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The mouse Smcx gene exhibits developmental and tissue specific variation in degree of escape from X inactivation.

The Smcx gene is the first known example of a non-pseudoautosomal X-linked gene in mouse that normally escapes X chromosome inactivation. We have analysed the kinetics of escape at different stages of development, and in adult tissues. Our results demonstrate that Smcx exhibits partial escape from X inactivation in embryos, in extraembryonic lineages where paternally imprinted X inactivation occurs and also in adult tissues. The degree of escape in different tissues is highly variable, the level of transcript from the inactive X allele representing between 20% and 70% of the active X allele. Partial escape is also seen in clones derived from haematopoietic stem cells, suggesting that partial repression of the inactive X allele is at the level of individual cells. This contrasts with classical position effect variegation (PEV), where a given gene is either active or silent in a given cell and its clonal derivatives. We discuss the implications of these results with respect to mechanisms of X inactivation and escape.

Alleles↗

Coupling gene expression and multicellular morphogenesis during fruiting body formation in Myxococcus xanthus.

A recurring theme in morphogenesis is the coupling of the expression of genes that drive morphogenesis and the morphogenetic process per se. This coupling ensures that gene expression and morphogenesis are carried out in synchrony. Morphogenesis of the spore-filled fruiting bodies in Myxococcus xanthus illustrates this coupling in the construction of a multicellular structure. Fruiting body formation involves two stages: aggregation of cells into mounds and the position-specific sporulation of cells that have accumulated inside mounds. Developmental gene expression propels these two processes. In addition, gene expression in individual cells is adjusted according to their spatial position. Progress in the understanding of the cell surface-associated C-signal is beginning to reveal the framework of an intercellular signalling system that allows the coupling of gene expression and multicellular morphogenesis. Accumulation of the C-signal is tightly regulated and involves transcriptional activation of the csgA gene and proteolysis of the full-length CsgA protein to produce the shorter cell surface-associated 17 kDa C-signal protein. The C-signal induces aggregation, sporulation and developmental gene expression at specific thresholds. The ordered increase in C-signalling levels, in combination with the specific thresholds, allows the C-signal to induce these three processes in the correct temporal order. The contact-dependent C-signal transmission mechanism, in turn, guarantees that C-signalling levels reflect the spatial position of individual cells relative to other cells and, thus, allows the cells to decode their spatial position during morphogenesis. By this mechanism, individual cells can tailor their gene expression profile to one that matches their spatial position. In this scheme, the molecular device that keeps gene expression in individual cells in register with morphogenesis is the C-signalling system, and the morphological structure, which is assessed, is the spatial position of individual cells relative to that of other cells.

Gene Expression Regulation, Bacterial↗

Expression of cytosolic acetyl-CoA synthetase gene is developmentally regulated.

Acetyl-CoA synthetase (AceCS) provides acetyl-CoA for different physiological processes, such as fatty acid and cholesterol synthesis, as well as the citric acid cycle. We show here that the cytosolic isoform of this enzyme, AceCS1, is expressed during mouse development. In the embryonic stage E9.5 AceCS1 transcripts localize in the cephalic region. At E10.5 the cephalic expression intensifies and transcripts appear also in the spinal cord and in the dorsal root ganglions. During organogenesis AceCS1 is expressed in the liver from E11.5. The AceCS1 gene is expressed also in the testes from E12.5 onwards and expression localizes in the interstitial Leydig cells. In the ovaries, expression is transient and AceCS1 transcripts are detected from E13.5 to E15.5 in the ovarian interstitial component. In the kidneys AceCS1 transcripts appear in a subset of the renal tubules at E16.5 and remains in these structures in newborns. Hence, expression of AceCS1 is developmentally regulated suggesting a role for AceCS1 during embryogenesis.

Acetate-CoA Ligase↗

The responsiveness of embryonic stem cells to alpha and beta interferons provides the basis of an inducible expression system for analysis of developmental control genes.

Embryonic stem (ES) cells, derived from the inner cell mass of the preimplantation mouse embryo, are used increasingly as an experimental tool for the investigation of early mammalian development. The differentiation of these cells in vitro can be used as an assay for factors that regulate early developmental decisions in the embryo, while the effects of altered gene expression during early embryogenesis can be analyzed in chimeric mice generated from modified ES cells. The experimental versatility of ES cells would be significantly increased by the development of systems which allow precise control of heterologous gene expression. In this paper, we report that ES cells are responsive to alpha and beta interferons (IFNs). This property has been exploited for the development of inducible ES cell expression vectors, using the promoter of the human IFN-inducible gene, 6-16. The properties of these vectors have been analyzed in both transiently and stably transfected ES cells. Expression was minimal or absent in unstimulated ES cells, could be stimulated up to 100-fold by treatment of the cells with IFN, and increased in linear fashion with increasing levels of IFN. High levels of induced expression were maintained for extended periods of time in the continuous presence of the inducing signal or following a 12-h pulse with IFN. Treatment of ES cells with IFN did not affect their growth or differentiation in vitro or compromise their developmental potential. This combination of features makes the 6-16-based expression vectors suitable for the functional analysis of developmental control control genes in ES cells.

Animals↗

Quantitative expression of candidate genes for developmental competence in bovine two-cell embryos.

Only competent oocytes are able to undergo complete maturation and normal embryonic development. Therefore, the identification of genes that are differentially expressed in competent oocytes would contribute to our understanding of the factors controlling competency. It is well known that time of cleavage after insemination in vitro is highly correlated with embryonic developmental potential and this can be used to distinguish between oocytes of different quality. The main objective of this study was to identify genes associated with competency and rapid cleavage. We examined the expression of 16 candidate genes (IDH, YEAF Cathepsin B, RAD50, TCP1 NCOR1, HUEL, STK6, ZNF403, AOP2, EEF1A1, Hsp90, Hsp40, AKR1B1, PGRMC1, and DMRT2) in early and late cleaving embryos, by real time PCR. These transcripts were derived from previous study in our laboratory using cDNA coming from a suppressive subtraction hybridization (SSH) between early cleaving versus late cleaving embryos spotted on a microarray slide. Of the 16 genes evaluated, 3 (IDH, YEAF, and H2A) showed statistical difference (P < 0.05) between early and late cleaving embryos. However, some genes such as Cathepsin B (P = 0.0677), RAD50 (P = 0.0899), and TCP1 (P = 0.0824) tended to show higher expression in the early cleaving than in the late cleaving embryo. In conclusion, we have identified three genes (YEAF, IDH, H2A) that were differentially expressed in the early cleaving embryos, and their expression can be associated with greater developmental competence.

Aldehyde Reductase↗

A genetic approach for investigating vagal sensory roles in regulation of gastrointestinal function and food intake.

Sensory innervation of the gastrointestinal (GI) tract by the vagus nerve plays important roles in regulation of GI function and feeding behavior. This innervation is composed of a large number of sensory pathways, each arising from a different population of sensory receptors. Progress in understanding the functions of these pathways has been impeded by their close association with vagal efferent, sympathetic, and enteric systems, which makes it difficult to selectively label or manipulate them. We suggest that a genetic approach may overcome these barriers. To illustrate the potential value of this strategy, as well as to gain insights into its application, investigations of CNS pathways and peripheral tissues involved in energy balance that benefited from the use of gene manipulations are reviewed. Next, our studies examining the feasibility of using mutations of developmental genes for manipulating individual vagal afferent pathways are reviewed. These experiments characterized mechanoreceptor morphology, density and distribution, and feeding patterns in four viable mutant mouse strains. In each strain a single population of vagal mechanoreceptors innervating the muscle wall of the GI tract was altered, and was associated with selective effects on feeding patterns, thus supporting the feasibility of this strategy. However, two limitations of this approach must be addressed for it to achieve its full potential. First, mutation effects in tissues outside the GI tract can contribute to changes in GI function or feeding. Additionally, knockouts of developmental genes are often lethal, preventing analysis of mature innervation and ingestive behavior. To address these issues, we propose to develop conditional gene knockouts restricted to specific GI tract tissues. Two genes of interest are brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3), which are essential for vagal afferent development. Creating conditional knockouts of these genes requires knowledge of their GI tract expression during development, which little is known about. Preliminary investigation revealed that during development BDNF and NT-3 are each expressed in several GI tract regions, and that their expression patterns overlap in some tissues, but are distinct in others. Importantly, GI tissues that express BDNF or NT-3 are innervated by vagal afferents, and expression of these neurotrophins occurs during the periods of axon invasion and receptor formation, consistent with roles for BDNF or NT-3 in these processes and in receptor survival. These results provide a basis for targeting BDNF or NT-3 knockouts to specific GI tract tissues, and potentially altering vagal afferent innervation only in that tissue (e.g., smooth muscle vs. mucosa). Conditional BDNF or NT-3 knockouts that are successful in selectively altering a vagal GI afferent pathway will be valuable for developing an understanding of that pathway's roles in GI function and food intake.

Afferent Pathways↗

Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells.

Epigenetic mechanisms, such as histone modifications and DNA methylation, have been shown to play a key role in the regulation of gene transcription. Results of recent studies indicate that a novel "bivalent" chromatin structure marks key developmental genes in embryonic stem cells (ESCs), wherein a number of untranscribed lineage-control genes, such as Sox1, Nkx2-2, Msx1, Irx3, and Pax3, are epigenetically modified with a unique combination of activating and repressive histone modifications that prime them for potential activation (or repression) upon cell lineage induction and differentiation. However, results of these studies also showed that a subset of lineage-control genes, such as Myf5 and Mash1, were not marked by these histone modifications, suggesting that distinct epigenetic mechanisms might exist for lineage-control genes in ESCs. In this review article, we summarize evidence regarding possible mechanisms that control these unique histone modifications at lineage-control gene loci in ESCs and consider their possible contribution to ESC pluripotency. In addition, we propose a novel "histone modification pulsing" model wherein individual pluripotent stem cells within the inner cell mass of blastocysts undergo transient asynchronous histone modifications at these developmental gene loci, thereby conferring differential responsiveness to environmental cues and morphogenic gradients important for cell lineage determination. Finally, we consider how these rapid histone modification exchanges become progressively more stable as ESCs undergo differentiation and maturation into specialized cell lineages.

Animals↗

Polycomb group genes control developmental timing of endosperm.

Polycomb (PcG) group proteins form modular complexes, which maintain repressed transcriptional states of target genes across cell divisions. As PcG complexes provide a memory of cell fate, such proteins might control temporal aspects of development. Loss-of-function of any of the FERTILIZATION INDEPENDENT SEED (FIS) PcG genes perturbs endosperm development. In this report we provide a detailed analysis of the phenotype of fis endosperm development using molecular and cellular markers. Wild type (WT) endosperm development undergoes a series of four major developmental phases timed by successive synchronous nuclei division. In fis endosperm the transition from phase 1, marked by a synchronous mode of nuclei divisions to phase 2, corresponding to the establishment of three mitotic domains, is absent. Accordingly, the expression of seven markers of phase 1 and phase 2 is temporally perturbed. In spite of such changes, specific sequences of developmental events still take place as in the WT. Overall, fis mutations are heterochronic mutations that cause a temporal deregulation in the ontogenic sequence of endosperm development.

Arabidopsis↗

Methylation of HoxA5 and HoxB5 and its relevance to expression during mouse development.

Expression and function of homeobox genes (Hox genes) in development have been subject to extensive study in a variety of organisms including mammals, however practically nothing is known regarding the methylation patterns of these genes. Here we describe the methylation patterns of HoxA5 and HoxB5 in various tissues of fetal and adult mice and their relevance to expression. Both genes exhibit tissue specific methylation patterns that are established postnatally. This methylation appears to play a role in stabilizing the newly acquired silent state of the genes. In contrast to the postimplantation wave of de novo methylation that takes place across the mammalian genome, the methylation of the Hox genes represents a different time window for de novo methylation which might be characteristic of developmental genes. In the case of HoxA5 this postnatal de novo methylation can cover a domain of at least 25 kb that includes several genes of the HoxA cluster and the CpG islands within. Our observations suggest that the establishment of tissue specific methylation patterns of HoxA5 and HoxB5 and the relationship between these methylation patterns and activity are different from what had been known for non-developmental genes. This may reflect the specialized functions played by Hox genes in development.

Animals↗

Cloning of rat vitamin K-dependent gamma-glutamyl carboxylase and developmentally regulated gene expression in postimplantation embryos.

Vitamin K-dependent carboxylase catalyzes the posttranslational modification of glutamate to gamma-carboxyglutamate (Gla) in its substrates, the vitamin K-dependent proteins (VKDPs). This modification is required for the activities of the VKDPs. Recent evidence demonstrates previously unrecognized roles for VKDPs as signaling molecules important in the regulation of cell growth, adhesion, and apoptosis, suggesting developmental functions for VKDPs and hence the carboxylase. The tissue distribution and functions of carboxylase in development are unknown. In this study, we isolated and characterized the full-length cDNA encoding the rat carboxylase and analyzed, at the cellular level, the expression of this gene in rat embryos by in situ hybridization. We demonstrate that the expression of this gene is highly regulated in a developmental and tissue-specific manner. Hepatocytes, the major site of synthesis of VKDPs of blood coagulation, express carboxylase mRNA late in gestation, in contrast to the central nervous system, mesenchymal, and skeletal tissues which express carboxylase mRNA early during rat embryogenesis. The tissue-specific temporal expression of the carboxylase gene during embryogenesis indicates that vitamin K-dependent carboxylation and the formation of Gla is developmentally regulated. These studies suggest that vitamin K-dependent carboxylation is an important modulator of embryonic VKDP function.

Amino Acid Sequence↗

Structural characterization of the mouse Hfh4 gene, a developmentally regulated forkhead family member.

Hepatocyte nuclear factor-3/forkhead homologue 4 (HFH-4) is a forkhead/winged-helix transcription factor family member that has a unique temporal and spatial pattern of gene expression in the developing and adult lung, choroid plexus, testis, and oviduct. To characterize HFH-4 further, mouse genomic clones were isolated and analyzed. The Hfh4 gene is encoded on a 5.5-kb region located on the distal end of mouse chromosome 11 and consists of two exons and one intron. Unlike most forkhead genes, the DNA binding domain is divided between two exons, and the intron position corresponds precisely to the site of gene translocations involving two known human forkhead homologues. Multiple putative transcription start sites are identified in a G+C-rich sequence that does not contain TATA or CAAT boxes. Within 2.1 kb of 5' flanking sequence are three identical E boxes and multiple putative transcription factor binding sites. Transfection of plasmids containing Hfh4 5' flanking sequence linked to a reporter gene results in promoter activity in lung epithelial cells but not in epithelial-like fibrosarcoma cells, suggesting that this 5' flanking sequence can function as a promoter with the proper cell-type specificity.

Amino Acid Sequence↗

Helix-loop-helix motif in GnRH associated peptide is critical for negative regulation of prolactin secretion.

The GnRH associated prolactin inhibiting factor (GAP) reveals the signature sequence associated with the helix-loop-helix structural motif. A number of different peptide fragments of GAP were designed, synthesized and analysed by circular dichroism and by an in vivo assay for prolactin secretion inhibiting activity. Peptides corresponding to the two individual alpha-helices and a 44-residue peptide comprising the entire helix-loop-helix motif show significant helical propensity in circular dichroism spectra. However, a peptide corresponding to the loop sequence shows no helical propensity. Albeit, the peptide corresponding to helix-loop-helix motif was found to inhibit prolactin secretion and augment circulating levels of gonadotropins in the in vivo assay; other shorter peptides did not show such activity. The activity profile of the 44-residue peptide was biphasic and very similar to that of the recombinant GAP. Thus, the prolactin inhibiting activity of this factor is defined by its helix-loop-helix motif as in the case of the transcription factors of developmental genes. The structural features of a homology-based model of GAP in complex with E47, a ubiquitous HLH-type developmental gene regulator, are consistent with the structural requirements of the negative regulation of transcription by helix-loop-helix proteins.

Amino Acid Sequence↗

A role for cyclic AMP in expression of developmentally regulated genes in Dictyostelium discoideum.

Starved cells of Dictyostelium discoideum begin to synthesize a new class of developmentally regulated proteins at about 13 hr of the 24-hr developmental program, concomitant with the formation of tips on the tight cell aggregates [Alton, T. H. & Lodish, H. F. (1977) Dev. Biol. 60, 180--206]. Continued synthesis of these proteins is normally dependent upon the integrity of the multicellular aggregates, because cells that have been disaggregated at 13 hr and shaken in suspension for 5 hr do not make these proteins. We show here that addition of 20 microM cyclic AMP to suspension cultures of disaggregated 13-hr cells caused synthesis of most of these late proteins to be maintained. Translation in an in vitro wheat germ system of total cellular RNA isolated from these cyclic AMP-stimulated suspension cells, or from normal aggregates, generated several proteins that were not encoded by the RNA isolated from equivalent suspension cells which had not been treated with cyclic AMP or from preaggregation cells. We conclude that cyclic AMP has a direct role in maintaining the synthesis of aggregation-dependent Dictyostelium proteins and in maintaining the level of the corresponding mRNAs.

Cell Aggregation↗

Gene expression and developmental competence of bovine embryos produced in vitro under varying embryo density conditions.

The objective of this study was to determine the effects of oocyte/embryo density (embryo number:medium volume ratio) on developmental competence and relative transcription of developmentally important genes in in vitro-produced bovine embryos. Using standard procedures, bovine oocytes were matured, fertilized and cultured in vitro in groups of 5, 10, 20 or 30 oocytes/embryos per 100 microL medium drop (embryo number/medium volume ratios of 1:20, 1:10, 1:5 and 1:3.3, respectively). A semi-quantitative RT-PCR assay was used to determine the relative abundance of Hsp 70.1 and Glut-1 transcripts in Day-6 morulae, and in Day-7 and Day-8 blastocysts and expanded blastocysts. Cleavage rates (55.9, 49.1, 47.1 and 34.6%, respectively) and blastocyst developmental rates (24.1, 18.9, 20.4 and 12.6%, respectively) were higher in groups containing 5, 10 and 20 embryos versus 30 embryos per drop, but there were no significant differences among groups in hatching rates. The relative abundance of Hsp 70.1 transcripts in Day-7 blastocysts was higher in embryos produced in the 20-embryo than in the 5-embryo groups. There were no differences among embryos from all groups in the amount of Glut-1 mRNA (regardless of embryonic stage). However, there were differences in the pattern of Hsp 70.1 gene expression between distinct stages of embryo development and embryo density; these dissimilarities appeared to be associated with compromised development at higher embryo densities. In conclusion, the increase in embryo density during IVM, IVF, and IVC phases of in vitro embryo production might negatively affect embryo development and the pattern of gene expression of in vitro-produced bovine embryos.

Animals↗

Molecular cloning and nucleotide sequence of a developmentally regulated gene from the cyanobacterium Calothrix PCC 7601: a gas vesicle protein gene.

Since the gas vesicle protein (GVP) is highly conserved among the different gas-vacuolate prokaryotes, a 29-mer oligonucleotide corresponding to a portion of the Anabaena flos-aquae GVP gene was synthesized and used to isolate the GVP structural gene from Calothrix PCC 7601 (= Fremyella diplosiphon). Gas vacuole production in this filamentous cyanobacterium is restricted to hormogonia which occur at a specific stage during the developmental cell cycle. The GVP gene (gvpA) was localized on a 709 bp HindIII-HincII fragment. Nucleotide sequence analysis revealed a 213 bp open reading frame whose deduced amino-acid sequence shows a very high homology with that of the Anabaena flos-aquae GVP. Assuming that the first methionine residue is proteolytically processed, the molecular mass of the Calothrix GVP is 7375 daltons. Sequences resembling the Escherichia coli consensus promoter were found upstream from the gvpA gene. The initiator codon of the gvpA gene is preceded by a polypurine sequence assumed to be the ribosome binding site. Southern hybridizations with a probe specific for the gvpA gene indicated that this gene is not plasmid-borne, and that another homologous gene is present in the Calothrix genome.

Amino Acid Sequence↗

Cardiac abnormalities induced by zinc deficiency are associated with alterations in the expression of genes regulated by the zinc-finger transcription factor GATA-4.

Zinc (Zn) deficiency during pregnancy results in a wide variety of developmental abnormalities. The objective of this study was to determine if expression of cardiac developmental genes regulated by Zn-finger transcription factors could be modulated during dietary Zn deficiency. Rats were fed 0.5 (low Zn) or 90 (controls) microg Zn/g diet throughout pregnancy. Fetal development was examined and RNA isolated at gestation day (GD) 13 and 20. Cardiac abnormalities were detected at GD 20 in 82% of fetuses from dams fed low Zn diets compared with only 2% in controls. Cardiac developmental gene expression regulated by the Zn-finger transcription factor, GATA-4, was measured by quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). In GD 13 and 20 hearts, two genes critical for heart development, alpha-myosin heavy chain (alpha-MHC) and cardiac troponin I (cTnI), were down-regulated in Zn-deficient fetuses. Expression of alpha-MHC was 66 and 40% lower at GD 13 and 20, respectively, in fetuses from dams fed low Zn diets compared with fetuses from control dams (p<0.05). Fetal cardiac TnI RNA levels were reduced 40 and 45% at GD 13 and 20 in the Zn-deficient group compared with controls (p<0.05). Fetal cardiac transcript levels of GATA-4 and MHox, a gene regulated by a helix-loop-helix transcription factor, whose expressions are not Zn-dependent, were unaffected by diet. These data indicated that alterations in gene regulation might be an underlying mechanism of cardiac abnormalities. Dysfunction of other Zn-dependent transcription factors may be an integral part of the extensive teratogenesis associated with Zn deficiency.

Abnormalities, Multiple↗

Suppression of a yeast cyclic AMP-dependent protein kinase defect by overexpression of SOK1, a yeast gene exhibiting sequence similarity to a developmentally regulated mouse gene.

Saccharomyces cerevisiae cyclic AMP-dependent protein kinase (A kinase) activity is essential for growth and cell cycle progression. Dependence on A kinase function can be partially relieved by the inactivation of a second kinase encoded by the gene YAK1. We have isolated two new genes, SOK1 and SOK2 (suppressor of kinase), as gene dosage suppressors of the conditional growth defect of several temperature-sensitive A kinase mutants. Overexpression of SOK1, like lesions in YAK1, also restores growth to a strain (tpk1 tpk2 tpk3) lacking all A kinase activity. The SOK1 gene is not essential, but a sok1::HIS3 disruption abrogates suppression of an A kinase defect by yak1. These results suggest that Yak1 and Sok1 define a linear pathway that is partially redundant with that of the A kinase. Activation of Sok1, by SOK1 overexpression or by inactivation of the negative regulator Yak1, renders a cell independent of A kinase function. The implications of such a model are particularly intriguing in light of the nuclear localization pattern of the overexpressed Sok1 protein and the primary sequence homology between SOK1 and a recently described, developmentally regulated mouse gene.

Amino Acid Sequence↗

Two early replicated, developmentally controlled genes of Physarum display different patterns of DNA replication by two-dimensional agarose gel electrophoresis.

The nature of replication origins in eukaryotic chromosomes has been examined in some detail only in yeast, Drosophila, and mammalian cells. We have used highly synchronous cultures of plasmodia of the myxomycete Physarum and two-dimensional agarose gel electrophoresis to examine replication of two developmentally controlled, early replicated genes over time in S-phase. A single, discrete origin of replication was found within 4.8 kb of the LAV1-5 gene, which encodes a homolog of profilin. In contrast, the LAV1-2 gene appears to be surrounded by several origins. Two origins were identified within a 15 kb chromosomal domain and appear to be inefficiently used. Replication forks collide at preferred sites within this domain. These terminating structures are long lived, persisting for at least 2 h of the 3 h S-phase. Analysis of restriction fragment length polymorphisms (RFLPs) within the LAV1-2 domain indicates that replication of alleles on different parental chromosomes is a highly coordinated process. Our studies of the these two early replicated, plasmodium-specific genes indicate that both a fixed, narrow origin region and a broader zone containing two closely spaced origins of DNA replication occur in Physarum.

Animals↗