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At least 235 records · Page 13Linked to original sources
PubMed1989

Sequence organization in regulatory regions of DNA of minute virus of mice.

Analysis of the nucleotide sequence of minute virus of mice (MVM) DNA indicates that the DNA termini contain clusters of potential DNA regulatory elements and that there are repetitive DNA elements highly reiterated throughout the entire genome, which may also have a role in DNA function. The left end of MVM DNA, which contains the promoter for the nonstructural genes, has a cluster of DNA elements that includes homologies to the polyoma virus enhancer, three copies of an E1A-inducible transcription factor (ATF) binding site, and a potential Z-DNA element. The MVM right end, which contains the origin of DNA replication, has a cluster of DNA elements that includes several homologies to the polyoma virus replication origin and a potential Z-DNA element. In addition, oligonucleotide frequency analysis indicates the presence of highly recurring sequence elements throughout the entire MVM genome that may be involved in regulation. This computer-aided analysis suggests similarities and significant differences in regulatory sequence organization between MVM and polyoma virus, and identifies specific DNA elements for future genetic characterization.

Activating Transcription Factors↗
PubMed1995

A portable regulatory element directs specific expression of the Caenorhabditis elegans ubiquitin gene ubq-2 in the somatic gonad.

The Caenorhabditis elegans ubq-2 gene encodes a fusion of ubiquitin and a 52-amino-acid ribosomal protein. This single copy gene is both cis- and trans-spliced. It is expressed in all life stages of the worm and its transcript abundance is unaffected by heat stress. Transgenic analysis shows that expression of ubq-2 is regulated by an upstream promoter and a downstream element. The downstream element is required for ubq-2 promoter activity in embryos and in cells of the somatic gonad, including the distal tip cells, sheath cells, spermathecal cells, and cells of the uterus. The gonad-specific activity of the downstream regulator is transferable to a stress gene promoter such that heat-inducible expression of the transgene occurs in the somatic gonad. Stress-inducible beta-galactosidase expression in the gonad does not occur in all life stages, but is initiated late in the second or early in the third larval stage, when differentiation of gonadal tissues begins. Expression of a beta-galactosidase fusion protein from constructs containing the downstream ubq-2 regulator causes abnormalities of the gonad and embryonic lethality. Gonad abnormalities include arrested development and general disorganization. These abnormalities may be related to the overexpression of ubiquitin in the gonad.

Amino Acid Sequence↗
PubMed2002

Wnt and Bmp signalling cooperatively regulate graded Emx2 expression in the dorsal telencephalon.

Pattern formation of the dorsal telencephalon is governed by a regionalisation process that leads to the formation of distinct domains, including the future hippocampus and neocortex. Recent studies have implicated signalling proteins of the Wnt and Bmp gene families as well as several transcription factors, including Gli3 and the Emx homeobox genes, in the molecular control of this process. The regulatory relationships between these genes, however, remain largely unknown. We have used transgenic analysis to investigate the upstream mechanisms for regulation of Emx2 in the dorsal telencephalon. We have identified an enhancer from the mouse Emx2 gene that drives specific expression of a lacZ reporter gene in the dorsal telencephalon. This element contains binding sites for Tcf and Smad proteins, transcriptional mediators of the Wnt and Bmp signalling pathway, respectively. Mutations of these binding sites abolish telencephalic enhancer activity, while ectopic expression of these signalling pathways leads to ectopic activation of the enhancer. These results establish Emx2 as a direct transcriptional target of Wnt and Bmp signalling and provide insights into a genetic hierarchy involving Gli3, Emx2 and Bmp and Wnt genes in the control of dorsal telencephalic development.

Animals↗
PubMed1997

Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila.

The mechanisms allowing remote enhancers to regulate promoters several kilobase pairs away are unknown but are blocked by the Drosophila suppressor of Hairy-wing protein (Suhw) that binds to gypsy retrovirus insertions between enhancers and promoters. Suhw bound to a gypsy insertion in the cut gene also appears to act interchromosomally to antagonize enhancer-promoter interactions on the homologous chromosome when activity of the Chip gene is reduced. This implicates Chip in enhancer-promoter communication. We cloned Chip and find that it encodes a homolog of the recently discovered mouse Nli/Ldb1/Clim-2 and Xenopus Xldb1 proteins that bind nuclear LIM domain proteins. Chip protein interacts with the LIM domains in the Apterous homeodomain protein, and Chip interacts genetically with apterous, showing that these interactions are important for Apterous function in vivo. Importantly, Chip also appears to have broad functions beyond interactions with LIM domain proteins. Chip is present in all nuclei examined and at numerous sites along the salivary gland polytene chromosomes. Embryos without Chip activity lack segments and show abnormal gap and pair-rule gene expression, although no LIM domain proteins are known to regulate segmentation. We conclude that Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development. We suggest that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions.

Amino Acid Sequence↗
PubMed1995

Enhancer-trap targeting at the Broad-Complex locus of Drosophila melanogaster.

Here, we describe the exact replacement of a defective unmarked P element by an enhancer-trap transposon marked by the miniwhite gene and carrying lacZ as a reporter gene. The original defective P element was located in an intron of the Broad-Complex (BRC), a key gene involved in metamorphosis. Replacement events resulted from conversions induced by the P-element transposase from a donor enhancer-trap element located on another chromosome. Six independent conversion events were selected. In all converted chromosomes, the enhancer-trap transposon was in the same orientation as the original P element. From the pattern of X-gal staining observed, lacZ expression likely reflects the regulatory influence of BRC enhancers on the convertant transposon. Reversion to wild type was achieved by excision of the enhancer-trap transposon. The six convertants were analyzed in detail at the nucleotide level. The occurrence of a polymorphism at position 33 of the P-element sequences led us to propose a conversion mechanism involving homologous P sequences for repair. This is in contrast to previously analyzed P-element transposase-induced conversion events and proposed models relying on sequence identity between genomic Drosophila sequences. The lack of any homology requirement other than between P element sequences means that our findings can be easily generalized. Targeting a marked P-element derivative at a precise site without loss or addition of genetic information makes it possible to exploit the hundreds of defective P elements scattered throughout the Drosophila genome by replacing them with engineered P elements, already available.

Animals↗
PubMed1998

Muscle and nerve-specific regulation of a novel NK-2 class homeodomain factor in Caenorhabditis elegans.

We have identified a new Caenorhabditis elegans NK-2 class homeobox gene, designated ceh-24. Distinct cis-acting elements generate a complex neuronal and mesodermal expression pattern. A promoter-proximal enhancer mediates expression in a single pharyngeal muscle, the donut-shaped m8 cell at the posterior end of the pharynx. A second mesodermal enhancer is active in a set of eight nonstriated vulval muscles used in egg laying. Activation in the egg laying muscles requires an 'NdE-box' consensus motif (CATATG) which is related to, but distinct from, the standard E-box motif bound by the MyoD family of transcriptional activators. Ectodermal expression of ceh-24 is limited to a subset of sublateral motor neurons in the head of the animal; this activity requires a cis-acting activator element that is distinct from the control elements for pharyngeal and vulval muscle expression. Activation of ceh-24 in each of the three cell types coincides with the onset of differentiation. Using a set of transposon-induced null mutations, we show that ceh-24 is not essential for the formation of any of these cells. Although ceh-24 mutants have no evident defects under laboratory conditions, the pattern of ceh-24 activity is apparently important for Rhabditid nematodes: the related species C. briggsae contains a close homologue of C. elegans ceh-24 including a highly conserved and functionally equivalent set of cis-acting control signals.

Amino Acid Sequence↗
PubMed2025

A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types.

The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell-type taxonomies from mouse and human to define marker genes and putative enhancers and create a large toolkit of transgenic lines and enhancer adeno-associated viruses (AAVs) for selective targeting of cortical cell populations. We report creation and evaluation of fifteen transgenic driver lines, two reporter lines, and >1,000 different enhancer AAV vectors covering most subclasses of cortical cells. The tools reported here have been made publicly available, and along with the scaled process of tool creation, evaluation, and modification, they will enable diverse experimental strategies toward understanding mammalian cortex and brain function.

Animals↗
PubMed2002

Enhancer-dependent transcription in Salmonella enterica Typhimurium: new members of the sigmaN regulon inferred from protein sequence homology and predicted promoter sites.

DNA-looping mediated by regulatory proteins is a ubiquitous mode of transcriptional control that allows interactions between genetic elements separated over long distances in DNA. In prokaryotes, one of the best-studied examples of regulatory proteins that use DNA-looping is the NtrC family of enhancer-binding proteins (EBPs), which activate transcription from sigmaN (sigma-N, sigma-54) dependent promoters. The completely sequenced genome of food-borne pathogen Salmonella enterica serovar Typhimurium LT2 contains seven novel EBPs of unknown function. Four of these EBPs have a similar domain organisation to NtrC whilst surprisingly the remaining three resemble LevR in Bacillus subtilis. Probable transcriptional targets are identified for each of the EBPs, including novel homologues of phosphotransferase system Enzyme II (EII) and several virulence-associated functions. Comparisons are made with the related enteric bacteria Salmonella Typhi, Escherichia coli and Yersinia pestis.

Bacterial Proteins↗
PubMed2006

Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos.

Genes involved in vertebrate development are unusually enriched for highly conserved non-coding sequence elements. These regions are readily detected in silico, by genome-wide sequence comparisons between different vertebrates, from mammals to fish (phylogenetic footprinting). It follows that sequence conservation must be the result of positive selection for an essential physiological role. An obvious possibility is that these conserved sequences possess regulatory or structural functions important for gene expression and, thus, an in vivo assay becomes necessary. We have developed a rapid testing system using zebrafish and Xenopus laevis embryos that allows us to assign transcriptional regulatory functions to conserved non-coding sequence elements. The sequences are cloned into a vector containing a minimal promoter and the GFP reporter, and are assayed for their putative cis-regulatory activity in zebrafish or Xenopus transgenic experiments. Vectors used include plasmid DNA and the Tol2 transposon system in fish and X. laevis. We have followed this logic to detect and analyze conserved elements in an intergenic region present in the Iroquois (Irx) gene clusters of zebrafish, Xenopus tropicalis, Fugu rubripes and mouse. We have assayed approximately 50 of these conserved elements and shown that the majority behave as modular positive regulatory elements (enhancers) that contribute to specific temporal and spatial domains that are part of the endogenous gene expression pattern. Moreover, comparison of the activity of cognate Irx enhancers from different organisms demonstrates that conservation of sequence is accompanied by in vivo functional conservation across species. Finally, for some of the most conserved elements, we have been able to identify a critical core sequence, essential for correct enhancer function.

Animals↗
PubMed2002

A cell type-specific allele of the POU gene Oct-6 reveals Schwann cell autonomous function in nerve development and regeneration.

While an important role for the POU domain transcription factor Oct-6 in the developing peripheral nerve has been well established, studies into its exact role in nerve development and regeneration have been hampered by the high mortality rate of newborn Oct-6 mutant animals. In this study we have generated a Schwann cell-specific Oct-6 allele through deletion of the Schwann cell-specific enhancer element (SCE) in the Oct-6 locus. Analysis of mice homozygous for this allele (deltaSCE allele) reveals that rate-limiting levels of Oct-6 in Schwann cells are dependent on the SCE and that this element does not contribute to Oct-6 regulation in other cell types. We demonstrate a Schwann cell autonomous function for Oct-6 during nerve development as well as in regenerating nerve. Additionally, we show that Krox-20, an important regulatory target of Oct-6 in Schwann cells, is activated, with delayed kinetics, through an Oct-6-independent mechanism in these mice.

Alleles↗
PubMed1999

Identification of regulatory regions driving the expression of the Drosophila spalt complex at different developmental stages.

The zinc finger transcription factors Spalt and Spalt-related have been implicated in multiple developmental processes. In the wing they are regulated by the secreted protein Decapentaplegic and participate in the positioning of the wing veins. The function of Spalt has been also analyzed during tracheal development and embryonic segmentation. Here, we present the isolation and characterization of novel spalt/spalt-related alleles, which analysis indicates that these genes cannot substitute for each other in the developmental processes studied. The mutants present embryonic or pupal lethality, with phenotypes consistent with the loss of spalt function. We also present a detailed functional analysis of the DNA regions implicated in the regulation of these genes. This regulation is complex, integrating the information from both negative and positive regulators, and it is modular, with discrete fragments of DNA directing expression to discrete regions in embryonic and larval tissues.

Alleles↗
PubMed2001

Transcriptional and posttranscriptional regulation of the gene for Dally, a Drosophila integral membrane proteoglycan.

"division abnormally delayed"(dally), a Drosophila member of the glypican family, has been implicated in Dpp and Wg signaling. Here, we report the genomic structure and regulation of the dally gene. The dally gene is composed of nine exons, and its expression is controlled by a TATA-less promoter. Analysis of transgenic flies bearing the dally promoter fused to the lacZ reporter gene showed that a 371 bp sequence of the dally 5' flanking region was capable of mimicking the patterns of dally enhancer trap expression in developing tissues, including embryonic epidermis and imaginal discs. The tissue-specific enhancers that drive marker gene expression in embryo and the wing disc are mapped in the 5' upstream region of dally gene. We propose that dally gene expression is also regulated posttranscriptionally by controlling the translation efficiency and stability of its mRNA.

Amino Acid Sequence↗
PubMed2026

Rb-driven transcription limits its tumour-suppressive effects in breast cancer.

The retinoblastoma protein (Rb) is a tumour suppressor best known for repressing E2F transcription factors and halting cell cycle progression1. In hormone receptor-positive (HR+) breast cancer, CDK4/6 inhibitors activate Rb by preventing its phosphorylation, forming a key component of current endocrine therapy regimens2. How pharmacologically activated Rb remodels chromatin and influences transcription beyond cell cycle arrest remains poorly understood. Here we show that CDK4/6 inhibition induces redistribution of hypophosphorylated Rb to promoters and enhancers. Although Rb predictably binds to cell cycle gene promoters to repress transcription, at other sites, it unexpectedly promotes expression of oestrogen-responsive genes by integrating into oestrogen receptor (ER)-rich transcriptional hubs. CDK4/6 inhibition enhances ER target gene expression in breast cancer cells, patient-derived xenografts and clinical HR+ breast cancer samples in an Rb-dependent manner. This reprogramming is mediated in part by KDM5A, whose interaction with Rb contributes to gene regulation at these loci. Critically, components of this Rb-driven ER transcriptional program are pro-proliferative. In endocrine-sensitive tumours, this effect can be neutralized with anti-oestrogen therapy, explaining therapeutic synergy. In endocrine-resistant settings such as ESR1-mutant breast cancer, the program persists, limiting the therapeutic efficacy of CDK4/6 inhibition. These findings reframe Rb as a dual-function transcriptional regulator that, although enforcing cell cycle arrest, can also activate programs that counteract its tumour suppressor function.

Humans↗
PubMed2000

Tissue-specific expression of a type I adenylyl cyclase rescues the rutabaga mutant memory defect: in search of the engram.

Most attempts to localize physical correlates of memory in the central nervous system (CNS) rely on ablation techniques. This approach has the limitation of defining just one of an unknown number of structures necessary for memory formation. We have used the Drosophila rutabaga type I Ca(2+)/CaM-dependent adenylyl cyclase (AC) gene to determine in which CNS region AC expression is sufficient for memory formation. Using pan-neural and restricted CNS expression with the GAL4 binary transcription activation system, we have rescued the memory defect of the rutabaga mutant in a fast robust spatial learning paradigm. The ventral ganglion, antennal lobes, and median bundle are likely the CNS structures sufficient for rutabaga AC- dependent spatial learning.

Adenylyl Cyclases↗