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PubMed2005

Gene expression analysis of Tek/Tie2 signaling.

The elaboration of the vasculature during embryonic development involves restructuring of the early vessels into a more complex vascular network. Of particular importance to this vascular remodeling process is the requirement of the Tek/Tie2 receptor tyrosine kinase. Mouse gene-targeting studies have shown that the Tie2-deficient embryos succumb to embryonic death at midgestation due to insufficient sprouting and remodeling of the primary capillary plexus. To identify the underlying genetic mechanisms regulating the process of vascular remodeling, transcriptomes modulated by Tie2 signaling were analyzed utilizing serial analysis of gene expression (SAGE). Two libraries were constructed and sequenced using embryonic day 8.5 yolk sac tissues from Tie2 wild-type and the Tie2-null littermates. After tag extraction, 45,689 and 45,275 SAGE tags were obtained for the Tie2 wild-type and Tie2-null libraries, respectively, yielding a total of 21,376 distinct tags. Close to 62% of the tags were uniquely annotated, whereas 10% of the total tags were unknown. Using semiquantitative PCR, the differential expression of eight genes was confirmed that included Elk3, an important angiogenic switch gene which was upregulated in the absence of Tie2 signaling. The results of this study provide valuable insight into the potential association between Tie2 signaling and other known angiogenic pathways as well as genes that might have novel functions in vascular remodeling.

Animals↗
PubMed2006

Drosophila melanogaster male somatic cells feminized solely by TraF can collaborate with female germ cells to make functional eggs.

Female differentiation of Drosophila germ cells is induced by cell-nonautonomous signals generated in the gonadal soma that work with germ-cell-autonomous signals determined by germ-cell X chromosome dose. Generation of the nonautonomous feminizing signals was known to involve female-specific protein encoded by the master sex-determination gene Sex-lethal (Sxl) acting on its switch-gene target transformer (tra) to produce Tra(F) protein. However, it was not known whether Sxl's action on tra alone would suffice to trigger a fully feminizing nonautonomous signal. We developed a constitutively feminizing tra transgene that allowed us to answer this question. In gynanders (XX//XO mosaics) feminized by this Tra(F) transgene, functionally Sxl- haplo-X (chromosomally male) somatic cells collaborated successfully with diplo-X (chromosomally female) germ cells to make functional eggs. The fertility of such gynanders shows not only that Tra(F) is sufficient to elicit a fully feminizing nonautonomous signal, but also that haplo-X somatic cells can execute all other somatic functions required for oogenesis, despite the fact that their genome is not expected to be dosage compensated for such diplo-X-specific functions. The unexpected observation that some Tra(F)-feminized gynanders failed to lay their eggs showed there to be diplo-X cells outside the gonad for which Tra(F)-feminized haplo-X cells cannot substitute.

Animals↗
PubMed1998

Rules for the evolution of gene circuitry.

Cells possess the genes required for growth and function in a variety of contexts. In any given context there is a corresponding pattern of gene expression in which some genes are OFF and others ON. The ability of cells to switch genes ON and OFF in a coordinate fashion to produce the required patterns of expression is the fundamental basis for complex processes like normal development and pathogenesis. The molecular study of gene regulation has revealed a plethora of mechanisms and circuitry that have evolved to perform what appears to be the same switching function. To some this implies the absence of rules. However, simple rules capable of relating molecular design to the natural environment have begun to emerge through the analysis of elementary gene circuits. Two of these rules are reviewed in this paper. These simple rules have the ability to unify understanding across several different levels of biological organization--molecular, physiological, developmental, ecological.

Base Sequence↗
PubMed2002

Extragenic suppressors of a dominant masculinizing her-1 mutation in C. elegans identify two new genes that affect sex determination in different ways.

SUMMARY: The her-1 regulatory switch gene in C. elegans sex determination is normally active in XO animals, resulting in male development, and inactive in XX animals, allowing hermaphrodite development. The her-1(n695gf) mutation results in the incomplete transformation of XX animals into phenotypic males. We describe four extragenic mutations that suppress the masculinized phenotype of her-1(n695gf) XX. They define two previously undescribed genes, sup-26 and sup-27. All four mutations exhibit semidominance of suppression and by themselves have no visible effects on sex determination in otherwise genotypically wild-type XX or XO animals. Analysis of interactions with mutations in the major sex-determining genes show that sup-26 and sup-27 influence sex determination in fundamentally different ways. sup-26 appears to act independently of her-1 to negatively modulate synthesis or function of tra-2 in both XX and XO animals. sup-27 may play a role in X-chromosome dosage compensation and influence sex determination indirectly.

Animals↗
PubMed1992

Growth-regulated expression of rhoG, a new member of the ras homolog gene family.

Cellular transition from the resting state to DNA synthesis involves master switches genes encoding transcriptional factors (e.g., fos, jun, and egr genes), whose targets remain to be fully characterized. To isolate coding sequences specifically accumulated in late G1, a differential screening was performed on a cDNA library prepared from hamster lung fibroblasts stimulated for 5 h with serum. One of the positive clones which displayed a sevenfold induction, turned out to code for a protein sharing homology to Ras-like products. Cloning and sequence analysis of the human homolog revealed that this putative new small GTPase, referred to as rhoG, is more closely related to the rac, CDC42, and TC10 members of the rho (ras homolog) gene family and might have diverged very early during evolution. rhoG mRNA accumulates in proportion to the mitogenic strength of various purified growth factors used for the stimulation, as a consequence of transcriptional activation. G1-specific RNA accumulation is impaired upon addition of antimitogenic cyclic AMP and is enhanced when protein synthesis is inhibited, mainly as a result of RNA stabilization. rhoG mRNA expression is observed in a wide variety of human organs but reaches a particularly high level in lung and placental tissues.

Amino Acid Sequence↗
PubMed1990

Isotype switching of an immunoglobulin heavy chain transgene occurs by DNA recombination between different chromosomes.

Transgenic mice carrying an immunoglobulin mu heavy chain transgene exhibit isotype switching of the transgene. We have now characterized the mechanism of transgene switching in these mice. The site of mu transgene insertion in one transgenic line has been localized to chromosome 5 using a series of polymorphic endogenous retroviruses as genetic markers in backcross mice. The endogenous immunoglobulin heavy chain locus resides on mouse chromosome 12, which shows that transgene isotype switching can occur between two different chromosomes even though normal antibody gene switching has generally been thought to occur within one chromosome. We find that transgene isotype switching involves interchromosomal DNA recombination, and our data suggest that the same enzymatic mechanisms mediate both normal isotype switch recombination and interchromosomal transgene switching. Our findings also support the notion that the isotype switching mechanism can induce chromosomal translocations such as observed for the c-myc gene in some B cell tumors.

Animals↗
PubMed2001

Molecular identification of virilizer, a gene required for the expression of the sex-determining gene Sex-lethal in Drosophila melanogaster.

Sex-lethal (Sxl) is a central switch gene in somatic sexual development of Drosophila melanogaster. Female-specific expression of Sxl relies on autoregulatory splicing of Sxl pre-mRNA by SXL protein. This process requires the function of virilizer (vir). Besides its role in Sxl splicing, vir is essential for male and female viability and is also required for the production of eggs capable of embryonic development. We have identified vir molecularly and found that it produces a single transcript of 6 kb that is ubiquitously expressed in male and female embryos throughout development. This transcript encodes a nuclear protein of 210 kD that cannot be assigned to a known protein family. VIR contains a putative transmembrane domain, a coiled-coil region and PEST sequences. We have characterized five different alleles of vir. Those alleles that affect both sexes are associated with large truncations of the protein, while alleles that affect only the female-specific functions are missense mutations that lie relatively close to each other, possibly defining a region important for the regulation of Sxl.

Alleles↗
PubMed1999

Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.

We have taken a comprehensive approach to the generation of novel DNA binding zinc finger domains of defined specificity. Herein we describe the generation and characterization of a family of zinc finger domains developed for the recognition of each of the 16 possible 3-bp DNA binding sites having the sequence 5'-GNN-3'. Phage display libraries of zinc finger proteins were created and selected under conditions that favor enrichment of sequence-specific proteins. Zinc finger domains recognizing a number of sequences required refinement by site-directed mutagenesis that was guided by both phage selection data and structural information. In many cases, residues not expected to make base-specific contacts had effects on specificity. A number of these domains demonstrate exquisite specificity and discriminate between sequences that differ by a single base with >100-fold loss in affinity. We conclude that the three helical positions -1, 3, and 6 of a zinc finger domain are insufficient to allow for the fine specificity of the DNA binding domain to be predicted. These domains are functionally modular and may be recombined with one another to create polydactyl proteins capable of binding 18-bp sequences with subnanomolar affinity. The family of zinc finger domains described here is sufficient for the construction of 17 million novel proteins that bind the 5'-(GNN)6-3' family of DNA sequences. These materials and methods should allow for the rapid construction of novel gene switches and provide the basis for a universal system for gene control.

Animals↗
PubMed2005

Identification of sex-specific transcripts of the Anopheles gambiae doublesex gene.

The understanding of the molecular mechanisms of sex differentiation in the mosquito Anopheles gambiae could identify important candidate genes for inducing selective male sterility in transgenic lines or for sex-controlled expression of lethal genes. In many insects, doublesex (dsx) is the double-switch gene at the bottom of the somatic sex-determination cascade that determines the differentiation of sexually dimorphic traits. We report here on the identification of the dsx homologue in A. gambiae and on the characterization of its sex-specific transcripts. Agdsx consists of seven exons, distributed over an 85 kb region on chromosome 2R, which are sex-specifically spliced to produce the female and male AgdsxF and AgdsxM transcripts. AgdsxF contains a 795 bp ORF, coding for a protein of 265 amino acids, while AgdsxM comprises a much longer (1866 bp) ORF, coding for a 622 aa protein. Differences in the exon/intron organization suggest that Agdsx sex-specific splicing results from a different mechanism from Drosophila melanogaster dsx. These findings represent an important step towards the understanding of sex differentiation in Anopheles and will facilitate the use of gene transfer technologies to manipulate sex ratios for vector control programs based on the sterile insect technique.

Amino Acid Sequence↗
PubMed2001

Conditional transgenic technologies.

Transgenic technology has been revolutionised by the development of techniques that allow temporo-spatial control of gene deletion or expression in transgenic animals. The ability to switch gene expression 'on' or 'off' in restricted tissues at specific times allows unprecedented flexibility for exploring gene function in both health and disease. As use of these techniques grows in all areas of biomedical research, an understanding of this topic is essential. In this review we examine the theory, application and limitations of these strategies, with particular reference to endocrine research.

Animals↗
PubMed1975

Activation and inactivation of genes determining hemoglobin types.20s.

Globin gene switching in sheep and goats has been used as a model system for examining gene expression in differentiating red blood cells. Sheep and goats switch from the synthesis of hemoglobin A to hemoglobin C in response to erythropoietin. The regulatory mechanism producing this switch in hemoglobin types could occur at the cellular, nuclear, or cytoplasmic level. Evidence is presented which suggests that regulation is occurring, in fact, at the nuclear level. Sheep and goat erythroid colonies have been grown in plasma clot culture in order to study the synthesis of individual globin chains. Erythropoietin is required for colony formation. The switch from hemoglobin A to hemoglobin C synthesis requires not only colony formation but also a higher concentration of erythropoietin than is required just for the production of colonies. A cell-free transcriptional system using bone marrow chromatin and mammalian DNA-dependent RNA polymerase has been developed in order to examine the nuclear control mechanisms in more detail.

Amino Acid Sequence↗
PubMed1993

Role of gene order in developmental control of human gamma- and beta-globin gene expression.

To determine the effect of gene order on globin gene developmental regulation, we produced transgenic mice containing two tandemly arranged gamma- or beta-globin or gamma beta- and beta gamma-globin genes linked to a 2.5-kb cassette containing sequences of the locus control region (LCR). Analysis of constructs containing two identical gamma or beta genes assessed the effect of gene order on globin gene expression, while analysis of constructs containing tandemly arranged gamma and beta genes assessed any additional effects of the trans-acting environment. When two gamma genes were tandemly linked to the LCR, expression from the proximal gamma gene was three- to fourfold higher than expression from the distal gamma gene, and the ratio of proximal to distal gene expression remained unchanged throughout development. Similarly, when two beta genes were tandemly linked to the LCR, the proximal beta gene was predominantly expressed throughout development. These results indicate that proximity to LCR increases gene expression, perhaps by influencing the frequency of interaction between the LCR and globin gene promoters. An arrangement where the gamma gene was proximal and the beta gene distal to the LCR resulted in predominant gamma-gene expression in the embryo. When the order was reversed and the gamma gene was placed distally to the LCR, gamma-gene expression in the embryo was still up to threefold higher than expression of the LCR-proximal beta gene. These findings suggest that the embryonic trans-acting environment interacts preferentially with the gamma genes irrespective of their order or proximity to the LCR. We conclude that promoter competition rather than gene order plays the major role in globin gene switching.

Animals↗
PubMed2000

Human gamma-globin gene promoter element regulates human beta-globin gene developmental specificity.

The persistence of fetal hemoglobin in many patients with deletion type beta thalassemias and the expression patterns of human globin genes in transgenic mice suggest that gamma- to beta-globin gene switching results primarily from competition of gamma- and beta-globin genes for interaction with the beta-globin locus control region (LCR). To define regulatory sequences that are essential for the competitive advantage of the gamma gene at early developmental stages, stable transgenic mouse lines were produced with LCR gamma-beta constructs containing deletions of gamma 5'-flanking DNA. All constructs contained the full 22 kb LCR, a 4.1 kb beta-globin gene and a gamma-globin gene with 1348, 383, 202, 130, 72 or 52 bp of 5'-flanking sequence. Primer extension analysis of yolk sac, fetal liver and blood RNA from these lines demonstrated that a region between -202 and -130 of the human gamma-globin gene promoter was required to suppress beta-globin gene expression at early developmental stages. Four transcription factor binding sites within this region [GATA(p), Oct1, GATA(d) and CACCC] were mutated independently in LCR gamma-beta constructs and transgenic mouse lines were produced. Only the gamma CACCC box mutation resulted in high levels of beta-globin gene expression in early embryos. These results demonstrate that the CACCC box of the human gamma-globin gene plays a critical role in human beta-globin gene developmental specificity. The data also suggest that gamma CACCC box binding factors mediate LCR-gamma interactions which normally enhance gamma-globin and suppress beta-globin gene expression in fetal erythroid cells.

Animals↗
PubMedDate not supplied

[Genome instability].

The paper deals with the various manifestations and the role of genome changes, mainly in eukaryotes. I. Hereditary changes: 1) multiplication of genes in animals; 2) multiplication of genes in prokaryotes; 3) microsymbionts, mobile elements and supermutability; 4) extrachromosomal element delta in Drosophila; 5) hybrid dysgenesis in Drosophila; 6) mobile and unstable genes in drosophila; 7) controlling elements in planrs. II. Genome changes as a regulatory factor of genetic activity: 1) immunoglobulin genes; 2) mating types in yeast; 3) the inversion mechanism of switching gene activity in prokaryotes; 4) ribosomal and histone genes; 5) changes of DNA fractions in ontogenesis; 6) regulation of genome changes.

Animals↗
PubMed1996

Transcription factors and the cardiac gene programme.

During the past decade, major advances have been made in uncovering the mechanisms that switch genes on and off. Gene methylation and histones play an important role in gene (in)activation. Following gene activation, the initiation of transcription by RNA polymerase requires the assembly of multiple protein complexes on the promoter region of a gene. How a cell type-specific gene expression pattern can be induced is a key question in cardiovascular biology today. Members of the helix-loop-helix-family of the transcription factors play a dominant role in skeletal muscle formation. In cardiac muscle the situation is less obvious. Recent studies identified muscle transcription factors like MEF-2, TEF-1 and MNF, which are common to both the skeletal and cardiac muscle lineages. A few transcription factors, among which Nkx 2.5 and GATA-4, are expressed predominantly in the heart. The absence of master regulators in the heart points to the importance of interaction between ubiquitous factors and tissue restricted factors to initiate the cardiac gene programme and to lock these cells in their differentiated state. The recent development of murine transgenic and gene-targeting technology provides tools to study the role of mammalian transcription factors in vivo. Interesting cardiac phenotypes are found in gene targeted mice, indicating a crucial role for retinoic acid and homeobox genes in murine cardiogenesis.

Animals↗
PubMedDate not supplied

Mechanisms mediating antigenic variation in Trypanosoma brucei.

Antigenic variation in Trypanosoma brucei is a highly sophisticated survival strategy involving switching between the transcription of one of an estimated thousand variant surface glycoprotein (VSG) genes. Switching involves either transcriptional control, resulting in switching between different VSG expression sites; or DNA rearrangement events slotting previously inactive VSG genes into an active VSG expression site. In recent years, considerable progress has been made in techniques allowing us to genetically modify infective bloodstream form trypanosomes. This is allowing us to reengineer VSG expression sites, and look at the effect on the mechanisms subsequently used for antigenic variation. We can now begin a dissection of a highly complicated survival strategy mediated by many different mechanisms operating simultaneously.

Animals↗
PubMed1995

Transdifferentiation induced by gene transfer.

While for many tissues the differentiation process is well characterized, little is known about 'master switch' genes determining a specific differentiation pathway and having the potential to induce this process in a cell designed for a different differentiation pathway. Based on heterokaryon and 5-aza-cytidine-induced hypomethylation experiments, the muscle determination gene MyoD1 was identified and isolated, which was shown to induce myogenic differentiation even in cells of ectodermal lineage. Since transdifferentiation studies could also be performed in drosophila in vivo by 'false' expression of developmental genes, it is tempting to speculate that experimentally induced transdifferentiation mimics processes during embryonic development and tissue maturation.

Animals↗
PubMed1986

Mapping of VSG genes on large expression-site chromosomes of Trypanosoma brucei separated by pulsed-field gradient electrophoresis.

We have modified the conditions for pulsed-field gradient electrophoresis of Trypanosoma brucei (strain 427) to resolve large chromosomes, which previously comigrated, into five distinct chromosome bands. Mapping of four different variant surface glycoprotein (VSG) genes, which were duplicatively activated in eight independent VSG gene switching events during later stages of infection, has shown that the activated gene is invariably translocated to the same chromosome band. Also, we have examined the chromosomal location of two VSG genes which were activated without duplication during early infection. The location of each is constant in its active and inactive state. These data identify a single chromosome band which is preferentially used for VSG gene expression during chronic infections in this trypanosome strain and support the concept that the transcription and the translocation of VSG genes are independently regulated.

Animals↗