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PubMed1995

Characterization of the cis-regulatory region of the Drosophila homeotic gene Sex combs reduced.

The Drosophila homeotic gene Sex combs reduced (Scr) controls the segmental identity of the labial and prothoracic segments in the embryo and adult. It encodes a sequence-specific transcription factor that controls, in concert with other gene products, differentiative pathways of tissues in which Scr is expressed. During embryogenesis, Scr accumulation is observed in a discrete spatiotemporal pattern that includes the labial and prothoracic ectoderm, the subesophageal ganglion of the ventral nerve cord and the visceral mesoderm of the anterior and posterior midgut. Previous analyses have demonstrated that breakpoint mutations located in a 75-kb interval, including the Scr transcription unit and 50 kb of upstream DNA, cause Scr misexpression during development, presumably because these mutations remove Scr cis-regulatory sequences from the proximity of the Scr promoter. To gain a better understanding of the regulatory interactions necessary for the control of Scr transcription during embryogenesis, we have begun a molecular analysis of the Scr regulatory interval. DNA fragments from this 75-kb region were subcloned into P-element vectors containing either an Scr-lacZ or hsp70-lacZ fusion gene, and patterns of reporter gene expression were assayed in transgenic embryos. Several fragments appear to contain Scr regulatory sequences, as they direct reporter gene expression in patterns similar to those normally observed for Scr, whereas other DNA fragments direct Scr reporter gene expression in developmentally interesting but non-Scr-like patterns during embryogenesis. Scr expression in some tissues appears to be controlled by multiple regulatory elements that are separated, in some cases, by more than 20 kb of intervening DNA. Interestingly, regulatory sequences that direct reporter gene expression in an Scr-like pattern in the anterior and posterior midgut are imbedded in the regulatory region of the segmentation gene fushi tarazu (ftz), which is normally located between 10 and 20 kb 5' of the Scr transcription start site. This analysis provides an entry point for the study of how Scr transcription is regulated at the molecular level.

Amino Acid Sequence↗
PubMed2000

Insect population control using a dominant, repressible, lethal genetic system.

A major modification to the sterile insect technique is described, in which transgenic insects homozygous for a dominant, repressible, female-specific lethal gene system are used. We demonstrate two methods that give the required genetic characteristics in an otherwise wild-type genetic background. The first system uses a sex-specific promoter or enhancer to drive the expression of a repressible transcription factor, which in turn controls the expression of a toxic gene product. The second system uses non-sex-specific expression of the repressible transcription factor to regulate a selectively lethal gene product. Both methods work efficiently in Drosophila melanogaster, and we expect these principles to be widely applicable to more economically important organisms.

Animals↗
PubMed2026

Conservation of Long G4-rich (LG4) genomic enhancer regulations.

Long G4-rich regions (LG4s) are defined as DNA sequences containing a high density of guanine triplets capable of forming non-B DNA structures called G-quadruplexes (G4s). These regions frequently overlap with enhancers, which are regulatory DNA elements that modulate gene expression by interacting with DNA regions that dictate where transcription is initiated known as promoters. While LG4s have now been well-characterized in the human genome, neither LG4 occurrence, nor the ability of LG4s to function as enhancers, in other species has been described. To address this, we screened the genomes of 16 different species from various taxa to identify LG4s and then determined if they were conserved, and additionally, we show the ability of one of the conserved LG4s to interact with its cognate promoter in vitro is functionally maintained across species. Our analyses characterized a number of previously unreported LG4s in the human genome as well as LG4s in 13 additional species. Of note, we identified a highly conserved LG4 enhancer predicted to regulate over 40 genes. This LG4 is embedded in the MAZ (Myc-Associated Zinc finger protein) locus, and we find this LG4 possesses the ability to directly interact with the same target promoter in both human and mouse. In summary, this work describes LG4s in the genomes of both unicellular and multicellular species including vertebrates, invertebrates, plants, and fungi, and finds many of these LG4 sequences highly conserved.

G-Quadruplexes↗
PubMed2026

Enhancer-mediated DDIT4 activation by SMYD2-dependent H3K4me1 promotes pazopanib resistance in clear cell renal cell carcinoma.

BACKGROUND: The progression and resistance to targeted therapy, including pazopanib, frequently lead to poor prognosis in clear cell renal cell carcinoma (ccRCC) patients. However, the underlying molecular mechanisms of these processes remain unclear. METHODS: In this study, we first performed RNA-seq to identify genes that were differentially expressed in both SMYD2-knockdown and pazopanib-resistant cells, indicating their potential role in SMYD2-mediated drug resistance. We analyzed TCGA-KIRC data and 150 patient samples to identify the relationship between SMYD2 and DDIT4 expression levels, as well as the prognostic significance of DDIT4. In vitro functional assays and murine models were applied to evaluate the effects of SMYD2 and DDIT4 on tumor growth and on pazopanib resistance. CUT&Tag and chromosome conformation capture (4 C) assays were applied to identify enhancers associated with SMYD2-mediated regulation of DDIT4, while the JASPAR database was utilized to predict transcription factors involved in the enhancer regulation. CRISPR-mediated enhancer deletion and ChIP-qPCR were subsequently performed to validate the regulatory roles of the identified enhancer and the transcription factor SPI1 in DDIT4 expression. RESULTS: Our study revealed that the expression level of DDIT4 is positively correlated with SMYD2. DDIT4 is highly expressed in renal cell carcinoma and is associated with poorer survival outcomes. Further research revealed that SMYD2 regulates H3K4me1 in a DDIT4 distal enhancer (chr10:72830412-72830891), promoting the recruitment of the transcription factor SPI1, thereby activating DDIT4 expression. We found that DDIT4 promotes the proliferation, metastasis, and pazopanib resistance of ccRCC, and DDIT4 knockdown enhances drug sensitivity in both in vitro and in vivo experiments. Furthermore, the SMYD2-DDIT4 axis activates the downstream STAT3 signaling pathway, thereby promoting tumor progression. In addition, DDIT4-related prognostic features showed potential associations with patient survival and predicted drug sensitivity in computational analyses. CONCLUSIONS: Our study identifies a previously unrecognized SMYD2-enhancer-DDIT4 regulatory axis, which promotes tumor progression and pazopanib resistance in ccRCC. These findings may provide potential therapeutic implications to overcome pazopanib resistance and improve treatment outcomes in ccRCC by targeting the SMYD2-enhancer-DDIT4 axis.

Carcinoma, Renal Cell↗
PubMed1998

Regulation of a hair follicle keratin intermediate filament gene promoter.

During hair growth, cortical cells emerging from the proliferative follicle bulb rapidly undergo a differentiation program and synthesise large amounts of hair keratin proteins. To identify some of the controls that specify expression of hair genes we have defined the minimal promoter of the wool keratin intermediate filament gene K2.10. The region of this gene spanning nucleotides -350 to +53 was sufficient to direct expression of the lacZ gene to the follicle cortex of transgenic mice but deletion of nucleotides -350 to -150 led to a complete loss of promoter activity. When a four base substitution mutation was introduced into the minimal functional promoter at the binding site for lymphoid enhancer factor 1 (LEF-1), promoter activity in transgenic mice was decreased but specificity was not affected. To investigate the interaction of trans-acting factors within the minimal K2.10 promoter we performed DNase I footprinting analyses and electrophoretic mobility shift assays. In addition to LEF-1, Sp1, AP2-like and NF1-like proteins bound to the promoter. The Sp1 and AP2-like proteins bound sequences flanking the LEF-1 binding site whereas the NF1-like proteins bound closer to the transcription start site. We conclude that the LEF-1 binding site is an enhancer element of the K2.10 promoter in the hair follicle cortex and that factors other than LEF-1 regulate promoter tissue- and differentiation-specificity.

Animals↗
PubMedDate not supplied

Analysis of heterologous and homologous promoters and enhancers in vitro and in vivo by gene transfer into Japanese medaka (Oryzias latipes) Xiphophorus.

Efficient expression systems are required for analysis of gene regulation and function in teleost fish. To develop such systems, a number of inducible or constitutive promoter and enhancer sequences of fish or higher vertebrate origin were tested for activity in a variety of fish cell lines and in embryos of the Japanese medaka fish (Oryzias latipes) and Xiphophorus. The activity of the different promoter-enhancer combinations were quantitated. Considerable differences were found for some constructs if tested in vitro or in vivo. Fro the data obtained, a set of expression vectors for basic research as well as for aquaculture purposes were established.

Animals↗
PubMed1990

Mutation of the core or adjacent LVb elements of the Moloney murine leukemia virus enhancer alters disease specificity.

Transcriptional enhancers of replication-competent mouse C-type retroviruses are potent determinants of the distinct disease-inducing phenotypes of different viral isolates and can also strongly influence the incidence and latent period of disease induction. To study the contribution of individual protein-binding sites to viral pathogenicity, we introduced mutations into each of the known nuclear factor-binding sites in the enhancer region of the Moloney murine leukemia virus and injected viruses with these mutations into newborn NFS mice. All viruses induced disease. Viruses with mutations in both copies of the leukemia virus factor a (LVa) site, leukemia virus factor c (LVc) site, or in just the promoter proximal copy of the glucocorticoid response element (GRE) had a latent period of disease onset and disease specificity indistinguishable from that of the wild-type Moloney virus. Viruses with mutations in two or three of the GREs, in both copies of the leukemia virus factor b (LVb) site, in two of the four nuclear factor 1 (NF1) consensus motifs, or in both copies of the conserved viral core element showed a significant delay in latent period of disease induction. Strikingly, viruses with mutations in the core element induced primarily erythroleukemias, and mutations in the LVb site also resulted in a significant incidence of erythroleukemias. These and other genetic and biochemical studies suggest models for how subtle alterations in the highly conserved structure of mouse C-type retrovirus enhancers can produce a dramatic effect on disease specificity.

Animals↗
PubMed2000

Activation of transcription factors in zebrafish cell cultures by environmental pollutants.

Many classes of environmental pollutants are found at significant levels in the aquatic environment. We are designing a fish model as an inexpensive and efficient system for the assessment of aquatic pollution. Three classes of environmental pollutants-halogenated and nonhalogenated aromatic hydrocarbons, heavy metals, and potent electrophiles-are known to upregulate particular mammalian genes via the activation of specific DNA motifs called aromatic hydrocarbon (AHREs), heavy metal (MREs), and electrophile (EPREs) response elements, respectively. We have made plasmid constructs, using these mammalian or trout response elements to drive the luciferase reporter gene. Here we show that transient transfection of the zebrafish ZEM2S cell line with these reporter constructs imparts dose-dependent gene induction upon exposure to a variety of chemicals within each of these three classes of inducers: [a] (AHRE-mediated) 2,3,7,8-tetrachlorodibenzo-p-dioxin, 3-methylcholanthrene, 3,4,5,3',4',5'-hexabromobiphenyl, Aroclor 1254, and benzo[a]pyrene; [b] (MRE-mediated) Cd(2+), Zn(2+), Hg(2+), and Al(3+); and [c] (EPRE-mediated) tert-butylhydroquinone, Hg(2+), Pb(2+), As(3+), Cu(2+), and Cd(2+). As expected, some agents gave a response to only one of the three classes, whereas others gave a mixed (AHRE- plus EPRE-mediated or MRE- plus EPRE-mediated) response. In response to several environmental agents, we found that differences in the electrophoretic mobility shift assay, using the AHRE or MRE as probe, were consistent with the degree of transcriptional activation seen with the reporter constructs. Our data suggest that these reporter constructs might be valuable for the generation of transgenic zebrafish in order to carry out mechanistic and developmental studies of transcriptional activation by environmental contaminants; moreover, such transgenic zebrafish lines might be useful as a sentinel for assessing aquatic pollution.

Animals↗
PubMed2004

The hybrid cytomegalovirus enhancer/chicken beta-actin promoter along with woodchuck hepatitis virus posttranscriptional regulatory element enhances the protective efficacy of DNA vaccines.

DNA vaccines represent a novel and powerful alternative to conventional vaccine approaches. They are extremely stable and can be produced en masse at low cost; more importantly, DNA vaccines against emerging pathogens or bioterrorism threats can be quickly constructed based solely upon the pathogen's genetic code. The main drawback of DNA vaccines is that they often induce lower immune responses than traditional vaccines, particularly in nonrodent species. Thus, improving the efficacy of DNA vaccines is a critical issue in vaccine development. In this study we have enhanced the efficacy of DNA vaccines by adopting strategies that increase gene expression. We generated influenza-hemagglutinin (HA)-encoding DNA vaccines that contain the hybrid CMV enhancer/chicken beta-actin (CAG) promoter and/or the mRNA-stabilizing post-transcriptional regulatory element from the woodchuck hepatitis virus (WPRE). Mice were immunized with these DNA vaccines, and the influenza-HA-specific cellular and humoral immune responses were compared with a conventional, HA-encoding DNA vaccine whose gene expression was driven by the CMV immediate-early promoter (pCMV-HA). CAG promoter-driven DNA vaccines elicited significantly higher humoral and cellular immune responses compared with the pCMV-HA vaccine. DNA vaccines consisting of both CAG and WPRE elements (pCAG-HA-WPRE) induced the highest level of protective immunity, such that immunization with 10-fold lower DNA doses prevented death in 100% of the mice upon lethal viral challenge, whereas all mice immunized with the conventional pCMV-HA vaccine succumbed to influenza infection.

Actins↗
PubMed2006

An autoregulatory loop directs the tissue-specific expression of p63 through a long-range evolutionarily conserved enhancer.

p63, a p53 family member, is essential for the development of various stratified epithelia and is one of the earliest markers of many ectodermal structures, including the epidermis, oral mucosa, apical ectodermal ridge, and mammary gland. Genetic regulatory mechanisms controlling p63 spatial expression during development have not yet been defined. Using a genomic approach, we identified an evolutionarily conserved cis-regulatory element, located 160 kb downstream of the first p63 exon, which functions as a keratinocyte-specific enhancer and is sufficient to recapitulate expression of the endogenous gene during mouse embryogenesis. Dissection of the p63 enhancer activity revealed a positive autoregulatory loop in which the p63 proteins directly bind to and are essential regulators of the enhancer. Accordingly, transactivating p63 isoforms induce endogenous p63 expression in cells that do not normally express this gene, whereas dominant negative isoforms suppress p63 expression in keratinocytes. In addition the transcription factor AP-2 also binds to the enhancer and cooperates with p63 to induce its activity. These results demonstrate that a long-range autoregulatory loop is involved in the regulation of p63 expression during embryonic development and in adult cells.

Amino Acid Sequence↗
PubMed2003

A novel boundary element may facilitate independent gene regulation in the Antennapedia complex of Drosophila.

The intrinsic enhancer-promoter specificity and chromatin boundary/insulator function are two general mechanisms that govern enhancer trafficking in complex genetic loci. They have been shown to contribute to gene regulation in the homeotic gene complexes from fly to mouse. The regulatory region of the Scr gene in the Drosophila Antennapedia complex is interrupted by the neighboring ftz transcription unit, yet both genes are specifically activated by their respective enhancers from such juxtaposed positions. We identified a novel insulator, SF1, in the Scr-ftz intergenic region that restricts promoter selection by the ftz-distal enhancer in transgenic embryos. The enhancer-blocking activity of the full-length SF1, observed in both embryo and adult, is orientation- and enhancer-independent. The core region of the insulator, which contains a cluster of GAGA sites essential for its activity, is highly conserved among other Drosophila species. SF1 may be a member of a conserved family of chromatin boundaries/insulators in the HOM/Hox complexes and may facilitate the independent regulation of the neighboring Scr and ftz genes, by insulating the evolutionarily mobile ftz transcription unit.

Animals↗
PubMed2006

Genetics of pigment cells: lessons from the tyrosinase gene family.

In mammals, the melanin pigment is produced in two cell types of distinct developmental origins. The melanocytes of the skin originate form the neural crest whereas the retinal pigment epithelium (RPE) of the eye originates from the optic cup. The genetic programs governing these two cell types are thus quite different but have evolved to allow the expression of pigment cell-specific genes such as the three members of the tyrosinase-related family. Tyrosinase, Tyrp1 and Dct promoters contain a motif termed E-box which is bound by the transcription factor Mitf. These E-boxes are also found in the promoters of the corresponding fish genes, thus highlighting the pivotal role of Mitf in pigment cell-specific gene regulation. Mitf, which displays cell type-specific isoforms, transactivates the promoters of the tyrosinase gene family in both pigment cell lineages. However, specific DNA motifs have been found in these promoters, and they correspond to binding sites for RPE-specific factors such as Otx2 or for melanocyte-specific factors such as Sox10 or Pax3. The regulation of pigment cell-specific expression is also controlled by genetic elements located outside of the promoter, such as the tyrosinase distal regulatory element located at -15 kb which acts as a melanocyte-specific enhancer but also protects from spreading of condensed chromatin. Thus, by using the tyrosinase gene family as a model, it is possible to define the transcription factor networks that govern pigment production in either melanocytes or RPE.

Animals↗
PubMed1999

Cubitus interruptus is necessary but not sufficient for direct activation of a wing-specific decapentaplegic enhancer.

In Drosophila, the imaginal discs are the primordia for adult appendages. Their proper formation is dependent upon the activation of the decapentaplegic (dpp) gene in a stripe of cells just anterior to the compartment boundary. In imaginal discs, the dpp gene has been shown to be activated by Hedgehog signal transduction. However, an initial analysis of its enhancer region suggests that its regulation is complex and depends upon additional factors. In order to understand how multiple factors regulate dpp expression, we chose to focus on a single dpp enhancer element, the dpp heldout enhancer, from the 3' cis regulatory disc region of the dpp locus. In this report, we present a molecular analysis of this 358 bp wing- and haltere-specific dpp enhancer, which demonstrates a direct transcriptional requirement for the Cubitus interruptus (Ci) protein. The results suggest that, in addition to regulation by Ci, expression of the dpp heldout enhancer is spatially determined by Drosophila TCF (dTCF) and the Vestigial/Scalloped selector system and that temporal control is provided by dpp autoregulation. Consistent with the unexpectedly complex regulation of the dpp heldout enhancer, analysis of a Ci consensus site reporter construct suggests that Ci, a mediator of Hedgehog transcriptional activation, can only transactivate in concert with other factors.

Animals↗
PubMed2004

Dissection of cis-regulatory elements in the C. elegans Hox gene egl-5 promoter.

Hox genes are highly conserved segmental identity genes well known for their complex expression patterns and divergent targets. Here we present an analysis of cis-regulatory elements in the Caenorhabditis elegans Hox gene egl-5, which is expressed in multiple tissues in the posterior region of the nematode. We have utilized phylogenetic footprinting to efficiently identify cis-regulatory elements and have characterized these with gfp reporters and tissue-specific rescue experiments. We have found that the complex expression pattern of egl-5 is the cumulative result of the activities of multiple tissue or local region-specific activator sequences that are conserved both in sequence and near-perfect order in the related nematode Caenorhabditis briggsae. Two conserved regulatory blocks analyzed in detail contain multiple sites for both positively and negatively acting factors. One of these regions may promote activation of egl-5 in certain cells via the Wnt pathway. Positively acting regions are repressed in inappropriate tissues by additional negative pathways acting at other sites within the promoter. Our analysis has allowed us to implicate several new regulatory factors significant to the control of egl-5 expression.

Animals↗
PubMed1992

The Drosophila sloppy paired locus encodes two proteins involved in segmentation that show homology to mammalian transcription factors.

The sloppy paired locus is involved in the establishment of the metameric body plan of the Drosophila embryo. We have cloned the sloppy paired locus by P-element-mediated enhancer detection. The locus is composed of two genes, slp1 and slp2, that are structurally and functionally related. They belong to a novel class of putative transcription factors containing a fork head domain that has also been found in mammalian hepatocyte transcription factors. The spatial expression patterns of the two transcripts are very similar, suggesting common regulation of the two genes. We recovered additional sloppy paired alleles by remobilization of an enhancer detector transposon. Genetic analysis suggests that both genes contribute to the segmentation phenotype that has characteristics of both, pair-rule and segment polarity genes, and that they interact functionally. The two genes appear to share an enhancer element situated upstream of slp1 that acts on both the proximal slp1 promoter and the distal slp2 promoter.

Amino Acid Sequence↗
PubMed1991

Mechanism of site-specific DNA inversion in bacteria.

A wealth of new information regarding the structure of the synaptic complex, the mechanism of DNA strand exchange, and the role of the recombinational enhancer in promoting DNA inversion has been obtained from a combination of approaches. These include: electron microscopy of reaction intermediates, topological analysis of recombination products, and X-ray crystallography coupled with genetic analysis.

Bacteria↗