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PubMed2003

Multiple levels of transcriptional and post-transcriptional regulation are required to define the domain of Hoxb4 expression.

Hox genes are key determinants of anteroposterior patterning of animal embryos, and spatially restricted expression of these genes is crucial to this function. In this study, we demonstrate that expression of Hoxb4 in the paraxial mesoderm of the mouse embryo is transcriptionally regulated in several distinct phases, and that multiple regulatory elements interact to maintain the complete expression domain throughout embryonic development. An enhancer located within the intron of the gene (region C) is sufficient for appropriate temporal activation of expression and the establishment of the correct anterior boundary in the paraxial mesoderm (somite 6/7). However, the Hoxb4 promoter is required to maintain this expression beyond 8.5 dpc. In addition, sequences within the 3' untranslated region (region B) are necessary specifically to maintain expression in somite 7 from 9.0 dpc onwards. Neither the promoter nor region B can direct somitic expression independently, indicating that the interaction of regulatory elements is crucial for the maintenance of the paraxial mesoderm domain of Hoxb4 expression. We further report that the domain of Hoxb4 expression is restricted by regulating transcript stability in the paraxial mesoderm and by selective translation and/or degradation of protein in the neural tube. Moreover, the absence of Hoxb4 3'-untranslated sequences from transgene transcripts leads to inappropriate expression of some Hoxb4 transgenes in posterior somites, indicating that there are sequences within region B that are important for both transcriptional and post-transcriptional regulation.

Animals↗
PubMed1998

The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins.

The route taken by transcripts from synthetic sites in the nucleus to the cytoplasm has been under scrutiny for years, but details of the pathway remain obscure. A new high-resolution method for mapping the pathway is described; HeLa cells are grown in Br-U so that the analogue is incorporated into RNA and exported to the cytoplasm, before Br-RNA is localized by immuno-electron microscopy. After exposure to low concentrations of Br-U for short periods, cells grow normally. Br-RNA is first found in several thousand extra-nucleolar transcription sites or factories (diameter 50-80 nm), before appearing in several hundred new downstream sites (diameter 50-80 nm) each minute; subsequently, progressively more downstream sites become labelled. These sites can be isolated on sucrose gradients as large nuclear ribonucleoprotein particles of approximately 200 S. Later, Br-RNA is seen docked approximately 200 nm away from approximately 20% nuclear pores, before exiting to the cytoplasm. Individual downstream sites are unlikely to contain individual transcripts; rather, results are consistent with groups of transcripts being shipped together from synthetic sites to pores. A subset of SR proteins are excellent markers of this pathway; this subset is concentrated in tens of thousands of sites, which include transcription, downstream and docking sites. Growth in high concentrations of Br-U for long periods is toxic, and Br-RNA accumulates just inside nuclear pores.

Bromouracil↗
PubMed2003

Synthesis of adenosine derivatives as transcription initiators and preparation of 5' fluorescein- and biotin-labeled RNA through one-step in vitro transcription.

Expanding our previous finding of an adenosine-initiated transcription system, we now demonstrate that either the 5' site or the N6 site of adenosine nucleotides can be modified extensively without abolishing their ability to initiate transcription under the T7 phi2.5 promoter. Two series of amino derivatives of adenosine nucleotides were synthesized. Fluorescein and biotin groups were coupled to AMP derivatives through linkers of different sizes and hydrophobicities. Both fluorescein- and biotin-conjugated (at either the 5' or N6 site) adenosine nucleotides can act as efficient transcription initiators, producing fluorescein- and biotin-labeled RNA at the specific 5' end by a one-step transcription procedure, eliminating posttranscriptional modification. Furthermore, N6-modified adenosine derivative-initiated transcription synthesizes 5' end modified RNA with a free phosphate group, providing the possibility for further derivatization. The current finding makes easily available a variety of site-specifically functionalized RNA, which may be used in nucleic acid detection, RNA structural and functional investigation, and generation and isolation of novel functional RNA.

Adenosine↗
PubMed2002

Analysis of transcription of plant 7SL RNA gene variants in HeLa in vitro transcription system.

We have performed an analysis of transcription of hop 7SL RNA genes in heterologous human extract from HeLa cells. Several variants of the Hl7SL-1 gene with a truncated or mutated 5' non-transcribed part revealed a crucial importance of TATA box for transcription. The USE element was found important but dispensable for transcription. Transcription of mutants in the A-like box and experiments with hop 7SL RNA pseudogenes E44 and G32 revealed the importance of internal elements. The A-like box and possibly CG doublet at position +15/+16 described by Bredow et al. (1990a) are according to our results indispensable for in vitro transcription of plant 7SL RNA genes in human extract.

Base Sequence↗
PubMed2006

Reverse serial analysis of gene expression (SAGE) characterization of orphan SAGE tags from human embryonic stem cells identifies the presence of novel transcripts and antisense transcription of key pluripotency genes.

Serial analysis of gene expression (SAGE) is a powerful technique for the analysis of gene expression. A significant portion of SAGE tags, designated as orphan tags, however, cannot be reliably assigned to known transcripts. We used an improved reverse SAGE (rSAGE) strategy to convert human embryonic stem cell (hESC)-specific orphan SAGE tags into longer 3' cDNAs. We show that the systematic analysis of these 3' cDNAs permitted the discovery of hESC-specific novel transcripts and cis-natural antisense transcripts (cis-NATs) and improved the assignment of SAGE tags that resulted from splice variants, insertion/deletion, and single-nucleotide polymorphisms. More importantly, this is the first description of cis-NATs for several key pluripotency markers in hESCs and mouse embryonic stem cells, suggesting that the formation of short interfering RNA could be an important regulatory mechanism. A systematic large-scale analysis of the remaining orphan SAGE tags in the hESC SAGE libraries by rSAGE or other 3' cDNA extension strategies should unravel additional novel transcripts and cis-NATs that are specifically expressed in hESCs. Besides contributing to the complete catalog of human transcripts, many of them should prove to be a valuable resource for the elucidation of the molecular pathways involved in the self-renewal and lineage commitment of hESCs.

Cells, Cultured↗
PubMed2004

Potentiation of androgen receptor transcriptional activity by inhibition of histone deacetylation--rescue of transcriptionally compromised mutants.

Androgens are critical in the development and maintenance of the male reproductive system and important in the progression of prostate cancer. The effects of androgens are mediated by the androgen receptor (AR), which is a ligand-modulated transcription factor that belongs to the nuclear receptor superfamily. We and others have previously shown that CREB-binding protein (CBP) can function as a coactivator for AR. Similar to some other nuclear receptor coactivators and/or the proteins that they interact with, CBP has histone acetyl transferase (HAT) activity that is thought to contribute to transcriptional activation by nuclear receptors. We have therefore assessed whether an increase in the histone acetylation status in the cell can influence AR transcriptional activity, by using the histone deacetylase (HDAC) inhibitors (HDACIs) trichostatin A (TSA), sodium butyrate (Na-But) and depsipeptide (FR901228). We found that inhibition of HDAC activity significantly increased the ability of endogenous AR in LNCaP cells, or ectopically expressed AR in HeLa cells, to activate transcription from AR-dependent reporter constructs. In addition, HDACIs increased the androgen-dependent activation of the prostate-specific antigen (PSA) gene in LNCaP cells, an increase that was not due to an increase in nuclear AR protein levels. Moreover, the viral oncoprotein E1A that inhibits CBP HAT activity fully repressed the ability of HDACIs to stimulate AR-mediated transcription, indicating that CBP is involved in this process. Deletional mutagenesis of AR indicated that whereas the AF-2 domain in the C-terminus is dispensable, the AF-1 domain in the N-terminus is required for augmentation of AR action by HDACIs, an observation which is in concordance with the reduced ability of CBP to activate AR N-terminal deletion mutants. Furthermore, HDACI treatment rescued the deficiency in the transactivation potential of AF-2 mutants. Taken together, our findings suggest that a change in the level of histone acetylation of target genes is an important determinant of AR action, possibly mediated by CBP.

Acetylation↗
PubMed1999

[Analysis of transcript mutations due to transcriptional slippage in rat p53 tumor suppressor gene with the use of yeast functional assay].

Transcriptional slippage was previously found in Escherichia coli during RNA elongation at runs of 10 or more As or Ts, resulting in the addition of untemplated A or U residues. To evaluate the incidence of transcriptional slippage in vivo, we employed a yeast functional assay, and analyzed the frequency and spectrum of mutations in mRNA of the tumor suppressor p53 in rat tissues. In this assay, yeast are transfected with p53 PCR products and a gapped p53 expression vector, which allow homologous recombination in vivo and yield a percentage of red colonies which reflects the proportion of mutant PCR products. Insertion mutations of single base of adenine (A) at stretches of 6 As were frequently detected in the liver samples of LEC rats which develop spontaneous hepatitis and hepatocellular carcinoma. For excluding the possibility of artifacts involvement, p53 cDNA was amplified by PCR from plasmids containing wild-type p53 and tested with the yeast functional assay, which resulted in no A insertion after sequencing 23 mutant clones. Furthermore, in vitro transcript of wild-type p53 was synthesized by SP6 RNA polymerase, and then, reverse-transcribed, PCR-amplified, and tested with the yeast functional assay. The overall rate of A insertion was much lower than that in the LEC rat liver. Since A insertions were found predominantly at nucleotides 293-298 in exon 4, an exon 4-specific yeast functional assay was developed. A insertion was detected in 4.8% of the PCR product of mRNA but 0-0.1% from genomic DNA, which suggested that such A insertion was caused by transcriptional slippage in vivo. The A insertion rate abruptly increased in acute hepatitis stage in the LEC rat liver, while the rate slowly increased by aging in control WKAH rat liver. It was suggested that cell damage and aging were primarily responsible for the increased rate of transcriptional slippage.

Adenine↗
PubMed1992

Catabolite gene activator protein (CAP) is not an "acidic activating region" transcription activator protein. Negatively charged amino acids of CAP that are solvent-accessible in the CAP-DNA complex play no role in transcription activation at the lac promoter.

It has been suggested that the catabolite gene activator protein (CAP) uses an "acidic activating region" transcription activation mechanism and that Glu171 of CAP is the critical amino acid of the "acidic activating region" of CAP (Irwin, N., and Ptashne, M. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8315-8319). In this paper, we show, contrary to the previously published report, that substitution of Glu171 of CAP fails to result in a specific defect in transcription activation at the lac promoter. Furthermore, in this paper, we show that substitution of each other negatively charged amino acid of CAP that is solvent-accessible in the CAP-DNA complex fails to result in a specific defect in transcription activation at the lac promoter. We conclude that CAP does not use an acidic activating region transcription activation mechanism in transcription activation at the lac promoter.

Amino Acids↗
PubMed1991

Transcriptional regulation of the apolipoprotein A-I gene. Species-specific expression correlates with rates of gene transcription.

Previous studies have shown that the abundance of apoA-I mRNA in liver and intestine correlates with a 2-3-fold species-specific difference in the plasma concentration of high density lipoprotein and apoA-I. In order to determine the role of gene transcription in regulating the tissue, steady state apoA-I mRNA abundance nuclear run-on assays were conducted using nuclei from two species of nonhuman primates. The transcriptional activity expressed as the ratio of apoA-I signal intensity to that for the constitutively expressed glyceraldehyde-3-phosphate dehydrogenase was calculated for seven individual animals in each of the two nonhuman primate species. The African green monkey showed a ratio of 4.18 +/- 0.35, and the cynomolgus monkey showed 2.03 +/- 0.13 (n = 7, p less than 0.004). To identify possible cis-acting elements that may be involved in transcriptional regulation of the apoA-I gene, a portion of the apoA-I regulatory region, corresponding to nucleotides -231 to +263 (where +1 is the start site of transcription), was isolated from both species using the polymerase chain reaction. The nucleotide sequence of this region was compared between monkey species, as well as with the same region from the apoA-I gene isolated from human genomic DNA. In this region, the African green monkey apoA-I gene showed 95% similarity, whereas the cynomolgus monkey showed 94% similarity to the human sequence. Although a high degree of sequence similarity was observed among all species, numerous sequence specific differences were noted in the first intron between the two primate species and between nonhuman and human primate sequences. Results from studies measuring relative promoter strength indicated that the African green monkey 5'-regulatory region had a consistently higher level of activity (1.4-3.0-fold) than the same region from the cynomolgus monkey. Interestingly, the African green monkey promoter also showed a significantly higher transcriptional activity than the human or rabbit promoter, suggesting the presence of a nonhuman primate specific cis-acting element(s) regulating apoA-I gene expression. These results demonstrate that a portion of the species-specific difference in apoA-I gene expression may be explained by sequence divergence in the 5'-regulatory region including exon/intron 1 of the apoA-I gene.

Animals↗
PubMed1990

Osmotic control of proU transcription is mediated through direct action of potassium glutamate on the transcription complex.

Osmoregulated transcription from the proU promoter of Escherichia coli has been successfully reconstituted from purified components in a simple in vitro system consisting of plasmid DNA template, RNA polymerase, and nucleotides in the absence of any other protein factor. proU transcription is stimulated by addition of high concentrations of potassium glutamate, the ionic compound accumulated in vivo during hyperosmotic stress. Transcription from the nonosmoregulated promoters beta la, lac, and pepN is inhibited under the same conditions, demonstrating the specificity of potassium glutamate as an inducer of proU transcription. proU transcription requires a circular DNA template, but stable alterations in the degree of supercoiling are unnecessary for this potassium glutamate-dependent signaling. These results agree well with previous data obtained in an S-30 coupled transcription/translation system and suggest that physiological changes in the ionic composition of the intracellular millieu can regulate gene expression.

Escherichia coli↗
PubMed1989

Transcription termination directed by heteroduplex thr attenuator templates. Evidence that the transcript stem and loop structure is the termination signal.

We have constructed both homoduplex and heteroduplex restriction fragment templates that contained mutations in the G + C-rich region of dyad symmetry in the Escherichia coli thr operon attenuator and have studied their termination properties in an in vitro transcription system. We found that the DNA sequence of the template strand determines the transcription termination efficiency. We also constructed two double mutant heteroduplex templates to examine the role of possible complementary base pairs between the nontranscribed DNA strand and the nascent RNA in the transcription bubble. There was no indication that the potential DNA-RNA interactions in the G + C-rich region are involved in transcription termination. Taken together, our results are consistent with and extend those obtained by Ryan and Chamberlin (Ryan, T., and Chamberlin, J. (1983) J. Biol. Chem. 258, 4690-4693) for the trp operon attenuator and argue strongly against models that propose that DNA hairpin formation in the nontranscribed DNA strand or pairing of the nascent RNA with the nontranscribed DNA strand are important for transcription termination.

Base Sequence↗
PubMed1987

Induction of the hepatic mixed-function oxidase system by synthetic glucocorticoids. Transcriptional and post-transcriptional regulation.

Quantitative evaluation of transcriptional rates in isolated nuclei and intranuclear and cytoplasmic mRNA levels demonstrates that the catatoxic steroids pregnenolone-16 alpha-carbonitrile (PCN) and dexamethasone modulate microsomal drug metabolizing enzymes both positively and negatively at the transcriptional level. Additionally, a strong post-transcriptional influence, believed to be message stabilization, was found to be exerted by dexamethasone. Both NADPH-cytochrome P-450b-homologous mRNA are induced 7- and 12-fold, respectively, presumably through message stabilization. Under these conditions, however, the oxidoreductase content of the cell is only marginally increased while the cytochrome P-450b level is actually decreased by 40% within three days after a single injection of dexamethasone. In contrast, genes coding for cytochromes P-450PCN show a definite increase in transcription following administration of either pre gnenolone-16 alpha-carbonitrile or dexamethasone, whereas transcription of the epoxide hydrolase gene is markedly reduced by administration of these compounds.

Animals↗
PubMed1983

[Coupling of transcription and translation as the factor regulating the transcription of genes rpoBC in Escherichia coli cells].

The natural transcription polarity of proximal and distal elements of the rplJL-rpoBC operon is increased when translation is inhibited in Escherichia coli cells. It is shown that transcription uncoupling to translation terminates within EcoRI-2,6 fragment of the operon which contains the transcription attenuator. We suggest that transcription attenuation in the rplJL-rpoBC operon is regulated by the coupling of transcription to translation of the intergenic fragment which overlaps the attenuator sequence.

Chloramphenicol↗
PubMed1995

Products of alternatively spliced transcripts of the Wilms' tumor suppressor gene, wt1, have altered DNA binding specificity and regulate transcription in different ways.

The Wilms' tumor susceptibility gene, wt1, encodes a transcription factor of the zinc finger protein family. Mutations in the WT1 gene product have been detected in both sporadic and familial Wilms' tumors, suggesting that alterations in WT1 may disrupt its normal function as a transcriptional regulator. The transcripts of wt1 are alternatively spliced; however, roles of the alternatively spliced forms have not been defined. The major transcript of wt1 encodes a WT1 protein [WT1(+KTS)+17AA] that contains three amino acids (+KTS) between the third and fourth zinc fingers and a serine-rich, 17 amino acid (+17AA) domain N-terminal to the zinc finger region. We now show that the WT1 (+KTS) forms functionally bind to a unique G+C-rich sequence within the PDGF A-chain promoter. We also show that WT1 (+KTS)+17AA functions as a strong transcriptional repressor and that +17AA alone fused to the zinc-finger domain of WT1 or to the heterologous DNA binding domain of GAL4 functions independently as a repressor. Deletion of four serine residues within +17AA abolishes the repressor activity of +17AA. These results indicate that wt1 products with +17AA contain an additional dominant repressor domain and that the presence or absence of +KTS determines alternative DNA binding specificity.

3T3 Cells↗
PubMed1994

A light-repressed transcript found in Synechococcus PCC 7002 is similar to a chloroplast-specific small subunit ribosomal protein and to a transcription modulator protein associated with sigma 54.

The gene encoding a novel light-repressed transcript (lrtA) contained within a 2.7-kbp EcoRI fragment has been cloned and sequenced from the unicellular cyanobacterium, Synechococcus PCC 7002. Northern analysis indicates that this transcript is synthesized rapidly in the dark, but upon 20 min of illumination, transcript levels fall below detectable limits. An open reading frame was located 378 bases from the start of the transcript which encodes a 21-kDa protein with significant homology to two hitherto different proteins. The protein sequence LrtA showed 37% sequence identity and 58% sequence similarity to the chloroplast-specific small subunit ribosomal protein, S30, and 37% sequence identity and 60% sequence identity and 60% sequence similarity to the reported transcription modulator protein of sigma 54 found in Klebsiella pneumonia and Azotobacter vinelandii. Expression of the lrtA gene product is not detectable within 1 h after placing the cells in the dark, however, within 2.5 min of illumination, [35S]methionine incorporated into a 21-kDa protein. To a lessor extent, [35S]methionine incorporation into a 17- and a 14-kDa protein was also seen which was followed by two other recognizable waves of translation at 5 and 10 min. This incorporation was not blocked by rifampicin added to dark-adapted cells prior to illumination. [35S]Methionine pulsed-labeling experiments suggested that the translation of lrtA occurred only during the first 10 min of reillumination of dark-adapted cells. The loss of initial [35S]methionine labeling in the light of the 21-kDa protein in a kanamycin-interrupted lrtA gene mutant suggests that the lrtA codes for the 21-kDa protein.

Amino Acid Sequence↗
PubMed1993

Priming of human monocytes with leukotriene B4 enhances their sensitivity in IL-2-driven tumor necrosis factor-alpha production. Transcriptional and post-transcriptional up-regulation of IL-2 receptors.

Cytotoxic activity of monocytes may be mediated by their production of TNF-alpha, and IL-2 has been shown to induce TNF-alpha production in monocytes and alveolar macrophages. Unstimulated human monocytes constitutively express the beta-chain of the IL-2R (IL-2R beta), but little or no IL-2R alpha. When monocytes were pretreated with leukotriene (LT) B4, they responded to IL-2 with both enhanced production of TNF-alpha (two- to threefold) and, more strikingly, with augmented sensitivity (1000-fold) to IL-2. Treatment of monocytes with LTB4 induced IL-2R alpha gene transcription at 30 min and augmented expression of IL-2R alpha gene transcripts by 3 h, maximal at 10(-8) M LTB4. LTB4 induced increased shedding of the IL-2R alpha in the culture supernatants and a modest induction of IL-2R alpha protein expression on monocytes. On the other hand, although LTB4 could stimulate the cell membrane expression of IL-2R beta and the accumulation of IL-2R beta mRNA, LTB4 did not significantly affect IL-2R beta gene transcription. The augmented expression of IL-2R on monocytes was associated with augmented binding of 125I-labeled IL-2 to LTB4-pretreated monocytes. Our data present direct evidence that the inflammatory lipid mediator LTB4 can induce the expression of IL-2R alpha in human monocytes by activating IL-2R alpha gene transcription; it can also stimulate the expression of IL-2R beta, through post-transcriptional regulation; this augmented expression of both alpha- and beta-chains of the IL-2R is associated with enhanced sensitivity of monocytes to IL-2 in terms of TNF-alpha production and may be relevant to the proinflammatory actions of LTB4.

Cells, Cultured↗
PubMed1993

Ionizing radiation down-regulates histone H1 gene expression by transcriptional and post-transcriptional mechanisms.

The cellular response to ionizing radiation includes growth arrest and DNA repair. However, little is known about the regulation of gene expression by this agent. The present studies demonstrate that exposure to ionizing radiation is associated with a dose-dependent decrease in histone H1 gene expression. Following treatment with 20 Gy, this effect was transient, detectable at 15-30 min, and maximal at 6 h. Nuclear run-on assays demonstrate that this down-regulation is controlled at least in part by transcriptional mechanisms. We also demonstrate that inhibition of protein synthesis with cycloheximide abrogates the down-regulation of both histone H1 gene transcription and mRNA levels in irradiated cells. The results demonstrate that treatment with ionizing radiation is associated with a decrease in the stability of the histone H1 transcript, and that this effect is reversed by inhibition of protein synthesis. These findings demonstrate that ionizing radiation activates at least two distinct signaling pathways that control histone H1 expression at the transcriptional and post-transcriptional levels.

Dose-Response Relationship, Radiation↗
PubMed1996

IL-7 differentially modulates the expression of IFN-gamma and IL-4 in activated human T lymphocytes by transcriptional and post-transcriptional mechanisms.

We investigated the role of IL-7 on the expression of IFN-gamma and IL-4 in human T lymphocytes. IL-7 alone did not induce IFN-gamma or IL-4 mRNA. However, IL-7 dose-dependently up-regulates the anti-CD3- or anti-CD3/anti-CD28-induced IFN-gamma and IL-4 mRNA expression. Used at an optimal concentration, IL-7 (5 ng/ml) increased the accumulation of IFN-gamma (eightfold) and IL-4 (2.5-fold) mRNAs, which could not be blocked by anti-IL-12 treatment. The enhanced IFN-gamma mRNA accumulation was observed within 3 to 6 h, without altering the pattern of the kinetics. However, longer exposure (> 12 h) did not result in different IFN-gamma expression for anti-CD3/anti-CD28 vs anti-CD3/anti-CD28 plus IL-7-stimulated T lymphocytes. mRNA stability studies revealed that IL-7 stabilizes both IFN-gamma and IL-4 mRNA transcripts: 40 and 60 min in anti-CD3/anti-CD28-stimulated T cells vs 120 and 90 min in T cells costimulated with anti-CD3/anti-CD28 plus IL-7. Nuclear run-on assays revealed that the transcription rate of the IFN-gamma gene increased approximately twofold in the presence of IL-7, without affecting the transcription rate of the IL-4 gene. The IL-7-mediated IFN-gamma up-regulation could not be inhibited by cycloheximide treatment, in contrast to IL-4 gene expression. However, the promotive effect of IL-7 on IFN-gamma and IL-4 gene expression could be blocked by genistein and cyclosporin A. Finally, it was demonstrated that the effect of IL-7 on IFN-gamma mRNA accumulation was also reflected at the protein level. In summary, these data demonstrate that IL-7 preferentially up-regulates IFN-gamma expression in activated T lymphocytes, which is accomplished at transcriptional and post-transcriptional levels.

Cells, Cultured↗