of osteoblast-enriched cells from fetal rat calvariae (Ob cells). Treatment with TGF beta1 at 0.4 nM decreased steady state collagenase mRNA levels after 2 to 24 h. This dose-dependent effect was observed at TGF beta1 concentrations of 4 pM to 1.2 nM, and was accompanied by decreased levels of immunoreactive procollagenase. The protein synthesis inhibitor cycloheximide increased collagenase transcripts, but did not prevent the effect of TGF beta1 on collagenase mRNA levels. TGF beta1 accelerated the decay of collagenase mRNA in transcriptionally arrested Ob cells. In addition, TGF beta1 decreased the levels of collagenase heterogeneous nuclear RNA and the rate of collagenase gene transcription in Ob cells. TGF beta1 enhanced the expression of tissue inhibitors of metalloproteinases (TIMP) 1 and 3 and caused a modest decrease of TIMP 2 mRNA levels. In conclusion, TGF beta1 decreases interstitial collagenase transcripts and protease levels in Ob cells by transcriptional and post-transcriptional mechanisms, and this effect may contribute to its actions on bone matrix.

Animals↗

Infidelity in the structure of ectopic transcripts: a novel exon in lymphocyte dystrophin transcripts.

Ectopic (or "illegitimate") transcripts have recently become popular as a means of facilitating the study of transcripts normally considered to have a pattern of expression restricted to one or a few tissues. It has been generally assumed that the structure of an ectopic transcript faithfully represents that of its tissue-specific counterpart. We describe here the inclusion of a novel exon in 50% of ectopic dystrophin transcripts from human peripheral blood lymphocytes. The novel sequence resembles a conserved region in the 3' untranslated region of members of the carcinoembryonic antigen gene family and lies within the first intron of the human dystrophin gene. This constitutes a significant departure from the expected in vivo splicing behaviour in an ectopic transcript and suggests that there may be exceptions to the assumption that ectopic transcripts are processed in a similar way to their tissue-specific counterparts.

Amino Acid Sequence↗

Rat ribosomal RNA gene can utilize primate RNA polymerase I transcription machinery: lack of absolute species specificity in rDNA transcription.

The transcriptional activity of rodent ribosomal RNA gene (rDNA) in the primate cell was examined in the light of reported species specificity of eukaryotic ribosomal RNA synthesis. The present study showed that rat rDNA can be transcribed in HeLa nuclear extract whereas mouse rDNA was not transcribed in the heterologous extract. Rat and mouse rDNA transcription factors were interchangeable with respect to efficiency and accuracy of transcription. The initiation of rat ribosomal gene transcription by RNA polymerase I occurred at the +1 site in the heterologous extract. Initiation of transcription at the correct site also occurred in vivo following transfection of cloned rat rDNA into the primate (COS-7) cells. These data indicate that rat ribosomal RNA gene can be expressed in the primate system in vitro and in vivo. The absolute lack of species specificity in rDNA transcription has been discussed based on the present data and other reports.

Animals↗

Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro.

To determine the role of ppGpp in both negative and positive regulation of transcription initiation during exponential growth in Escherichia coli, we examined transcription in vivo and in vitro from the growth-rate-dependent rRNA promoter rrnB P1 and from the inversely growth-rate-dependent amino acid biosynthesis/transport promoters PargI, PhisG, PlysC, PpheA, PthrABC, and PlivJ. rrnB P1 promoter activity was slightly higher at all growth-rates in strains unable to synthesize ppGpp (deltarelAdeltaspoT) than in wild-type strains. Consistent with this observation and with the large decrease in rRNA transcription during the stringent response (when ppGpp levels are much higher), ppGpp inhibited transcription from rrnB P1 in vitro. In contrast, amino acid promoter activity was considerably lower in deltarelAdeltaspoT strains than in wild-type strains, but ppGpp had no effect on amino acid promoter activity in vitro. Detailed kinetic analysis in vitro indicated that open complexes at amino acid promoters formed much more slowly and were much longer-lived than rrnB P1 open complexes. ppGpp did not increase the rates of association with, or escape from, amino acid promoters in vitro, consistent with its failure to stimulate transcription directly. In contrast, ppGpp decreased the half-lives of open complexes at all promoters, whether the half-life was seconds (rrnB P1) or hours (amino acid promoters). The results described here and in the accompanying paper indicate that ppGpp directly inhibits transcription, but only from promoters like rrnB P1 that make short-lived open complexes. The results indicate that stimulation of amino acid promoters occurs indirectly. The accompanying paper evaluates potential models for positive control of amino acid promoters by ppGpp that might explain the requirement of ppGpp for amino acid prototrophy.

Amino Acids↗

Site of transcriptional activation of virB on the large plasmid of Shigella flexneri 2a by VirF, a member of the AraC family of transcriptional activators.

VirB plays a central role in the regulation of virulence of Shigella flexneri. It acts as a transcriptional activator and is itself transcriptionally activated by another virulence protein, VirF. Experiments were performed in order to identify the site upstream of virB at which VirF binds in order to activate transcription. Progressive 5' deletions of the DNA upstream of the transcription start point of virB were constructed by subcloning and Bal31 deletion. These deletion derivatives were cloned into the chloramphenicol acetyltransferase (CAT) reporter gene plasmid pKK232-8 and the resulting plasmids were analysed using a CAT activity assay. This allowed identification of minimal regions required for VirB promoter activity and regions required for full enhancement of promoter activity by VirF. A region approximately 100 bp upstream from the transcription start point of virB was identified as being necessary for full activation of this promoter by VirF. This region encompasses at least one inverted repeat which may play a role in transcription repression in the absence of the activator protein, VirF.

Bacterial Proteins↗

Characterizations of coronavirus cis-acting RNA elements and the transcription step affecting its transcription efficiency.

Seven to eight species of viral subgenomic mRNAs are produced in coronavirus-infected cells. These mRNAs are produced in different quantities, and their molar ratios remain constant during viral replication. We studied RNA elements that affect coronavirus transcription efficiency by characterizing a series of cloned coronavirus mouse hepatitis virus (MHV) defective interfering (DI) RNAs containing an inserted intergenic sequence, from which subgenomic DI RNA is transcribed in MHV-infected cells. Certain combinations of upstream and downstream flanking sequences of the intergenic sequence suppressed subgenomic DI RNA transcription, yet changing one of the flanking sequences to a different sequence eliminated transcription suppression. The suppressive effect of certain combinations of flanking sequences, but not all combinations, could be counteracted by altering the intergenic sequence. Thus, the combination of intergenic sequence and flanking sequence affected transcription efficiency. We also characterized another set of DI RNAs designed to clarify which transcription step determines the relative molar ratios of coronavirus mRNAs. Our study indicated that if subgenomic mRNAs were exclusively synthesized from negative-strand genomic RNA, then the relative molar ratios of coronavirus mRNAs were most likely determined after synthesis of the genomic-sized template RNA. If negative-strand subgenomic RNAs were templates for subgenomic mRNAs, then the relative molar ratios of coronavirus mRNAs probably were determined after synthesis of the genomic-sized template RNA used for subgenomic-sized RNA transcription but prior to the completion of the synthesis of subgenomic-sized RNAs containing the leader sequence. The relative molar ratios of coronavirus mRNAs, therefore, seem to have been established prior to a putative replicon-type amplification of subgenomic mRNAs.

Animals↗

Antibodies directed against an epitope in the N-terminal region of the H4L subunit of the vaccinia virus RNA polymerase inhibit both transcription initiation and transcription termination, in vitro.

The vaccinia virus virion RNA polymerase that is active in early gene transcription contains a unique subunit encoded by the H4L gene. Prior studies demonstrated that this protein is required both for early gene transcription initiation and for transcription termination. Polyclonal antibodies raised against H4L amino acids 1 to 256 prevent both initiation and termination of transcription, in vitro. Pretreatment of the anti-H4L antibody with a H4L fragment containing amino acids 1 to 99 prevents antibody inhibition of both steps, mapping the inhibitory antibody-binding site to this region. A combination of immunoprecipitation and competition studies of antibody binding to wild-type and site-specific mutations of H4L(1-195) mapped the strong epitope to a site that includes Y18. H4L fragments containing an Y18A mutation exhibit diminished ability to block antibody inhibition of transcription initiation and termination. Antibodies inhibit preinitiation complex (PIC) formation but not the activity of preformed PICs, indicating that this region of H4L interacts with one or more factors during active PIC formation. Furthermore, isolated H4L(1-195) directly inhibits PIC activity, supporting this model. Anti-H4L antibody inhibition of transcription termination is only observed in the absence of the essential termination cofactor NPH I. In contrast, antibody inhibition of PIC formation is unaffected by NPH I, demonstrating that the inhibitory antibody and NPH I can bind to H4L at the same time.

Animals↗

Mapping and characterization of Paracentrotus lividus mitochondrial transcripts: multiple and overlapping transcription units.

This paper reports the mapping of both mature and precursor Paracentrotus lividus mitochondrial transcripts. Several mtRNAs were found to have 5' and 3' termini which differ from those inferred through DNA sequencing (Cantatore et al. 1989). The 3' ends of the two rRNAs (12S and 16S) overlap with the downstream transcripts (tRNAGlu and CoI mRNA) by 5 and 10 nt respectively. The 132 nt non-coding region is extensively transcribed: in particular it contains a 124 nt RNA and the 5' end of a possible precursor of 13 clustered tRNAs. This latter overlaps by 7 nt with the 3' end of the 124 nt RNA. In addition to the mature RNAs, 32 high molecular weight RNAs, which are probably the precursors of the smaller more abundant mature species, were detected by Northern blotting. The mapping of these transcripts indicates that they are processed at the level of tRNA or tRNA-like sequences and suggests the existence of two transcription initiation sites upstream of the ND1 and the cytochrome b genes respectively. In the light of these results it appears that P. lividus mitochondrial DNA transcription takes place via multiple and probably overlapping transcription units. Moreover, the wide variation in the steady-state levels of the mature mRNAs indicates that sea urchin mitochondrial DNA expression is also regulated at the level of RNA decay.

Animals↗

Cloning and transcription analysis of the entire glycerol utilization (gylABX) operon of Streptomyces coelicolor A3(2) and identification of a closely associated transcription unit.

The entire glycerol utilization (gylABX) operon of Streptomyces coelicolor A3(2) was cloned and its transcriptional organization and regulation was analyzed by Northern blotting, S1 nuclease mapping and transcriptional fusions. Transcription of the operon is glycerol-inducible and glucose-repressible; glyA (presumptively encoding glycerol kinase), gylB (encoding sn-glycerol-3-phosphate dehydrogenase) and gylX (a non-essential 1.1 kb sequence) are transcribed consecutively to give a 5.4 kb mRNA. Two alternative transcription termination or gyl mRNA processing sites are located within the operon; one (a discrete site) lies between gylB and gylX and the other (a heterogeneous site) positioned 3 kb into the operon, may correspond to the gylA-gylB intercistronic region. A 0.9 kb glycerol-inducible transcription unit is located immediately upstream of gylABX. Transcriptional fusion studies employing an attP site-deleted phage vector provided complementary evidence for the organization of the operon.

Chromosome Mapping↗

Distinct post-transcriptional modifications result into seven alternative transcripts of the CC-NBS-LRR gene JA1tr of Phaseolus vulgaris.

The generation of splice variants has been reported for various plant resistance (R) genes, suggesting that these variants play an important role in disease resistance. Most of the time these R genes belong to the Toll and mammalian IL-1 receptor-nucleotide-binding site-leucine-rich repeat (TIR-NBS-LRR) class of R genes. In Phaseolus vulgaris, a resistance gene cluster (referred to as the B4 R-gene cluster) has been identified at the end of linkage group B4. At this complex resistance cluster, three R specificities (Co-9, Co-y and Co-z) and two R QTLs effective against the fungal pathogen Colletotrichum lindemuthianum, the causal agent of anthracnose, have been identified. At the molecular level, four resistance gene candidates encoding putative full-length, coiled-coil (CC)-NBS-LRR R-like proteins, with LRR numbers ranging from 18 to 20, have been previously characterized. In the present study, seven cDNA corresponding to truncated R-like transcripts, belonging to the CC-NBS-LRR class of plant disease R genes, have been identified. These seven transcripts correspond to a single gene named JA1tr, which encodes, at most, only five LRRs. The seven JA1tr transcript variants result from distinct post-transcriptional modifications of JA1tr, corresponding to alternative splicing events of two introns, exon skipping and multiple 'aberrant splicing' events in the open reading frame (ORF). JA1tr was mapped at the B4 R-gene cluster identified in common bean. These post-transcriptional modifications of the single gene JA1tr could constitute an efficient source of diversity. The present results provide one of the few reports of transcript variants with truncated ORFs resulting from a CC-NBS-LRR gene.

Alternative Splicing↗

Grr1p is required for transcriptional induction of amino acid permease genes and proper transcriptional regulation of genes in carbon metabolism of Saccharomyces cerevisiae.

The F-box protein Grr1p is involved in cell cycle regulation, glucose repression and transcriptional induction of the amino acid permease (AAP) gene AGP1. We investigated the role of Grr1p in amino acid-mediated induction of AAP genes by performing batch cultivations with a wild-type strain and a grr1Delta strain and adding citrulline in the exponential phase. Whole-genome transcription analyses were performed on samples from each cultivation, both immediately before and 30 min after citrulline addition. Transcriptional induction of the AAP genes AGP1, BAP2, BAP3, DIP5, GNP1 and TAT1 is fully dependent on Grr1p. Comparison of the grr1Delta strain with the reference strain in the absence of citrulline revealed that GRR1 disruption leads to increased transcription of numerous genes. These encode enzymes in the tricarboxylic acid cycle, the pentose-phosphate pathway and both glucose and starch metabolism. Promoter analysis showed that many of the genes with increased transcription display Mig1p- and/or Msn2p/Msn4p-binding sites. Increased expression of glucose-repressed genes in the grr1Delta strain may be explained by the reduced expression of the hexose transporter genes HXT1, HXT2, HXT3 and HXT4 and a subsequent lowering of the glucose uptake; and the effect of GRR1 deletion on general carbon metabolism may therefore be indirect. Finally, none of the genes known to be primarily involved in cell cycle regulation displayed different expression levels in the grr1Delta cells as compared with the reference strain, suggesting that the role of Grr1p in cell cycle regulation does not include any transcriptional component.

Amino Acid Transport Systems↗

Three linked myosin heavy chain genes clustered within 370 kb of each other show independent transcriptional and post-transcriptional regulation during differentiation of a mouse muscle cell line.

We have examined myosin heavy chain gene transcription in the mouse muscle cell line C2/7 under different culture conditions. Gene-specific probes for embryonic (MHCemb), perinatal (MHCpn), and adult (MHCIIB) MHC sequences were used in nuclear run-on experiments, and transcriptional levels compared with cytoplasmic RNA accumulation of the transcripts during muscle cell differentiation. Transcripts are not detectable in myoblasts. These three MHC genes are physically linked within 370 kb of each other. However, they are not activated coordinately, but show independent transcriptional regulation as muscle cells differentiate into myotubes and as myotubes mature in culture. Post-transcriptional mechanisms also regulate cytoplasmic RNA accumulation of these MHC genes.

Animals↗

Transcriptional and post-transcriptional regulation of c-myc, c-myb, and p53 during proliferation and differentiation of murine erythroleukemia cells treated with DFMO and DMSO.

The proto-oncogenes myc, myb, and p53 produce nuclear proteins which have been implicated in the regulation of proliferation or differentiation in a number of systems. The expression of these proto-oncogenes was studied in murine erythroleukemia (MEL) cells during (i) normal replication, (ii) DMSO-induced differentiation and (iii), alpha-difluoromethylornithine (DFMO)-restricted cell division and differentiation. The RNA levels of c-myc, c-myb, and p53 were all elevated during normal cellular proliferation; only c-myc expression declined when the cells stopped dividing although the rate of transcription for the gene was unaltered. In contrast, treatment of the cells with DFMO resulted in gradual cessation of cell replication and a decrease in transcription of c-myc, c-myb and p53. When the MEL cells were induced to differentiate with dimethyl sulfoxide (DMSO), a transient reduction in c-myc and c-myb RNA levels occurred immediately prior to the G1 arrest with a concomitant decrease in transcriptional activity, while p53 mRNA production was elevated without an increase in transcription. Similar changes of the proto-oncogene levels were observed when the MEL cells were incubated with DFMO and then later induced with DMSO, a protocol which restricts differentiation of the MEL cells. From these experiments we conclude that (i) c-myc, c-myb, and p53 are regulated independently at both the transcriptional and post-transcriptional levels, (ii) DFMO inhibits MEL cell proliferation and expression of several genes, including c-myc, c-myb and p53, and (iii) DFMO suppresses terminal differentiation but is unable to alter proto-oncogene changes associated with the early stages of differentiation.

Animals↗

The 5' and 3' limits of transcription in the pseudorabies virus latency associated transcription unit.

While latent in sensory neurons of infected pigs, pseudorabies virus expresses transcripts from a limited genomic area. These RNAs are transcribed from the strand opposite to that which encodes the pseudorabies immediate-early protein. Using a combination of in situ nucleic acid hybridization performed on latently infected pig trigeminal ganglia and DNA sequencing, 5' and 3' limits of transcription for the pseudorabies LAT transcription unit have been defined. The 5' limit of transcription has been localized to a NarI-BamHI subfragment of the BamHI-6 fragment. Several promoter elements in the correct orientation for the transcript are present including consensus TATA and CAAT boxes and an SP1 site. The 3' limit of transcription has been localized to a HindIII-KpnI subfragment of the BamHI-5 fragment which contains a consensus polyadenylation signal and two termination codones in the correct orientation. From these results we conclude that the region of pseudorabies virus DNA which is active during latency can be no longer than 12.6 kb and completely overlaps the gene encoding the pseudorabies immediate-early protein.

Animals↗

Transcription of Cauliflower mosaic virus DNA: detection of promoter sequences, and characterization of transcripts.

Four RNA transcripts encoded by cauliflower mosaic virus DNA have been detected in the polyadenylated RNA from virus-infected turnip leaves. Two of these transcripts, the major 35S and the 8S species, have the same 5' termini, at nucleotide 7435. A viral DNA fragment encompassing this region directs transcription initiation at this point in vitro. The 5' terminus of the 19S transcript is at nucleotide 5764, and a corresponding viral DNA fragment also directs transcription initiation in vitro. The major 35S RNA is a complete transcript of the circular viral genome, and is 3'-coterminal with 19S RNA at nucleotide 7615. The 8S RNA has its 3' extremity at delta 1, the single-stranded interruption in the transcribed strand of virion DNA. A minor 35S RNA has also been detected that has its 5' and 3' termini at delta 1.

Base Sequence↗