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PubMed1999

Mechanisms of developmental control of transcription in the murine alpha- and beta-globin loci.

We have characterized mRNA expression and transcription of the mouse alpha- and beta-globin loci during development. S1 nuclease and primary transcript in situ hybridization analyses demonstrate that all seven murine globin genes (zeta, alpha1, alpha2, epsilony, betaH1, betamaj, and betamin) are transcribed during primitive erythropoiesis, however transcription of the zeta, epsilony, and betaH1 genes is restricted to the primitive erythroid lineage. Transcription of the betamaj and betamin genes in primitive cells is EKLF-dependent demonstrating EKLF activity in embryonic red cells. Novel kinetic analyses suggest that multigene expression in the beta locus occurs via alternating single-gene transcription whereas coinitiation cannot be ruled out in the alpha locus. Transcriptional activation of the individual murine beta genes in primitive cells correlates inversely with their distance from the locus control region, in contrast with the human beta locus in which the adult genes are only activated in definitive erythroid cells. The results suggest that the multigene expression mechanism of alternating transcription is evolutionarily conserved between mouse and human beta globin loci but that the timing of activation of the adult genes is altered, indicating important fundamental differences in globin gene switching.

Animals↗
PubMed2004

Plasticity of gene expression in injured human dorsal root ganglia revealed by GeneChip oligonucleotide microarrays.

Root avulsion from the spinal cord occurs in brachial plexus lesions. It is the practice to repair such injuries by transferring an intact neighbouring nerve to the distal stump of the damaged nerve; avulsed dorsal root ganglia (DRG) are removed to enable nerve transfer. Such avulsed adult human cervical DRG ( [Formula: see text] ) obtained at surgery were compared to controls, for the first time, using GeneChip oligonucleotide arrays. We report 91 genes whose expression levels are clearly altered by the injury. This first study provides a global assessment of the molecular events or "gene switches" as a consequence of DRG injuries, as the tissues represent a wide range of surgical delay, from 1 to 100 days. A number of these genes are novel with respect to sensory ganglia, while others are known to be involved in neurotransmission, trophism, cytokine functions, signal transduction, myelination, transcription regulation, and apoptosis. Cluster analysis showed that genes involved in the same functional groups are largely positioned close to each other. This study represents an important step in identifying new genes and molecular mechanisms in human DRG, with potential therapeutic relevance for nerve repair and relief of chronic neuropathic pain.

Adult↗
PubMed1993

Regulated splicing of the Drosophila sex-lethal male exon involves a blockage mechanism.

In Drosophila melanogaster, sex determination in somatic cells is controlled by a cascade of genes whose expression is regulated by alternative splicing [B. S. Baker, Nature (London) 340:521-524, 1989; J. Hodgkin, Cell 56:905-906, 1989]. The master switch gene in this hierarchy is Sex-lethal. Sex-lethal is turned on only in females, and an autoregulatory feedback loop which controls alternative splicing maintains this state (L. R. Bell, J. I. Horabin, P. Schedl, and T. W. Cline, Cell 65:229-239, 1991; L. N. Keyes, T. W. Cline, and P. Schedl, Cell 68:933-943, 1992). Sex-lethal also promotes female differentiation by controlling the splicing of RNA from the next gene in the hierarchy, transformer. Sosnowski et al. (B. A. Sosnowski, J. M. Belote, and M. McKeown, Cell 58:449-459, 1989) have shown that the mechanism for generating female transformer transcripts is not through the activation of the alternative splice site but by the blockage of the default splice site. We have tested whether an activation or a blockage mechanism is involved in Sex-lethal autoregulation. The male exon of Sex-lethal with flanking splice sites was placed into the introns of heterologous genes. Our results support the blockage mechanism. The poly(U) run at the male exon 3' splice site is required for sex-specific splicing. However, unlike transformer, default splicing to the male exon is sensitive to the sequence context within which the exon resides. This and the observation that the splice signals at the exon are suboptimal are discussed with regard to alternate splicing.

Alternative Splicing↗
PubMedDate not supplied

Optimal temperature control policy for a two-stage recombinant fermentation process.

The optimal temperature control policy to be followed in the operation of a two-stage fermentation system in which gene expression is induced by a temperature-sensitive gene switching system was studied. A genetically structured model was used to describe product formation, and kinetic equations based on experimental data were used to quantify the specific gene expression rate and parameters that affect plasmid instability. A constant temperature control policy and temperature profiling control policy including temperature cycling were studied and compared. Maximum average production rate was obtained from a temperature control policy in which the second stage was operated initially at about 40.5 degrees C and the temperature decreased slightly to a constant value at 40.0 degrees C. The maximum average production rate, which corresponds to the optimal temperature control policy, for an operation of 180 h was 29.7 units of protein (mg of cells)-1 h-1.

DNA, Recombinant↗
PubMed2003

XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators.

In Caenorhabditis elegans, an X chromosome-counting mechanism specifies sexual fate. Specific genes termed X-signal elements, which are present on the X chromosome, act in a concerted dose-dependent fashion to regulate levels of the developmental switch gene xol-1. In turn, xol-1 levels determine sexual fate and the activation state of the dosage compensation mechanism. The crystal structure of the XOL-1 protein at 1.55 A resolution unexpectedly reveals that xol-1 encodes a GHMP kinase family member, despite sequence identity of 10% or less. Because GHMP kinases, thus far, have only been characterized as small molecule kinases involved in metabolic pathways, for example, amino acid and cholesterol synthesis, XOL-1 is the first member that controls nonmetabolic processes. Biochemical investigations demonstrated that XOL-1 does not bind ATP under standard conditions, suggesting that XOL-1 acts by a mechanism distinct from that of other GHMP kinases. In addition, we have cloned a XOL-1 ortholog from Caenorhabditis briggsae, a related nematode that diverged from C. elegans approximately 50-100 million years ago. These findings demonstrate an unanticipated role for GHMP kinase family members as mediators of sexual differentiation and dosage compensation and, possibly, other aspects of differentiation and development.

Adenosine Triphosphatases↗
PubMed2006

Internal promoter characterization and expression of the Deinococcus radiodurans pprI-folP gene cluster.

PprI is a general gene switch responsible for the extraordinary radioresistance of Deinococcus radiodurans. From NCBI DNA sequence analysis, it was predicted that the translation start codon of the downstream folP (DR0168) gene overlaps the pprI (DR0167) stop codon, suggesting that these genes may form an operon. In this study, we show that a mutant containing an inserted sequence in folP does not grow unless folate is added to the medium, but is not affected in extreme radioresistance, whereas a pprI disruptant strain could grow in the absence of folate. It was found that expression of a pprI-lacZ fusion is constitutive and unaltered following ionizing radiation as is the production of the PprI protein. PprI protein is not expressed if its promoter is deleted and the transcription from the entire pprI promoter is essential for radioresistance of D. radiodurans. However, the deletion of pprI promoter has no effect on the expression of the folP-lacZ fusion. Primer extension analysis of the folP promoter region shows that folP is transcribed from its own promoter located within the pprI structural gene. All these results do support neither the existence of a pprI-folP operon nor a regulatory role of FolP in pprI expression.

Bacterial Proteins↗
PubMed1984

Cardiac myosin heavy chain isozymic transitions during development and under pathological conditions are regulated at the level of mRNA availability.

We have shown that the level of two ventricular MHC mRNAs, fetal and adult, can account for the observed isozymic transitions of the myosin protein during normal development and under pathological conditions. Moreover, these MHC mRNAs are encoded by two genes that are linked in the genome, less than 5 kilobases apart and are organized according to their developmental expression. The fact that the two ventricular MHC genes are very closely related at the nucleotide sequence level, and yet respond in opposite direction to the same stimulus, makes these genes an excellent model in which to study the possible mechanisms involved in the gene switching.

Animals↗
PubMed1985

Continued expression of neonatal myosin heavy chain in adult dystrophic skeletal muscle.

The expression of myosin heavy chain isoforms was examined in normal and dystrophic chicken muscle with a monoclonal antibody specific for neonatal myosin. Adult dystrophic muscle continued to contain neonatal myosin long after it disappeared from adult normal muscle. A new technique involving western blotting and peptide mapping demonstrated that the immunoreactive myosin in adult dystrophic muscle was identical to that found in neonatal normal muscle. Immunocytochemistry revealed that all fibers in the dystrophic muscle failed to repress neonatal myosin heavy chain. These studies suggest that muscular dystrophy inhibits the myosin gene switching that normally occurs during muscle maturation.

Age Factors↗
PubMed2006

Genome-wide approaches for identification of nuclear receptor target genes.

Large-scale genomics analyses have grown by leaps and bounds with the rapid advances in high throughput DNA sequencing and synthesis techniques. Nuclear receptor signaling is ideally suited to genomics studies because receptors function as ligand-regulated gene switches. This review will survey the strengths and limitations of three major classes of high throughput techniques widely used in the nuclear receptor field to characterize ligand-dependent gene regulation: expression profiling studies (microarrays, SAGE and related techniques), chromatin immunoprecipitation followed by microarray (ChIP-on-chip), and genome-wide in silico hormone response element screens. We will discuss each technique, and how each has contributed to our understanding of nuclear receptor signaling.

Journal Article↗
PubMed2003

Stochastic gene expression as a many-body problem.

Gene expression has a stochastic component because of the single-molecule nature of the gene and the small number of copies of individual DNA-binding proteins in the cell. We show how the statistics of such systems can be mapped onto quantum many-body problems. The dynamics of a single gene switch resembles the spin-boson model of a two-site polaron or an electron transfer reaction. Networks of switches can be approximately described as quantum spin systems by using an appropriate variational principle. In this way, the concept of frustration for magnetic systems can be taken over into gene networks. The landscape of stable attractors depends on the degree and style of frustration, much as for neural networks. We show the number of attractors, which may represent cell types, is much smaller for appropriately designed weakly frustrated stochastic networks than for randomly connected networks.

Algorithms↗
PubMed2000

Chromatin remodeling gene SMARCA5 is dysregulated in primitive hematopoietic cells of acute leukemia.

We identified a subset of genes involved in chromatin remodeling whose mRNA expression changes in differentiating mouse erythroleukemia (MEL) cells. We furthermore tested their mRNA expression patterns in normal and malignant CD34+ bone marrow cells. SMARCA5, imitation switch gene homologue, was rapidly silenced during in vitro erythroid differentiation of MEL cells whereas it was up-regulated in CD34+ hematopoietic progenitors of acute myeloid leukemia (AML) patients. Moreover, SMARCA5 mRNA levels decreased in AML CD34+ progenitors after the patients achieved complete hematologic remission. We detected high levels of SMARCA5 mRNA in murine bone marrow and spleen and monitored its expression in these hematopoietic tissues during accelerated hematopoiesis following hemolytic anemia induced by phenylhydrazine. SMARCA5 expression levels decreased after the onset of accelerated erythropoiesis. Our data suggest that both in vitro and in vivo induction of differentiation is followed by down-regulation of SMARCA5 expression. In CD34+ AML progenitors over-expression of SMARCA5 may thus dysregulate the genetic program required for normal differentiation.

Acute Disease↗
PubMed1998

Erythroid-specific transcription.

Over the past year, the range of research related to erythroid cell-specific transcription has expanded beyond isolation of its transcriptional players to studies that address more complex yet still fundamental questions: first, whether these factors form part of a larger protein-protein structure; second, how factor interactions with DNA affect the surrounding chromatin configuration; third, how this affects the mechanism of gene switching within the beta-like globin cluster; and finally, how these regulators are themselves transcriptionally controlled.

Animals↗
PubMed2000

Mosaic analysis of GL2 gene expression and cell layer autonomy during the specification of Arabidopsis leaf trichomes.

Homozygous glabra2 (gl2) mutant Arabidopsis thaliana Landsberg erecta plants with only a few rudimentary single spiked trichomes on the leaf margin were transformed with a genomic clone of GL2, resulting in partial restoration of the normal leaf trichome phenotype. The introduced GL2 transgene was configured as part of an FLP recombinase-responsive gene switch, which permitted visibly marked gl2 mutant clonal sectors to be generated by FLP recombinase-mediated deletion of the GL2 transgene with concomitant activation of a previously silent beta-glucuronidase (GUS) marker gene. GUS marked sectors extending through all three leaf cell layers (L1, L2, and L3) displayed the anticipated gl2 mutant phenotype, whereas immediately adjacent unmarked tissue, and unmarked tissues overlaying GUS sectors restricted to the L2 and/or L3 cell layers, retained the GL2 restored phenotype. These data support the view that the GL2 gene product acts in a region-autonomous manner within a single cell layer and indicate that GL2 gene expression in the L1 layer is sufficient for GL2-directed outgrowth of trichomes.

Arabidopsis↗
PubMed2004

Development of transgenic mice that inducibly express an active form of c-Src in the epidermis.

Recent work from our laboratory has shown that elevated src kinase activity enhances tumor promotion, malignant progression, and metastasis during multistage skin carcinogenesis. In this study, we have generated "gene-switch" src(530) transgenic mice to further analyze the role of this nonreceptor tyrosine kinase in multistage carcinogenesis. Target transgenic mice that have an activated form of the human c-src (src(530)) gene fused with GAL4 binding sites upstream of the thymidine kinase (TK) promoter were generated. Two lines of epidermis-specific transactivator mice were used that targeted the expression of GLVPc or GLp65 transactivators, fusion molecules containing a truncated progesterone receptor with a GAl4-DNA binding domain, with either a mouse loricrin (ML) or human keratin 14 (HK14) promoter, respectively. The transactivator mice (ML.GLVPc or HK14.GLp65) and the target mice (TK.src(530)) were mated to generate bitransgenic mice, and src(530) transgene expression was induced by topical application of RU486 (mifepristone, a progesterone receptor antagonist). In both ML.GLVPc/TK.src(530) and HK14.GLp65/TK.src(530) bitransgenic mice, histological analysis revealed that only the bitransgenic mice had marked epidermal hyperplasia and hyperkeratosis after treatment with RU486. Neither the nontransgenic mice nor the mice hemizygous for either the transactivator transgene or the target transgene alone showed any response to treatment with RU486. In addition, no differences were observed in the skin of the bitransgenic mice versus nontransgenic littermates without treatment of RU486. Interestingly, in HK14.GLp65/TK.src(530) bitransgenic mice, squamous cell carcinomas (SCCs) arose along the periphery of the area of the punch biopsies in 25% of the bitransgenic mice several weeks after taking the biopsy and subsequent to RU486 treatment. Collectively, the data support a role of c-src activation in epidermal hyperproliferation. Furthermore, the data support the conclusion that src activation can substitute for an initiating event in the presence of a tumor promoting stimulus (i.e., wounding). Finally, inducible src(530) transgenic mice provide a new tool for dissecting the role of src activation in multistage carcinogenesis by allowing temporal control of the expression of this oncogene.

Animals↗
PubMed2003

Cluster characterisation and temporal expression of porcine sarcomeric myosin heavy chain genes.

Members of the myosin heavy chain (MyHC) gene family are subjected to temporal regulation of gene switching during development. One strategy to the identification of cis-acting regulatory elements that are involved in temporal or fibre-type specific regulation is to undertake a comparative analysis of the MyHC gene family between the pig, an important target species, and other mammals, like human whose entire genome has been recently sequenced. Towards this end, we report here on the isolation, and characterisation of the porcine cardiac (MyHC slow/beta and alpha) and skeletal MyHC (embryonic, 2a, 2x, 2b and perinatal) gene clusters, and their structural comparisons with mouse and human clusters. The genome organisation of both clusters in the pig, human and mouse is conserved as having the same gene order, similar intergenic distances, and in the same head-to-tail orientation. For a period of pre-natal muscle growth, relative expression of MyHC isoforms, as determined by TaqMan real-time RT-PCR, correlated with the gene order in the skeletal MyHC cluster (embryonic > 2a > 2x > 2b) suggesting the possible presence of DNA elements on the same side as the MyHC embryonic gene that direct temporal regulation.

Alternative Splicing↗
PubMed2004

Targeted activation of c-Jun N-terminal kinase in vivo induces restrictive cardiomyopathy and conduction defects.

The stress-activated protein kinase, c-Jun N-terminal kinase (JNK), has been implicated in the process of cardiac hypertrophy and apoptosis, yet the specific roles of JNK in heart failure are unclear. To determine the effects of JNK activation in intact heart, we established transgenic animals using a Cre/loxP-mediated gene switch approach to achieve targeted expression of an upstream activator, mitogen-activated protein kinase kinase 7 (D) (MKK7D), in ventricular myocytes. MKK7D expression led to significant JNK activation, robust induction of the fetal gene program, and contractile dysfunction. The animals died approximately 7 weeks after birth with signs of congestive heart failure. Doppler mode echocardiography revealed a marked stiffening of JNK-activated hearts that was associated with the remodeling of specific extracellular matrix components. Gene expression analysis of MKK7D hearts revealed up-regulation of transforming growth factor beta signaling, offering a potential molecular mechanism underlying changes in extracellular matrix composition. In addition, we demonstrated that JNK activation led to specific loss of connexin 43 protein and gap junctions without affecting the expression or localization of other key intercalated disc proteins. This specific and localized gap junction remodeling resulted in significant slowing of ventricular electrical conduction in JNK-activated hearts. These results represent the first characterization of JNK-mediated cardiac pathology in vivo and support an important role for JNK signaling in specific aspects of cardiac remodeling in the pathogenesis of cardiac disease.

Animals↗
PubMed2005

Development of ecdysone-regulated lentiviral vectors.

We have engineered a lentivirus-based gene transfer system to achieve ecdysone-regulated transgene expression. The method combines the wide tropism of lentiviral vectors and the possibility of gene regulation by a small molecule with an excellent pharmacological profile. Using the hematopoietic tissue as a model, we transduced mouse progenitors with an ecdysone-regulated GFP expression cassette. The ecdysone gene switch efficiently turned GFP on and off in transplanted animals, showing low basal activity. This system allows the delivery of inducible transcriptional units in vitro and ex vivo and may be a useful tool for gene transfer purposes. Moreover, our work provides hints on the design of lentiviral vectors containing multiple expression cassettes with multiple promoters.

Animals↗
PubMed1996

The attenuated phenotype of a Salmonella typhimurium flgM mutant is related to expression of FliC flagellin.

The flgM gene of Salmonella typhimurium encodes a negative regulator of flagellin synthesis that acts by inhibiting the flagellum-specific sigma factor FliA (sigma 28), but only when a mutation in a flagellar basal body, hook, or switch gene is present. We previously showed that FlgM is also necessary for the virulence of S. typhimurium in the mouse model of typhoid fever and proposed that FlgM is required to modulate the activity of the FliA sigma factor, which, in turn, regulates a gene involved in virulence. In this investigation, we observed that (i) the in vitro generation times of flgM mutant and wild-type strains of S. typhimurium were indistinguishable, as were the amounts of flagellin produced by the strains; (ii) the 50% lethal doses of fliA mutant and wild-type strains of S. typhimurium were similar in orally infected mice; and (iii) inactivation of the FliA-regulated flagellin gene fliC in an flgM S. typhimurium mutant resulted in a virulent phenotype. Therefore, we now conclude that expression of the FliC flagellin subunit in an flgM strain is responsible for the attenuated phenotype of an flgM mutant and that FliA does not appear to positively regulate virulence genes in S. typhimurium. Our results suggest that the normal regulation of flagellum synthesis appears to be necessary for virulence and that there may be an advantage conferred in vivo by expression of a particular flagellar phenotype of S. typhimurium.

Animals↗