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PubMed2002

Ku is important for telomere maintenance, but not for differential expression of telomeric VSG genes, in African trypanosomes.

Trypanosome antigenic variation, involving differential expression of variant surface glycoprotein (VSG) genes, has a strong association with telomeres and with DNA recombination. All expressed VSGs are telomeric, and differential activation involves recombination into the telomeric environment or silencing/activation of subtelomeric promoters. A number of pathogen contingency gene systems associated with immune evasion involve telomeric loci, which has prompted speculation that chromosome ends provide conditions conducive for the operation of rapid gene switching mechanisms. Ku is a protein associated with eukaryotic telomeres that is directly involved in DNA recombination and in gene silencing. We have tested the hypothesis that Ku in trypanosomes is centrally involved in differential VSG expression. We show, via the generation of null mutants, that trypanosome Ku is closely involved in telomere length maintenance, more so for a transcriptionally active than an inactive telomere, but exhibits no detectable influence on DNA double strand break repair. The absence of Ku and the consequent great shortening of telomeres had no detectable influence either on the rate of VSG switching or on the silencing of the telomeric promoters of the VSG subset that is expressed in the tsetse fly.

Amino Acid Sequence↗
PubMed2002

Rhodospirillum centenum utilizes separate motor and switch components to control lateral and polar flagellum rotation.

Rhodospirillum centenum is a purple photosynthetic bacterium that is capable of differentiating from vibrioid swimming cells that contain a single polar flagellum into rod-shaped swarming cells that have a polar flagellum plus numerous lateral flagella. Microscopic studies have demonstrated that the polar flagellum is constitutively present and that the lateral flagella are found only when the cells are grown on solidified or viscous medium. In this study, we demonstrated that R. centenum contains two sets of motor and switch genes, one set for the lateral flagella and the other for the polar flagellum. Electron microscopic analysis indicated that polar and lateral flagellum-specific FliG, FliM, and FliN switch proteins are necessary for assembly of the respective flagella. In contrast, separate polar and lateral MotA and MotB motor subunits are shown to be required for motility but are not needed for the synthesis of polar and lateral flagella. Phylogenetic analysis indicates that the polar and lateral FliG, FliM, and FliN switch proteins are closely related and most likely arose as a gene duplication event. However, phylogenetic analysis of the MotA and MotB motor subunits suggests that the polar flagellum may have obtained a set of motor genes through a lateral transfer event.

Amino Acid Sequence↗
PubMed2004

Mechanisms of antigen receptor evolution.

The adaptive immune system, which utilizes RAG-mediated recombination to diversify immune receptors, arose in ancestors of the jawed vertebrates approximately 500 million years ago. Homologs of immunoglobulins (Igs), T cell antigen receptors (TCRs), major histocompatibility complex (MHC) I and II, and the recombination activating genes (RAGs) have been identified in all extant classes of jawed vertebrates; however, no definitive ortholog of any of these genes has been identified in jawless vertebrates or invertebrates. Although the identity of the "primoridal" receptor that likely was interrupted by the recombination mechanism in the common ancestor of jawed vertebrates may never be established, many different families of genes that exhibit predicted characteristics of such a receptor have been described both within and outside the jawed vertebrates. Various model systems point toward a range of immune receptor diversity, encompassing many different families of recognition molecules, including non-diversified and diversified Ig-type variable (V) regions, as well as diversified VJ domains, whose functions are integrated in an organism's response to pathogenic invasion. The transition from the primordial antigen receptor to the monomeric Ig-/TCR-like domain and subsequent antigen-specific heterodimer likely involved progressive refinement of unique intermolecular associations in parallel with the acquisition of combinatorial diversity and antigen-specific recognition through somatic modification of the V region. RAG-mediated recombination and associated junctional diversification of both Ig and TCR genes occurs in all jawed vertebrates. In the case of Igs, somatic variation is expanded further through class switching, gene conversion, and somatic hypermutation. Various approaches, including both genomic and protein functional analyses, currently are being applied in jawless vertebrates, protochordates and other invertebrate deuterostome model systems in order to examine both RAG-mediated and alternative forms of antigen receptor diversification. Such studies have uncovered previously unknown mechanisms of generating receptor diversity.

Animals↗
PubMed1994

The chicken beta/epsilon-globin enhancer directs autonomously regulated, high-level expression of the chicken epsilon-globin gene in transgenic mice.

In transiently transfected chicken erythroid cells, beta-like globin gene switching is mediated through differential activation of the cis-linked embryonic epsilon- and adult beta-globin genes by a shared enhancer. Two underlying mechanisms have been proposed: (i) tissue- and stage-specific factors activate the beta-globin promoter in adult erythroid cells (autonomous regulation); and (ii) the epsilon-globin promoter, although transcriptionally competent in both embryonic and adult cells, is suppressed at the adult stage through competition with the beta-globin promoter for interaction with the enhancer (competitive regulation). Analyses of transgenic mice carrying the chicken beta/epsilon-globin locus demonstrated that both genes depended on the enhancer for erythroid expression, but only the epsilon-globin gene exhibited developmentally appropriate transcription at levels comparable to the endogenous mouse globin genes. Surprisingly, the chicken epsilon-globin gene also appeared to be autonomously regulated, as has been observed for human embryonic and fetal beta-like globin genes in transgenic mice. These results suggest that the chicken beta/epsilon-globin enhancer possesses either embryonic stage or epsilon-globin gene specificity when incorporated into the murine germ line.

Animals↗
PubMed2004

The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms.

The adaptive immune system arose in ancestors of the jawed vertebrates approximately 500 million years ago. Homologs of immunoglobulins (Igs), T-cell antigen receptors (TCRs), major histocompatibility complex I (MHC I) and MHC II, and the recombination-activating genes (RAGs) have been identified in all extant classes of jawed vertebrates; however, no definitive homolog of any of these genes has been identified in jawless vertebrates or invertebrates. RAG-mediated recombination and associated junctional diversification of both Ig and TCR genes occurs in all jawed vertebrates. In the case of Igs, somatic variation is expanded further through class switching, gene conversion, and somatic hypermutation. Although the identity of the 'primordial' receptor that was interrupted by the recombination mechanism in jawed vertebrates may never be established, many different families of genes that exhibit predicted characteristics of such a receptor have been described both within and outside the jawed vertebrates. Recent data from various model systems point toward a continuum of immune receptor diversity, encompassing many different families of recognition molecules whose functions are integrated in an organism's response to pathogenic invasion. Various approaches, including both genomic and protein-functional analyses, currently are being applied in jawless vertebrates, protochordates, and other invertebrate deuterostome systems and may yield definitive evidence regarding the presence or absence of adaptive immune homologs in species lacking adaptive immune systems. Such studies have the potential for uncovering previously unknown mechanisms of generating receptor diversity.

Animals↗
PubMed1981

Human immunoglobulin heavy chain genes: evolutionary comparisons of C mu, C delta and C gamma genes and associated switch sequences.

Human immunoglobulin heavy chain constant region genes have been characterised in isolated clones. The human c mu gene comprises discrete domains for C mu 1, C mu 2, C mu 3 and C mu 4 + tp separated by short intervening sequences. The C delta gene has been located about 5 kb downstream of C mu 4. Furthermore, the coding segments for the membrane form of mu have been located 1.9 kb downstream of C mu 4. Tandemly repeated sequences implicated in the heavy chain class switch occur upstream of the C mu and the C gamma genes, but none were detected near the C delta gene. These tandem repeats are very homologous to those of mouse. Particularly common is the sequence G-A-G-C-T. These data suggest that the mu to gamma switch in humans involves DNA rearrangements of the CH-genes and subsequent deletion of DNA, but that the coexpression of C mu and C delta genes results from different mechanisms.

Amino Acid Sequence↗
PubMed1995

Enhancer sharing in a plasmid model containing the alpha-fetoprotein and albumin promoters.

It has been proposed that the alpha-fetoprotein (AFP) enhancers also regulate the adjacent albumin gene, since the -10 kbp albumin enhancer is inactive in a number of cell lines that express albumin. In transfection experiments, the AFP enhancers strongly stimulate the albumin promoter in cells that silence the AFP promoter. These observations led us to develop a plasmid model of AFP-albumin gene switching, in which the albumin and AFP promoters would compete for the three AFP enhancers. However, when AFPCAT + ALBgal genes were combined with the AFP enhancers in one plasmid, both genes were driven at full activity. There was no change in the relative promoter expression over a wide range of transfected DNA concentrations, demonstrating that relative promoter activity was independent of DNA concentration and of promoter concentration, and that neither promoter was limiting the expression of the other. In contrast, a control plasmid containing two albumin promoters showed mutual inhibition, indicating the expected promoter competition. The albumin and AFP promoters noncompetitively shared the three enhancers on this plasmid, resulting in high levels of transcription from both promoters.

Albumins↗
PubMed2006

Myogenic basic helix-loop-helix proteins regulate the expression of peroxisomal proliferator activated receptor-gamma coactivator-1alpha.

Peroxisomal proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha), a transcriptional coactivator, is selectively expressed in slow-twitch fibers in skeletal muscle. Ectopic expression of the PGC-1alpha gene in either a cell or an animal has been shown to promote fast to slow fiber-type switch. The expression of PGC-1alpha in muscle is regulated by myocyte enhancer factor 2 and Forkhead in rhabdomyosarcoma, two transcription factors implicated in terminal muscle differentiation. In this study we found that PGC-1alpha expression was activated during terminal muscle differentiation in both C2C12 and Sol8 myoblasts. Using retrovirus-mediated MyoD overexpression in C3H10T1/2 cells, we also demonstrated that MyoD, the master regulator of terminal differentiation, could activate PGC-1alpha expression in vivo. Our transient transfection results also show that myogenic basic helix-loop-helix (bHLH) proteins, especially MyoD, can activate PGC-1alpha expression by targeting its promoter. Myogenic bHLH protein target sites on PGC-1alpha promoter were localized to a short region (-49 to approximately +2) adjacent to the transcription start site, which contains two putative E boxes. Mutation of either site significantly reduced MyoD-mediated transactivation in the cells, suggesting that both sites are required for myogenic bHLH protein-mediated activation. However, only one site, the E2 box, was directly bound by glutathione-S-transferase-MyoD protein in EMSAs. Our results indicate that myogenic bHLH proteins not only are involved in lineage determination and terminal differentiation, but also are directly implicated in activation of the key fiber-type and metabolic switch gene, PGC-1alpha.

Animals↗
PubMed2004

Dominant-positive and dominant-negative heat shock factors.

Heat and other acute or chronic stresses provoke multiple cellular reactions, including activation of the heat shock or stress protein response. To date, no compounds have become available that specifically activate, or block activation of, the stress protein response. At the transcriptional level the response is mediated by heat shock factors, ubiquitously expressed transcription factors that are normally inactive but are activated in a cell experiencing a stress. Mutant heat shock factors that activate the stress protein response in the absence of a stress or that prevent stress activation of the response have proven useful for studying biological questions associated with a normal or abnormal stress protein response and have been incorporated in the design of gene switches with desirable new properties.

Animals↗
PubMed2000

Chemically regulated zinc finger transcription factors.

Ligand-dependent transcriptional regulators were generated by fusion of designed Cys(2)-His(2) zinc finger proteins and steroid hormone receptor ligand binding domains. To produce novel DNA binding domains, three-finger proteins binding specific 9-base pair sequences were constructed from modular building blocks. Fusion of these zinc finger proteins to a transcriptional activation domain and to modified ligand binding domains derived from either the estrogen or progesterone receptors yielded potent ligand-dependent transcriptional regulators. Together with optimized minimal promoters, these regulators provide 4-hydroxytamoxifen- or RU486-inducible expression systems with induction ratios of up to 3 orders of magnitude. These inducible expression systems are functionally independent, and each can be selectively switched on within the same cell. The potential use of zinc finger-steroid receptor fusion proteins for the regulation of natural promoters was also explored. A gene-specific six-finger protein binding an 18-base pair target sequence was converted into a ligand-dependent regulator by fusion with either two estrogen receptor ligand binding domains or one ecdysone receptor and one retinoid X receptor ligand binding domain. These single-chain receptor proteins undergo an intramolecular rearrangement, rather than intermolecular dimerization and are functional as monomers. Thus, the ability to engineer DNA binding specificities of zinc finger proteins enables the construction of ligand-dependent transcriptional regulators with potential for the regulation of virtually any desired artificial or natural promoter. It is anticipated that the novel chemically regulated gene switches described herein will find many applications in applied and basic research, where the specific modulation of gene expression can be exploited.

Amino Acid Sequence↗
PubMed2000

The Drosophila melanogaster sex determination gene sisA is required in yolk nuclei for midgut formation.

During sex determination, the sisterlessA (sisA) gene functions as one of four X:A numerator elements that set the alternative male or female regulatory states of the switch gene Sex-lethal. In somatic cells, sisA functions specifically in sex determination, but its expression pattern also hints at a role in the yolk cell, a syncytial structure believed to provide energy and nutrients to the developing embryo. Previous studies of sisA have been limited by the lack of a null allele, leaving open the possibility that sisA has additional functions. Here we report the isolation and molecular characterization of four new sisA alleles including two null mutations. Our findings highlight key aspects of sisA structure-function and reveal important qualitative differences between the effects of sisA and the other strong X:A numerator element, sisterlessB, on Sex-lethal expression. We use genetic, expression, clonal, and phenotypic analyses to demonstrate that sisA has an essential function in the yolk nuclei of both sexes. In the absence of sisA, endoderm migration and midgut formation are blocked, suggesting that the yolk cell may have a direct role in larval gut development. To our knowledge, this is the first report of a requirement for the yolk nuclei in Drosophila development.

Alleles↗
PubMed2006

Polyphyly and gene flow between non-sibling Heliconius species.

BACKGROUND: The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae), whose distributions overlap in Central and Northwestern South America. RESULTS: In these taxa, we sequenced 30-45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII), and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi), mannose-6-phosphate isomerase (Mpi) and cubitus interruptus (Ci) genes. A fifth gene, dopa decarboxylase (Ddc) produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. CONCLUSION: Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

Animals↗
PubMed1983

In vivo demethylation of chicken embryonic beta-type globin genes with 5-azacytidine.

We have studied the in vivo effects of the methyl-blocking cytotoxic pyrimidine analog 5-azacytidine upon DNA methylation and expression of the normally inactive embryonic beta-type globin genes in adult chickens. We find that 5 daily treatments with intravenous 5-azacytidine is capable of converting the normally completely methylated embryonic rho gene to a greater than 75% demethylated state as assayed by the restriction endonucleases HpaII, MspI, and HhaI. However, this change in methylation is not accompanied by activation of the embryonic rho gene at the level of globin protein or globin RNA. Although our analysis does not exclude a few copies of embryonic globin RNA per cell, this result is still in contrast with the results seen with the fetal gamma-globin genes in baboons and humans [17; see also other chapters in this volume]. Hence demethylation by 5-azacytidine treatment alone is not sufficient to activate the chicken embryonic beta-globin genes. We propose that these seemingly disparate results can be reconciled by a model in which certain genes in specific cell types (eg, human and baboon gamma-globin in adult erythroid cells, chicken ev-1 in MSB cells, mouse metallothionein-1 in lymphoblastoid cells) are in a poised state such that removal of specific methyl cytosines results in a high level of transcription. In contrast other genes (including chicken rho and epsilon embryonic globin genes in adult erythroid cells) are in a suppressed state that overrides activation by demethylation. Alternatively, 5-azacytidine could activate certain genes by a mechanism totally independent of DNA methylation. For instance, selection of specific early erythroid cell types could account for the results seen in baboon fetal globin gene activation. The availability of various eukaryotic DNA transformation systems, characterization of eukaryotic DNA methylases, and development of large-scale cultures of erythropoietic precursor cells should facilitate detailed examination of these various states of gene activation and allow the elucidation of the precise role of DNA methylation in the regulation of globin gene switching.

Animals↗
PubMed2005

The T-box transcription factor SEA-1 is an autosomal element of the X:A signal that determines C. elegans sex.

Sex is determined in C. elegans by a chromosome-counting mechanism that tallies X chromosome dose relative to the sets of autosomes, the X:A ratio. A group of genes on X called X signal elements (XSEs) communicates X chromosome number by repressing the activity of the master sex-determination switch gene xol-1 in a dose-dependent manner. xol-1 is repressed by transcriptional and posttranscriptional mechanisms and is inactive in XX animals (hermaphrodite) but active in XO animals (male). Prior to our work, the nature of the autosomal signal and its target(s) were unknown. Here we show the signal includes discrete, trans-acting autosomal signal elements (ASEs) that counter XSEs to coordinately control both sex determination and dosage compensation. sea-1, the first autosomal signal element, encodes a T-box transcription factor that opposes XSEs by activating transcription of xol-1. Hence, xol-1 integrates both X and autosomal signals to determine sexual fate.

Amino Acid Sequence↗
PubMed1998

Inducible control of gene expression: prospects for gene therapy.

A number of drug-related gene expression systems are available for controlling target gene transcription through the use of small-molecule inducing compounds. While the utility of such systems has been demonstrated in vitro and in transgenic mice, recent improvements are likely to make these systems more amenable for use in a therapeutic context, such as gene therapy. These improvements include further optimization of the antiprogestin-regulated gene switch, rendering it more sensitive to RU486, and the synthesis of nonimmunosuppressive rapamycin analogs for use in dimerization-based strategies of gene regulation.

Animals↗
PubMed1999

Erythroid Kruppel like factor: from fishing expedition to gourmet meal.

Erythroid Kruppel like factor (EKLF) is the founding member of a family of transcription factors which are defined by the presence of three C-terminal C2H2-type zinc fingers. Since its discovery 6 years ago, the study of EKLF has been intense. In this review I will revisit the discovery of EKLF, and highlight recent advances in our understanding of how it interacts with other proteins to regulate erythroid gene transcription. The current knowledge of the biological role/s of EKLF in erythroid cell differentiation and globin gene switching are summarized.

Amino Acid Sequence↗
PubMed1998

Coinduction of embryonic and adult-type globin mRNAs by sodium butyrate and trichostatin A in two murine interleukin-3-dependent bone marrow-derived cell lines.

Using an RNase protection assay, globin mRNA species expressed in clones derived from Ba/F3 and B6SUtA cells transfected with the erythropoietin receptor (EpoR) and selected with erythropoietin (Epo) were compared with globin mRNA species induced in corresponding parental cells by sodium butyrate (SB) and trichostatin A (TSA). betaMajor/betaminor- and -1/-2-globin mRNAs were the major species, with trace amounts of epsilon-globin mRNA, formed in Epo-stimulated EpoR+ Ba/F3 clones, whereas SB and TSA allowed expression of all species of globin mRNAs, ie, epsilon, betah1, betamajor/betaminor, zeta, and -1/-2, in parental Ba/F3 cells. In contrast, epsilon- and -1/-2-globin mRNAs were the major species present in Epo-stimulated EpoR+ B6SUtA clones, whereas SB and TSA activated epsilon-, betah1-, betaS/betaT-, and -1/-2-globin genes in parental B6SUtA cells; zeta-globin mRNA was not detected in SB- and TSA-treated B6SUtA cells. Because TSA is a specific inhibitor of histone deacetylase, the mimicry of action exhibited by SB and TSA suggests that the effects of SB are mediated through its ability to inhibit histone deacetylase and that histone deacetylase is an integral part of the repression of globin genes in these interleukin-3-dependent cells. Efficient coinduction of embryonic and adult types of globin mRNA in bone marrow cell lines derived from adult mice indicates that adult hematopoietic precursors possess an embryonic nature. These cell lines are useful models to study the mechanism(s) of developmental globin gene switching.

Animals↗
PubMed2005

Bisphosphonate modulates cementoblast behavior in vitro.

BACKGROUND: Cementum formation is deemed to be instrumental for the successful regeneration of periodontal tissues, and thus events and modifiers of cementum formation and mineralization need to be determined. This study aimed to determine whether the bisphosphonate 1-hydroxyethylidene-1,1-bisphosphonate (HEBP) altered the behavior of immortalized cementoblasts (osteocalcin-cementoblasts [OCCM]). METHODS: OCCM from transgenic mice were exposed to HEBP at concentrations ranging from 0.01 to 10.0 microM. The assays performed included the count of cell number for proliferation, Northern blot analysis for gene expression (up to 10 days for core binding factor alpha-1 [Cbfa1], bone sialoprotein [BSP], osteocalcin [OCN], and osteopontin [OPN], markers for cementoblast/osteoblast maturation/mineralization), von Kossa stain and alizarin red S stain for mineralization, and enzyme assay (p-nitrophenol phosphate cleavage) for alkaline phosphatase (ALP) activity. RESULTS: Mineral nodule formation was inhibited at the higher doses of HEBP (1.0 and 10.0 microM) only. At early stages (1, 3, and 6 days), gene expression assays revealed only subtle changes in treated cells versus untreated cells, but by day 10, groups treated with lower doses (0.01 and 0.1 microM) were markedly different at the gene expression level. OCN was significantly downregulated (70%) at the lowest dose, with less pronounced effects at higher doses. In concurrence, the master switch gene for osteoblasts, Cbfa1, was also downregulated at the lower doses. Inversely, OPN mRNA was enhanced at the lower doses. ALP activity was not altered by HEBP. CONCLUSION: Bisphosphonate alters cementoblast function in vitro through the regulation of gene expression and mineral formation.

Alkaline Phosphatase↗