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Results for “regulatory element transcripts”

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PubMed2004

Complementation of melanocyte development in SOX10 mutant neural crest using lineage-directed gene transfer.

An in vitro gene complementation approach has been developed to dissect gene function and regulation in neural crest (NC) development and disease. The approach uses the avian RCAS virus to express genes in NC cells derived from transgenic mice expressing the RCAS receptor TVA, under the control of defined promoter elements. Constructs for creating TVA transgenic mice were developed using site-specific recombination GATEWAY (GW), compatible vectors that can also be used to facilitate analysis of genomic fragments for transcriptional regulatory elements. By using these GW vectors to facilitate cloning, transgenic mouse lines were generated that express TVA in SOX10-expressing NC stem cells under the control of the Pax3 promoter. The Pax3-tv-a transgene was bred onto a Sox10-deficient background, and the feasibility of complementing genetic NC defects was demonstrated by infecting the Pax3-tv-a cells with an RCAS-Sox10 expression virus, thereby rescuing melanocyte development of Sox10-deficient NC cells. This system will be useful for assessing genetic hierarchies in NC development. Developmental Dynamics 229:54-62, 2004.

Animals↗

PubMed2006

Chlamydial type III secretion system is encoded on ten operons preceded by sigma 70-like promoter elements.

Many gram-negative bacterial pathogens employ type III secretion systems for infectious processes. Chlamydiae are obligate intracellular bacteria that encode a conserved type III secretion system that is likely requisite for growth. Typically, genes encoding type III secretion systems are located in a single locus; however, for chlamydiae these genes are scattered throughout the genome. Little is known regarding the gene regulatory mechanisms for this essential virulence determinant. To facilitate identification of cis-acting transcriptional regulatory elements, the operon structure was determined. This analysis revealed 10 operons that contained 37 genes associated with the type III secretion system. Linkage within these operons suggests a role in type III secretion for each of these genes, including 13 genes encoding proteins with unknown function. The transcriptional start site for each operon was determined. In conjunction with promoter activity assays, this analysis revealed that the type III secretion system operons encode sigma(70)-like promoter elements. Transcriptional initiation by a sigma factor responsible for constitutive gene expression indicates that undefined activators or repressors regulate developmental stage-specific expression of chlamydial type III secretion system genes.

Bacterial Proteins↗

PubMed2006

The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa.

BACKGROUND: An organ such as the bladder consists of complex, interacting set of tissues and cells. Inflammation has been implicated in every major disease of the bladder, including cancer, interstitial cystitis, and infection. However, scanty is the information about individual detrusor and urothelium transcriptomes in response to inflammation. Here, we used suppression subtractive hybridizations (SSH) to determine bladder tissue- and disease-specific genes and transcriptional regulatory elements (TRE)s. Unique TREs and genes were assembled into putative networks. RESULTS: It was found that the control bladder mucosa presented regulatory elements driving genes such as myosin light chain phosphatase and calponin 1 that influence the smooth muscle phenotype. In the control detrusor network the Pax-3 TRE was significantly over-represented. During development, the Pax-3 transcription factor (TF) maintains progenitor cells in an undifferentiated state whereas, during inflammation, Pax-3 was suppressed and genes involved in neuronal development (synapsin I) were up-regulated. Therefore, during inflammation, an increased maturation of neural progenitor cells in the muscle may underlie detrusor instability. NF-kappaB was specifically over-represented in the inflamed mucosa regulatory network. When the inflamed detrusor was compared to control, two major pathways were found, one encoding synapsin I, a neuron-specific phosphoprotein, and the other an important apoptotic protein, siva. In response to LPS-induced inflammation, the liver X receptor was over-represented in both mucosa and detrusor regulatory networks confirming a role for this nuclear receptor in LPS-induced gene expression. CONCLUSION: A new approach for understanding bladder muscle-urothelium interaction was developed by assembling SSH, real time PCR, and TRE analysis results into regulatory networks. Interestingly, some of the TREs and their downstream transcripts originally involved in organogenesis and oncogenesis were also activated during inflammation. The latter represents an additional link between inflammation and cancer. The regulatory networks represent key targets for development of novel drugs targeting bladder diseases.

Animals↗

PubMed2002

A novel transcriptional inhibitory element differentially regulates the cyclin D1 gene in senescent cells.

Senescent human diploid fibroblasts are unable to initiate DNA synthesis following mitogenic stimulation and adopt a unique gene expression profile distinct from young or quiescent cells. In this study, a novel transcriptional regulatory element was identified in the 5'-untranslated region of the cyclin D1 gene. We show that this element differentially suppresses cyclin D1 expression in young versus senescent fibroblasts. Electrophoretic mobility shift assays revealed abundant complexes forming with young cell nuclear extracts compared with senescent cell nuclear extracts. Binding was maintained in young quiescent cells, showing that loss of this activity was specific to senescent cells and not an effect of cell cycle arrest. Site-directed mutagenesis within this cyclin D1 inhibitory element (DIE) abolished binding activity and selectively increased cyclin D1 promoter activity in young but not in senescent cells. Sequences with homology to the DIE were found in the 5'-untranslated regions of other genes known to be up-regulated during cellular aging, suggesting that protein(s) that bind the DIE might be responsible for the coordinate increase in transcription of many genes during cellular aging. This study provides evidence that loss of transcriptional repressor activity contributes to the up-regulation of cyclin D1, and possibly additional age-regulated genes, during cellular senescence.

5' Untranslated Regions↗

PubMed1991

Cloning and characterization of the gene encoding bovine mitochondrial adenylate kinase isozyme 3.

The structure of the gene (AK3) encoding bovine mitochondrial (mt) adenylate kinase isozyme 3 (AK3) has been determined. The gene spans about 46 kb and splits into five exons. The 5'-flanking region of the gene lacks typical transcriptional regulatory elements such as TATA and CAAT boxes. The G + C content of this region is high (71%), and seven GC boxes are recognized. Possible sequences responsive to transcription factors, AP-1, AP-2, Myf-6 and MyoD1, are present in this region. In the 5'-flanking region, there are sequences (mt sequence) which were found in the genes encoding other mt proteins. Transcriptional mapping analyses revealed one major mRNA start point. The promoter activity measurement in Chinese hamster ovary cells by transient expression of the cat gene connected with the 5'-flanking region, showed presence of a functional promoter.

Adenylate Kinase↗

PubMed1990

Purified Drosophila transcription factor, Adh distal factor-1 (Adf-1), binds to sites in several Drosophila promoters and activates transcription.

Adh distal factor-1 (Adf-1) is a sequence-specific DNA-binding activity originally identified in Drosophila tissue culture cells and embryos. Adf-1 binds to upstream recognition elements in each of the two promoters of the Drosophila alcohol dehydrogenase gene (Adh), and binding of Adf-1 to the Adh distal promoter site activates transcription. We have carried out a mutational analysis of the Adh distal promoter using both an in vitro transcription assay and a transient transfection assay in Drosophila tissue culture cells, and in both cases find that deletion of sequences required for Adf-1 binding leads to a 3-4-fold drop in transcription. We have purified Adf-1 and demonstrate by a sodium dodecyl sulfate-gel renaturation assay that it is a 34-kDa protein. Purified Adf-1 activates Adh distal promoter transcription in vitro in a binding site-dependent manner. DNase I footprint analysis shows that the purified protein binds not only to the two previously characterized sites in Adh but also to transcriptional regulatory elements in the dopa decarboxylase (Ddc) and Antennapedia (Antp) P1 promoters. Thus, it appears that Adf-1 may play an important role not only in the regulation of Adh expression but also in the transcription of other Drosophila genes as well.

Alcohol Dehydrogenase↗

PubMed2004

CD14-mediated alterations in transcription and splicing of endogenous retroviruses after injury.

Increase in systemic levels of lipopolysaccharide (LPS) contributes to the pathogenesis of distant organ injury after burn. Stress signals elicited from burn influence transcriptional activities of mouse endogenous retroviruses (MuERVs) in various distant organs. The involvement of LPS pathways in the burn-mediated regulation of MuERVs in the spleen was investigated in this study. Spleen harbors substantial numbers of tissue macrophages, a key responder to LPS stimulation. Spleen tissues collected from CD14 (LPS receptor) knockout (KO) and wild type (WT) mice after burn were subjected to RT-PCR analysis of MuERV expression. There was a substantial induction of 2 bands and a marked downregulation of a band in CD14 KO mice compared to WT mice after burn. Sequence analysis of these CD14- and burn-dependent bands identified 3 new alternatively spliced and 2 defective env transcripts of MuERVs as well as novel splicing signals. Chromosomal loci of putative MuERVs sharing the unique U3 sequences of these transcripts were mapped by surveying the entire genome of C57BL/6J mice. In addition, coding potentials, transcriptional regulatory elements, and adjacent cellular genes of these putative MuERVs were analyzed. The results from these studies suggest that injury-triggered LPS/CD14 signaling events play roles in the transcriptional regulation of certain MuERVs carrying unique U3 promoter sequences.

Amino Acid Sequence↗

PubMed2004

Isolation and characterization of the human Cdc2L1 gene promoter.

CDK11 (cyclin-dependent kinase 11, formerly known as PITSLRE) is a member of the p34cdc2-related kinases. It has been previously shown to be involved in a variety of different cellular processes including RNA processing, apoptosis, and cell cycle progression. It is encoded by two different but highly similar genes, Cdc2L1 (cell division control 2 like 1) and Cdc2L2 (cell division control 2 like 2). Previous studies from our group identified and characterized the transcriptional regulation of the human Cdc2L2 gene promoter. The current studies identify and characterize the Cdc2L1 gene promoter. We cloned the promoter and elucidated the different transcriptional regulatory elements that reside within the 5' region of the gene. Deletion analysis of the promoter showed a region of nucleotides -152 to +11 to be necessary for basal transcription of the Cdc2L1 gene. Sequencing analysis found this region of the promoter to be highly GC-rich but is lacking both TATA and CAAT boxes. There are several different transcription factor binding sites that are consensus or near consensus found within this region. The potential binding sites include two Ets-1 sites, one Skn-1 site, and one E2F-1 site. Transfection studies of various site-directed mutagenesis clones for these different sites revealed that both Ets-1 sites play critical roles in sustained transcriptional activity as well as Skn-1. Chromatin immunoprecipitation of the endogenous promoter with Ets-1 and Skn-1 verified an in vivo association of Ets-1 and Skn-1 transcription factors with the endogenous promoter. These results, in addition to our Cdc2L2 results, lead to the further comprehension of the fundamental mechanisms dictating CDK11 gene expression through the Cdc2L1 gene promoter.

5' Flanking Region↗

PubMed2006

Expression of GATA-1 in a non-hematopoietic cell line induces beta-globin locus control region chromatin structure remodeling and an erythroid pattern of gene expression.

GATA-1 is a hematopoietic transcription factor expressed in erythroid, megakaryocytic, mast cell and eosinophil lineages. It is required for normal erythroid differentiation, the expression of erythroid-specific genes and for the establishment of an active chromatin structure throughout the beta-globin gene locus. GATA-1 is also necessary for the formation and function of the locus control region DNase I hypersensitive site (HS) core elements. To determine whether GATA-1 was sufficient to direct formation of the locus control region (LCR) and an erythroid pattern of gene expression, we expressed GATA-1 in the non-hematopoietic HeLa cell line that does not express other hematopoietic transcription factors but does express GATA-2, GATA-3, and GATA-6. We found that production of the GATA-1 protein resulted in the formation of LCR DNase I HSs 1-4 in their normal locations, and that histones became hyperacetylated within these regulatory elements. Transcription of several erythroid-specific genes was activated in HeLa cells expressing GATA-1, including those coding for alpha-globin, beta-globin, the erythropoietin receptor, the erythroid krüpple-like factor and p45 NF-E2. Despite increased expression of these genes at the mRNA level, their protein products were not detected. These results imply that GATA-1 is sufficient to direct chromatin structure reorganization within the beta-globin LCR and an erythroid pattern of gene expression in the absence of other hematopoietic transcription factors.

Acetylation↗

PubMed1993

A complex response element in intron 1 of the androgen-regulated 20-kDa protein gene displays cell type-dependent androgen receptor specificity.

The androgen-regulated 20-kDa protein gene consists of four exons that code for a major secretory protein of rat ventral prostate. Analysis of its potential cis-acting transcriptional regulatory elements revealed that a large intron 1 region (In-1) had stronger androgen response element (ARE) activity than did the 5'-flanking DNA. In cotransfected CV1 cells, In-1 and its most active subfragment In-1c functioned as AREs but not glucocorticoid response elements (GRE). Nevertheless several ARE/GRE-like partial palindromic sequences are present in In-1c, and it bound both androgen receptors and glucocorticoid receptors in mobility shift assays. A cluster of three ARE/GRE-like sequences contained within a 39-base pair sequence of In-1c had both ARE and GRE activities when analyzed as an isolated oligonucleotide, suggesting that other elements within In-1c determined its ARE specificity. In addition to ARE/GRE-like sequences, In-1c contains putative response elements for the transcription factors AP1, CREB, AP2, OCT-1, C/EBP, and a number of inverted and direct repeats. The ARE specificity of In-1c observed in CV1 cells was diminished in PC3 and HeLa cells transiently cotransfected with an androgen receptor or glucocorticoid receptor expression vector together with an In-1c reporter vector; however, the ARE activity of In-1c was greater than its GRE activity in these cell lines. Interestingly, a 131-base pair subfragment of In-1c retained ARE specificity in all three cell lines.

Amino Acid Sequence↗

PubMed1998

Preliminary analysis of the transcriptional regulation of the human beta 1-adrenergic receptor gene.

One open reading frame of a 13 kb genomic clone of the human beta 1-adrenergic receptor, which lacks introns, encodes the previously isolated cDNA. Transcript(s) between 4.7 and 5.1 kb are detected in total RNA, whereas a approximately 3 kb transcript is detected only in polyadenylated RNA. The poly (A+) transcript is most highly expressed in the pancreas, liver, heart, kidney, thalamus, adrenal, and salivary glands. Primer extension and ribonuclease protection analyses suggest that the major transcriptional start site is located at -263. Transient expression of luciferase reporter gene constructs indicates that the region from -444 to -360 possesses the primary promoter, consistent with the transcriptional start site at -263. Negative transcriptional regulatory elements are located from -3118 to -2730 and -2730 to -2241, while a positive element is located between -2241 and -1790. The present study suggests that, despite similarities, the expression and transcriptional regulation of the human gene are distinct from those of the genes of other species.

Animals↗

PubMed1997

The POU-domain factor Brn-3.0 recognizes characteristic sites in the herpes simplex virus genome.

The restriction of herpes virus latency to mammalian sensory ganglia has led to a search for tissue-specific regulatory molecules in these neurons which alter viral gene expression. We have recently shown that the POU-domain transcriptional regulator Brn-3.0 is abundantly expressed in the adult trigeminal ganglion. To begin to examine the hypothesis that Brn-3.0 might participate in the regulation of the HSV life-cycle, we used Brn-3.0 POU-domain protein as an affinity matrix, and biochemically screened the entire HSV genome for sites of Brn-3.0 binding. This screen identified several sites of the form TA/TA A T N A N TA/T, which significantly do not include the previously identified HSV octamer sequences. All of the selected sites occur in the <25% of the HSV genome which has not been assigned to open reading frames, suggesting that these sites may be transcriptional regulatory elements recognized by Brn-3.0 or another homeobox factor with similar DNA binding properties. However, these sites do not interact with Brn-3.0 with sufficiently high affinity to directly mediate transcriptional activation by Brn-3.0 alone in transfection assays. The experiments described also provide an effective general method for exhaustive screening of large viral genomes or sub-genomic fragments of eukaryotic DNA for sites of interaction with specific transcription factors.

Animals↗

PubMed2006

Constitutive expression of murine decay-accelerating factor 1 is controlled by the transcription factor Sp1.

The complement regulatory protein decay-accelerating factor (DAF or CD55) protects host tissue from complement-mediated injury by inhibiting the classical and alternative complement pathways. Besides its role in complement regulation, DAF has also been shown to be a key player in T cell immunity. Modulation of DAF expression could therefore represent a critical regulatory mechanism in both innate and adaptive immune responses. To identify and characterize key transcriptional regulatory elements controlling mouse Daf1 expression, a 2.5-kb fragment corresponding to the 5' flanking region of the mouse Daf1 gene was cloned. Sequence analysis showed that the mouse Daf1 promoter lacks conventional TATA and CCAAT boxes and displays a high guanine and cytosine content. RACE was used to identify one major and two minor transcription start sites 47, 20, and 17 bp upstream of the translational codon. Positive and negative regulatory regions were identified by transiently transfecting sequential 5'deletion constructs of the 5'flanking region into NIH/3T3, M12.4, and RAW264.7 cells. Mutational analyses of the promoter region combined with Sp1-specific ELISA showed that the transcription factor Sp1 is required for basal transcription and LPS-induced expression of the Daf1 gene. These findings provide new information on the regulation of the mouse Daf1 promoter and will facilitate further studies on the expression of Daf1 during immune responses.

5' Flanking Region↗

PubMed2005

Enhancing rAAV vector expression in the lung.

Despite favorable DNA transfer efficiency, gene expression from recombinant adeno-associated virus (rAAV2) vectors in the lung has been variable in the context of cystic fibrosis (CF) gene therapy. This is due, in part, to the large size of the CF transmembrane regulator (CFTR)-coding sequence which necessitates the use of compact endogenous promoter elements versus stronger exogenous promoters. We evaluated the possibility that gene expression from rAAV could be improved by using AAV capsid serotypes with greater tropism for the apical surface of airway cells (i.e. rAAV5 or rAAV1) and/or using strong promoters such as the cytomegalovirus (CMV) enhancer/chicken beta-actin hybrid (Cbeta) promoter. The relative activity of the CMV immediate-early (CMVie) promoter, the Cbeta promoter, and the Cbeta promoter with a downstream woodchuck hepatitis virus post-transcriptional regulatory element (wpre) were assessed in vitro and in vivo in C57\Bl6 mice using human alpha-1 antitrypsin (hAAT) as a secreted reporter. In vivo, the Cbeta-AAT-wpre group achieved maximum serum levels of 1.5 mg/ml of hAAT. AAV capsid serotypes were then compared in vivo utilizing the transcriptionally optimized CB-wpre cassette in rAAV serotype 1, 2 or 5 capsids (rAAV1, rAAV2, and rAAV5), utilizing luciferase as a reporter to compare expression over a wide dynamic range. The pulmonary luciferase levels at 8 weeks were similar in rAAV5 and rAAV1 groups (2.9 x 10(6) relative light units (RLU)/g tissue and 2.7 x 10(6) RLU/g tissue, respectively), both of which were much higher than rAAV2. Although the advantage of rAAV5 over rAAV2 in the lung has already been described, the availability of another serotype (rAAV1) capable of efficient gene transfer in the lung could be useful.

Animals↗

PubMed1997

Trans-suppression of terminal deficiency-associated position effect variegation in a Drosophila minichromosome.

Position effect variegation (PEV) is the clonal inactivation of euchromatic or heterochromatic genes that are abnormally positioned within a chromosome. PEV can be influenced by modifiers in trans, including single gene mutations and the total amount of heterochromatin present in the genome. Terminal deletions of a Drosophila minichromosome (Dp1187) dramatically increase PEV of a yellow+ body-color gene located in cis, even when the terminal break is > 100 kb distal to the yellow gene. Here we demonstrate that terminal deficiency-associated PEV can be suppressed by the presence of a second minichromosome, a novel phenomenon termed "trans-suppression." The chromosomal elements responsible for trans-suppression were investigated using a series of minichromosomes with molecularly characterized deletions and inversions. The data suggest that trans-suppression does not involve communication between transcriptional regulatory elements on the homologues, a type of transvection known to act at the yellow locus. Furthermore, trans-suppression is not accomplished by titration through the addition of extra centric heterochromatin, a general mechanism for PEV suppression. We demonstrate that trans-suppression is disrupted by significant changes in the structure of the suppressing minichromosome, including deletions of the yellow region and centric heterochromatin, and large inversions of the centric heterochromatin. We conclude that chromosome pairing plays an important role in trans-suppression and discuss the possibility that terminal deficiency-associated PEV and trans-suppression reflect changes in nuclear positioning of the chromosomes and the gene, and/or the activity and distribution of telomere-binding proteins.

Animals↗

PubMed1997

Differential expression of alpha-bungarotoxin-sensitive neuronal nicotinic receptors in adrenergic chromaffin cells: a role for transcription factor Egr-1.

Adrenomedullary chromaffin cells express at least two subtypes of acetylcholine nicotinic receptors, which differ in their sensitivity to the snake toxin alpha-bungarotoxin. One subtype is involved in the activation step of the catecholamine secretion process and is not blocked by the toxin. The other is alpha-bungarotoxin-sensitive, and its functional role has not yet been defined. The alpha7 subunit is a component of this subtype. Autoradiography of bovine adrenal gland slices with alpha-bungarotoxin indicates that these receptors are restricted to medullary areas adjacent to the adrenal cortex and colocalize with the enzyme phenylethanolamine N-methyl transferase (PNMT), which confers the adrenergic phenotype to chromaffin cells. Transcripts corresponding to the alpha7 subunit also are localized exclusively to adrenergic cells. To identify possible transcriptional regulatory elements of the alpha7 subunit gene involved in the restricted expression of nicotinic receptors, we isolated and characterized its 5' flanking region, revealing putative binding sites for the immediate early gene transcription factor Egr-1, which is known to activate PNMT expression. In reporter gene transfection experiments, Egr-1 increased alpha7 promoter activity by up to sevenfold. Activation was abolished when the most promoter-proximal of the Egr-1 sites was mutated, whereas modification of a close upstream site produced a partial decrease of the Egr-1 response. Because Egr-1 was found to be expressed exclusively in adrenergic cells, we suggest that this transcription factor may be part of a common mechanism involved in the induction of the adrenergic phenotype and the differential expression of alpha-bungarotoxin-sensitive nicotinic receptors in the adrenal gland.

Animals↗

PubMed2001

Cell type-specific expression and promoter activity of human endogenous retroviral long terminal repeats.

Evolution over millions of years has adapted several thousand copies of retrovirus-like elements and over 10 times as many solitary long terminal repeats (LTRs) to their present location in the human genome. Transcription of these human endogenous retroviruses (HERVs) has been detected in various cells and tissues, and in some cases their transcriptional control elements have been recruited by cellular genes. We used a retroviral pol-specific expression array to obtain a HERV transcription profile in a variety of human cells such as epidermal keratinocytes, liver cells, kidney cells, pancreatic cells, lymphocytes, and lung fibroblasts. This rapid screening test revealed a distinct HERV pol-expression pattern in each cell type tested so far. About 40 different U3/R regulatory sequences from the HERV-H and HERV-W families were then amplified from actively transcribed 3'HERV LTRs of various cell lines and tissues. Their promoter activities were compared with LTR sequences of other known HERV families in 12 human cell lines using a transient luciferase reporter system. Expression of the isolated HERV LTRs varied significantly in these cell lines, in some cases showing strict cell type specificity. These results suggest that endogenous retroviral LTRs may be a valuable source of transcriptional regulatory elements for the construction of targeted retroviral expression vectors.

Base Sequence↗

PubMed1999

Antisilencing: myelin proteolipid protein gene expression in oligodendrocytes is regulated via derepression.

Antisilencer or antirepressor elements have been described, thus far, for only a few eukaryotic genes and were identified by their ability not to augment gene expression per se but to override repression mediated via negative transcription regulatory elements. Here we report the first case of antisilencing for a neural-specific gene, the myelin proteolipid protein (PLP) gene (Plp). PLP is the most abundant protein found in CNS myelin. The protein is synthesized in oligodendrocytes, and its expression is regulated developmentally. Previously we have shown that a PLP-lacZ transgene (which includes the entire sequence for Plp intron 1) is regulated in mice, in a manner consistent with the spatial and temporal expression of the endogenous Plp gene. In the present report, we demonstrate by transfection analyses, using various PLP-lacZ deletion constructs, that Plp intron 1 DNA contains multiple elements that collectively regulate Plp gene expression in oligodendrocytes. One of these regulatory elements functions as an antisilencer element, which acts to override repression mediated by at least two negative regulatory elements located elsewhere within Plp intron 1 DNA. The mechanism for antisilencing appears to be complex as the intragenic region that mediates this function binds multiple nuclear factors specifically.

Animals↗