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PubMed2002

Regulation of fetal versus embryonic gamma globin genes: appropriate developmental stage expression patterns in the presence of HS2 of the locus control region.

The gamma genes provide the major contribution to beta-like globin chain production in the fetal liver of humans. However, the expression of gamma genes in the fetus is a recent evolutionary trend seen only in the primate lineage. In a previous study, it was shown that galago and human gamma genes retain their characteristic stage-specific expression patterns in transgenic mice (galago gamma is expressed exclusively in the embryo, whereas human gamma is expressed in the fetus). In that experiment, human and galago gamma genes were linked to hypersensitive site 3 (HS3) of the locus control region. To rule out the possibility that HS3 is required for these differential expression profiles, additional transgenic lines were tested in which human or galago gamma genes were linked to HS2. Once again, the galago gamma gene was embryonic and the human gamma gene was fetal, indicating that the stage specificity of these genes is driven by elements located within the 4-kb fragments that contain the human and galago gamma genes proper.

Age Factors↗
PubMed1997

Endochitinase and beta-1,3-glucanase genes are developmentally regulated during somatic embryogenesis in Picea glauca.

Two cDNAs isolated from white spruce [Picea glauca (Moench) Voss] somatic embryos, are predicted to encode a basic class IV chitinase and a beta-1,3-glucanase, respectively corresponding to genes PgChi-1 and PgGlu-1. Each represents a multigene family in spruce. Transcripts homologous to PgChi-1 or PgGlu-1 genes were highly abundant in embryogenic tissues and gradually decreased after tissues were placed on abscisic acid-containing maturation medium, with lowest abundance in globular embryos. Transcripts related to PgGlu-1 became highly abundant again in early cotyledonary embryos but decreased thereafter, whereas transcripts related to PgChi-1 were also highly abundant in late cotyledonary embryos and plantlets in vitro; transcripts were either low (PgChi-1) or were not detectable (PgGlu-1) in needles. Wounding, drying and flooding stresses enhanced PgChi-1- and PgGlu-1-related gene expression. Fungal cell wall suspension enhanced PgGlu-1-related transcript accumulation, but reduced PgChi-1-related transcript abundance within 24 h. PgChi-1 and PgGlu-1 and their homologues may have roles in plant defense, and possibly developmental roles during spruce somatic embryo maturation.

Amino Acid Sequence↗
PubMed1986

DNase I hypersensitivity and methylation of the 5'-flanking region of the alpha 1-fetoprotein gene during developmental and glucocorticoid-induced repression of its activity in rat liver.

Three major regions of DNase I hypersensitivity (DH) were found in alpha 1-fetoprotein (AFP) chromatin of rat liver. DH site I is located at the transcription initiation site and associated with ongoing AFP transcription. DH site II is located 2.5 kb upstream from the cap site: it is developmental stage-dependent but dissociable from ongoing AFP transcription. DH site III, 3.7 kb upstream from the cap site, behaves as hepatocyte-constitutive. DH sites are present in similar regions of liver albumin chromatin. Dexamethasone-induced AFP gene repression is accompanied by the selective loss of AFP DH site I, a likely result of glucocorticoid receptors binding to a DNA recognition sequence located 5'-adjacent to DH site I. Sl nuclease-hypersensitive sites were found on naked superhelical AFP and albumin DNA, but do not appear to contribute DH sites in liver chromatin. The extent of hypomethylation of HpaII sites at the 5'-end of the AFP gene correlates positively with the level of potential and actual expression of the gene. We conclude that developmental and hormonal regulation of the AFP gene is confined within congruent to 4 kb of 5'-flanking DNA, and we discuss possible hierarchical interactions among DH sites, in relation to DNA methylation and replication.

Aging↗
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↗
PubMed1983

The cloned dopa decarboxylase gene is developmentally regulated when reintegrated into the Drosophila genome.

The Drosophila dopa decarboxylase gene, Ddc, functions normally when reintroduced into flies. DNA containing a cloned Ddc gene inserted into a P element transposon was injected into early embryos. Transformants were identified by suppression of the cuticular phenotype of a Ddc mutant allele. The reintegrated genes are expressed in the proper tissue and at the proper stages during development even though their positions within the genome are different from that of the wild-type Ddc gene. Absolute levels of DDC enzyme activity are within 35% of that found in wild-type Canton S flies, the source of the transforming DNA. The transformants' Ddc RNA is indistinguishable from that of wild type. One reintegrated Ddc gene, inserted on the X chromosome, is affected by the dosage compensation mechanism that leads to sex-specific differences in the expression of many X-chromosome genes.

Animals↗
PubMed2003

A genomewide survey of developmentally relevant genes in Ciona intestinalis. IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail.

Many kinds of transcription factors and regulators play key roles in a variety of developmental processes. In the present survey, genes encoding proteins with conserved HMG-box, bZip domains, and some types of zinc finger motifs were surveyed in the completely sequenced genome of Ciona intestinalis. In the present analysis, 21 HMG-box-containing genes and 26 bZip genes were identified as well as four small groups of zinc finger genes in the Ciona genome. The results also showed that a less redundant set of genes is present in the Ciona genome compared with vertebrate genomes. In addition, cDNA clones for almost all genes identified have been cloned and distributed as a " Ciona intestinalis Gene Collection Release I". The present comprehensive analysis therefore provides a means to study the role of these transcription factors in developmental processes of basal chordates.

Animals↗
PubMed1986

Changes in the chromatin structure of Drosophila glue genes accompany developmental cessation of transcription in wild type and transformed strains.

Three Drosophila salivary gland glue genes show a dramatic transition in their DNAse I hypersensitive sites during the short period between the late third instar and the white prepupa, which correlates with the cessation of their transcription. In culture cells, where the genes are inactive, there is a chromatin configuration similar to that of prepupal salivary glands. In two transformed fly strains where the sgs3 gene is active at new chromosomal sites, including one in which 2.6 kb of sgs3 upstream sequences have been inverted, the same DNAase I hypersensitive sites and developmental transitions are seen over the same DNA regions. These results, together with the analysis of transformants carrying rearranged sgs3 genes, suggest that there is at least one distal DNAase I hypersensitive site associated with an element of regulation which may be exchanged between sgs genes.

Animals↗
PubMed1988

Expression of an activated ras gene causes developmental abnormalities in transgenic Drosophila melanogaster.

We describe the developmental effects of the expression of a normal and mutated Drosophila ras gene ras2 in transgenic Drosophila. A Gly14----Val14 mutant (Gly14 in ras2 is equivalent to Gly12 in mammalian ras proteins) was constructed in ras2 by site-directed mutagenesis. Inducible constructs of ras2 and ras2Val14 were made by coupling the hsp70 promoter to each of the genes. In addition, the endogenous ras2 promoter was placed upstream of the mutated ras2Val14. These constructs were introduced into the germ line of Drosophila to yield transgenic lines by P-element-mediated transformation. A wide variety of developmental disorders were displayed in flies carrying the mutated ras2 gene driven by either the endogenous or the hsp70 promoter. The basal level of transcription of mutated ras from the uninduced hsp70 promoter was sufficient to produce disturbances in the development of several tissue types. In contrast, phenotypic disturbances were not seen with the normal ras2 gene driven by the hsp70 promoter even when induced by heat shock to very high levels of transcription over normal ras2 levels. A subset of the tissues expressing ras2 during development was particularly sensitive to the expression of ras2Val14. The compound eye was found to develop a dorsal-to-ventral 'scar' correlated with the wave of differentiation occurring in the eye imaginal disc at the time of a single brief induction of the hsp70 promoted ras2Val14 construct.

Animals↗
PubMed2000

Cloning a novel developmental regulating gene, Xotx5: its potential role in anterior formation in Xenopus laevis.

The vertebrate Otx gene family is related to otd, a gene contributing to head development in Drosophila. In Xenopus, Xotx1, Xotx2, and Xotx4 have already been isolated and analyzed. Here the cloning, developmental expression and functions of the additional Otx Xenopus gene, Xotx5 are reported. This latter gene shows a greater degree of homology to Xotx2 than Xotx1 and Xotx4. Xotx5 was initially expressed in Spemann's organizer and later in the anterior region. Ectopic expression of Xotx5 had similar effects to other Xotx genes in impairing trunk and tail development, and especially similar effects to Xotx2 in causing secondary cement glands. Taken together, these findings suggest that Xotx5 stimulates the formation of the anterior regions and represses the formation of posterior structures similar to Xotx2.

Amino Acid Sequence↗
PubMed2005

Duplicated Pax6 genes in Glomeris marginata (Myriapoda: Diplopoda), an arthropod with simple lateral eyes.

Composite (facetted) eyes comprised by several units, termed ommatidia, are an ancestral feature in the arthropods. Some arthropods, however, do not possess composite eyes, obviously by secondary reduction. Reductions on the level of conserved eye developmental genes are one possibility to reduce the visual system. The genes of the Pax6 family have been shown to be key regulators of visual system development in a wide variety of animals. Reduction of Pax6 expression may therefore be expected in a species with reduced eyes. Here I have investigated the myriapod Glomeris marginata that displays very simple eyes. Glomeris, however, possesses two Pax6 genes that, based on their sequence, are similar to Drosophila eyeless (ey) and twin of eyeless (toy), respectively. Both genes are highly expressed in the optic lobes and the ventral nerve cord of developing embryos. Furthermore, homologs of other high-ranking eye developmental genes like hedgehog, decapentaplegic, dachshund, and homothorax are expressed in the optic lobes. This indicates that eye reduction in Glomeris is not realized at the level of the Pax6 genes or other genes on the upper levels of the eye development network. I suggest instead that the simple eyes of Glomeris are the product of changes at a much lower level in the network, probably at the level of genes directly regulating ommatidia development or ommatidia number and arrangement.

Animals↗
PubMed2001

Influence of neonatal estrogens on rat prostate development.

Brief exposure of rodents to estrogens during early development alters prostate branching morphogenesis and cellular differentiation in a dose-dependant manner. If estrogenic exposures are high, these disturbances lead to permanent imprints of the prostate, which include reduced growth, differentiation defects of the epithelial cells, altered secretory function and reduced responsiveness to androgens in adulthood. This process, referred to as neonatal imprinting or developmental estrogenization, is associated with an increased incidence of prostatic lesions with aging, which include hyperplasia, inflammation and dysplasia. To better understand how early estrogenic exposures can permanently alter prostate growth and function and predispose the gland to neoplasia, the effects of estrogens on prostatic steroid receptors, cell-cell communication molecules and key developmental genes were examined. Transient and permanent alterations in the expression of prostatic androgen receptors, estrogen receptors alpha (ERalpha) and beta, and retinoic acid receptors are observed. It is proposed that the estrogen-induced alterations in these critical transcription factors play a fundamental role in initiating prostatic growth and differentiation defects. Down-stream effects of the altered steroid receptor expression include disruption of TGFbeta paracrine communication, altered expression of gap junction connexin molecules and loss of epithelial cadherin on epithelial cells. Additionally, specific disruptions in the expression of prostatic developmental genes are observed in response to neonatal estrogen. An extended developmental period of hoxa-13 expression, a lack of hoxd-13 increase with maturation, and an immediate and sustained suppression of hoxb-13 was noted within prostatic tissue. A transient decrease in Nkx3.1 expression in the developing prostate was also observed. Thus subtle and overt alterations in Hox-13 and Nkx3.1 genes may be involved in the altered prostate phenotype in response to neonatal estrogen exposure. In summary, estrogen imprinting of the prostate gland is mediated through up-regulated levels of stromal ERalpha, which initiates alterations in steroid receptor expression within the developing gland. Rather than being an androgen-dominated process, as occurs normally, prostatic development is regulated by alternate steroids, including estrogens and retinoids, in the estrogenized animal. This, in turn, leads to disruptions in the coordinated expression of critical developmental genes including TGFbeta, Hox-13 genes and Nkx3.1. Since a precise temporal expression pattern of these and other molecules is normally required for appropriate differentiation of the prostatic epithelium and stroma, the estrogen-initiated disruption in this pattern would lead to permanent differentiation defects of the prostate gland. It is hypothesized that these molecular and cellular changes initiated early in life predispose the prostate to the neoplastic state upon aging.

Animals↗
PubMed1991

The tomato Cu,Zn superoxide dismutase genes are developmentally regulated and respond to light and stress.

The expression of the two Cu,Zn superoxide dismutase (SOD) genes of tomato was followed in different organs and plant developmental stages at the transcript and enzymatic activity levels. The cDNA clones used as probes code for the chloroplast Cu,Zn SOD (clone T1) and the cytosolic Cu,Zn SOD (clone P31). The two genes were found to display distinct expression patterns. While the T1 transcript was rare or absent from roots, stems and ripening fruits, the P31 transcript was very abundant in these organs. Shoot tips, flower buds, seedlings and young leaves contained high levels of the two mRNAs. During leaf expansion, the levels of both transcripts diminish markedly. Despite the diminished presence of transcripts, SOD activity levels of the corresponding cytosolic and chloroplast isozymes accumulated and were sustained throughout leaf expansion. In non-photosynthetic organs, the SOD-3 (cytosolic) isozyme contained most of the activity, while in the expanded leaf the SOD-1 (chloroplast) isozyme was more abundant. Light-regulated accumulation of both the P31 transcript (1.7-fold) and the T1 transcript (3-fold) was observed upon light exposure of etiolated seedlings. However, only SOD-1 activity was observed to increase, after a lag of a few hours. The levels of both transcripts increased in response to paraquat and mechanical wounding. The level of the cytosolic transcript and the respective isozyme activity increased dramatically during prolonged drought stress while the chloroplast transcript remained unaffected. The expression of both genes was enhanced by spraying tomato plants with ethephon--a compound that releases ethylene. Our data show that the expression of Cu,Zn SOD genes in tomato is modulated in response to a variety of factors and suggest the importance of oxyradical toxicity as well as the role of SOD in the defence mechanism of plants exposed to stress.

Blotting, Northern↗
PubMed2005

EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods.

To evaluate the molecular mechanisms during pod and seed formation in legumes, starting with the development of reproductive organs, we constructed two cDNA libraries from developing flowers (MtFLOW) and pods including seeds (MtPOSE) of the model plant Medicago truncatula Gaertner. A total of 2,516 expressed sequence tags (ESTs) clustered into 1,776 nonredundant sequences (2k-set), which were annotated and assigned to functional classes. While about 30% of the ESTs encoded proteins of yet unknown function, typical annotations pointed to seed storage proteins, LTPs and lipoxygenases. The 2k-set was used to upgrade Mt6k-RIT microarrays (Küster et al. in J Biotechnol 108: 95, 2004) to Mt8k versions representing approximately 6,300 nonredundant M. truncatula genes. These were used to perform time course expression profiling studies based on hybridizations of samples that covered eight different developmental stages from flower buds to almost mature pods versus leaves as a common reference. About 180 up- and 70 downregulated genes were typically found for each stage and in total, 782 genes were either twofold up- or downregulated in at least one of the eight stages investigated. Based on this set, a combination of self-organizing map and hierarchical clustering revealed genes displaying expression regulation during characteristic stages of M. truncatula flower and pod development. Amongst those, several genes encoded proteins related to seed metabolism and development including novel regulators and proteins involved in signaling.

Expressed Sequence Tags↗
PubMed1998

Expressed sequence tag analysis of the bradyzoite stage of Toxoplasma gondii: identification of developmentally regulated genes.

Toxoplasma gondii is a protozoan parasite responsible for widespread infections in humans and animals. Two major asexual forms are produced during the life cycle of this parasite: the rapidly dividing tachyzoite and the more slowly dividing, encysted bradyzoite. To further study the differentiation between these two forms, we have generated a large number of expressed sequence tags (ESTs) from both asexual stages. Previously, we obtained data on approximately 7,400 ESTs from tachyzoites (J. Ajioka et al., Genome Res. 8:18-28, 1998). Here, we report the results from analysis of approximately 2,500 ESTs from bradyzoites purified from the cysts of infected mice. We also report the results from analysis of 760 ESTs from parasites induced to differentiate from tachyzoites to bradyzoites in vitro. Comparison of the data sets from bradyzoites and tachyzoites reveals many previously uncharacterized sequence clusters which are largely or completely specific to one or other developmental stage. This class includes a bradyzoite-specific form of enolase. Combined with the previously identified bradyzoite-specific form of lactate dehydrogenase, this finding suggests significant differences in flux through the lower end of the glycolytic pathway in this stage. Thus, the generation of this data set provides valuable insights into the metabolism and growth of the parasite in the encysted form and represents a substantial body of information for further study of development in Toxoplasma.

Amino Acid Sequence↗
PubMed1988

The coupling between enhancer activity and hypomethylation of kappa immunoglobulin genes is developmentally regulated.

Previous studies have indicated that immunoglobulin enhancers are essential for establishing transcriptional competence but not for maintaining the activity of constitutively transcribed genes. To understand the basis for this developmental shift away from dependence on enhancer function, we have investigated the relationship between transcriptional activity and methylation status of the immunoglobulin kappa light-chain genes (kappa genes) in mouse cell lines representing different stages of B-cell maturation. Using pre-B-cell lines in which the level of a critical kappa enhancer-binding factor, NF-kappa B, was controlled by the administration or withdrawal of lipopolysaccharide and plasmacytoma lines that either contain or lack this factor, we studied the properties of endogenous kappa genes and of transfected kappa genes which were stably integrated into the genomes of these cells. In the pre-B cells, the exogenous (originally unmethylated) kappa genes, as well as endogenous kappa genes, were fully methylated and persistently dependent on enhancer function, even after more than 30 generations in a transcriptionally active state. In plasmacytoma cells, the endogenous kappa genes were invariably hypomethylated, whereas exogenous kappa genes were hypomethylated only in cells that contain NF-kappa B and are thus permissive for kappa enhancer function. These results indicate that the linkage of hypomethylation to enhancer-dependent activation of kappa transcription occurs after the pre-B-cell stage of development. The change in methylation status, together with associated changes in chromatin structure, may suffice to eliminate or lessen the importance of the enhancer for the maintenance of the transcriptionally active state.

Abelson murine leukemia virus↗
PubMed1989

Replication timing of 10 developmentally regulated genes in Physarum polycephalum.

We have tested the hypothesis which stipulates that only early-replicating genes are capable of expression. Within one cell type of Physarum - the plasmodium - we defined the temporal order of replication of 10 genes which were known to be variably expressed in 4 different developmental stages of the Physarum life cycle. Southern analysis of density-labeled, bromodesoxyuridine-substituted DNA reveals that 4 genes presumably inactive within the plasmodium, were not restricted to any temporal compartment of S-phase: 1 is replicated in early S-phase, 2 in mid S-phase and 1 in late S-phase. On the other hand, 4 out of 6 active genes analysed are duplicated early, with the first 30% of the genome. Surprisingly, the two others active genes are replicated late in S-phase. By gene-dosage analysis, based on quantitation of hybridization signals from early and late replicating genes throughout S-phase, we could pinpoint the replication of one of these two genes at a stage where 80-85% of the genome has duplicated. Our results demonstrate that late replication during S-phase does not preclude gene activity.

Blotting, Southern↗
PubMed1986

Identification and characterization of neuron-specific and developmentally regulated gene transcripts in the chick embryo spinal cord.

Clones corresponding to neuron-specific and developmentally regulated messenger RNA species in the chick have been isolated from a complementary DNA library prepared using polyadenylated RNA from 7-day embryonic spinal cord. The library was initially screened by differential complementary DNA hybridization procedures for clones identifying polyadenylated RNAs present in embryonic spinal cord but absent from or at low abundance in liver tissue. A high proportion of selected recombinant plasmids were found to identify different RNA species which, although present in 14-day embryonic spinal cord, could not be detected in a corresponding region of the developing chick CNS that is devoid of neuronal cell bodies, the optic nerve. The neuron-specific assignment of these mRNAs within the developing neuroectoderm was confirmed using bulk-isolated neuronal and glial-enriched cell fractions from 7-day embryonic spinal cord. In addition, several distinctive patterns of developmentally regulated expression of neuron-specific messenger RNA species have been observed in the chick spinal cord. The studies lay a foundation for detailed examination of the regional and temporal distribution and control of neuronal gene expression in the chick spinal cord during embryogenesis.

Animals↗