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BIR-1, the homologue of human Survivin, regulates expression of developmentally active collagen genes in C. elegans.

BIR-1 and Survivin are highly conserved members of the inhibitor of apoptosis protein family that regulate cell division in nematodes and mammals and inhibit apoptosis in mammals. In the C. elegans genome, bir-1 is organized in an operon together with transcription and splicing cofactor CeSKIP (skp-1) and is highly expressed during embryogenesis as well as in non-dividing cells during larval development. Previously we have shown that BIR-1 regulates transcription and development and its loss-of-function phenotype overlaps with loss of function of CeSKIP and nuclear hormone receptor CHR3 (NHR-23). Here we searched for genes whose expression is affected by BIR-1 loss of function using whole-genome microarray experiments and identified several collagen genes as candidate targets of bir-1 inhibition in L1 larval stage. The decreased expression of selected collagen genes in bir-l-inhibited larvae was confirmed by quantitative RT-PCR. Next, we generated transgenic lines expressing bir-1 mRNA under a heat shock-regulated promoter and tested whether bir-1 overexpression has the potential to augment the expression of genes that showed decreased expression in worms treated with bir-1 RNAi. Overexpression of bir-1 resulted in a pronounced increase (2 to 5 times) of the expression of these genes. Our findings support the concept that BIR-1, a protein generally regarded as a mitotic factor, is involved in the regulation of transcription during normal development of C. elegans and has a strong ability to affect transcription of developmentally active genes if overexpressed.

Animals↗

Interplay of mechanical deformation and patterned gene expression in developing embryos.

The shaping of the early embryo requires pattern formation as well as geometric and topological morphogenesis of the developing tissues. The morphogenetic movements that lead to geometric shape changes are controlled by patterned gene expression. How particular movements are related to patterning genes, and which underlying molecular and cellular mechanisms lead to coordinated macroscopic movements that induce morphogenesis, remain the challenging questions of embryonic development. How morphogenetic movements could modulate the expression of developmental genes is an emerging question, potentially opening new horizons in developmental biology. This question instigates the task of characterizing the molecular and cellular mechanisms underlying these mechano-transcription events.

Animals↗

Structure trees and species trees: what they say about morphological development and evolution.

The evolutionary history of morphological structures generally is equated with that of the taxa that carry them. It is argued here that, analogous to genes, developmental genetic pathways underlying morphological structures may be subject to developmental evolutionary changes that result, for instance, in duplication (serial homology analogous to gene duplication and paralogy). Entities that undergo evolution are expected to be related to each other as a tree. Just as with molecular evolution, "structure trees" and species trees sometimes may be incongruent, with implications for morphological homology concepts. Detection of structure trees through morphological evolutionary analyses may point to an entity that is maintained through evolution, possibly in part because it is a developmentally integrated structure ("individualized"). This idea is illustrated in a morphological evolutionary analysis of leaf primordia. These analyses suggest that leaf primordia in monocots and close relatives are related to each other as a tree and, therefore, are developmentally integrated, evolving entities. Among monocot primordia this tree structure breaks down, and it is concluded that there is no entity, the "monocot leaf primordium." However, one group of primordia is identified within monocots that have uniform characteristics and that are well represented by model species maize and rice. Such analyses of structure trees can facilitate the extrapolation and interpretation of results from molecular developmental and other comparative studies.

Flowers↗

Functional promiscuity of gene regulation by serpentine receptors in Dictyostelium discoideum.

Serpentine receptors such as smoothened and frizzled play important roles in cell fate determination during animal development. In Dictyostelium discoideum, four serpentine cyclic AMP (cAMP) receptors (cARs) regulate expression of multiple classes of developmental genes. To understand their function, it is essential to know whether each cAR is coupled to a specific gene regulatory pathway or whether specificity results from the different developmental regulation of individual cARs. To distinguish between these possibilities, we measured gene induction in car1 car3 double mutant cell lines that express equal levels of either cAR1, cAR2, or cAR3 under a constitutive promoter. We found that all cARs efficiently mediate both aggregative gene induction by cAMP pulses and induction of postaggregative and prespore genes by persistent cAMP stimulation. Two exceptions to this functional promiscuity were observed. (i) Only cAR1 can mediate adenosine inhibition of cAMP-induced prespore gene expression, a phenomenon that was found earlier in wild-type cells. cAR1's mediation of adenosine inhibition suggests that cAR1 normally mediates prespore gene induction. (ii) Only cAR2 allows entry into the prestalk pathway. Prestalk gene expression is induced by differentiation-inducing factor (DIF) but only after cells have been prestimulated with cAMP. We found that DIF-induced prestalk gene expression is 10 times higher in constitutive cAR2 expressors than in constitutive cAR1 or cAR3 expressors (which still have endogenous cAR2), suggesting that cAR2 mediates induction of DIF competence. Since in wild-type slugs cAR2 is expressed only in anterior cells, this could explain the so far puzzling observations that prestalk cells differentiate at the anterior region but that DIF levels are actually higher at the posterior region. After the initial induction of DIF competence, cAMP becomes a repressor of prestalk gene expression. This function can again be mediated by cAR1, cAR2, and cAR3.

Adenosine↗

Gonadotropins affect Oct-4 gene expression during mouse oocyte growth.

The transcription factor Oct-4 is required for the maintenance of stem cells pluripotency and is involved in the regulation of the expression of a number of developmental genes. Oct-4 is also expressed in the female gamete during folliculogenesis, but the role it plays is largely unknown. Its upstream and promoter regions have some characteristic features that make this gene a possible target of hormonal regulation. To further our understanding of Oct-4 gene expression during oocyte growth, we tested whether changes to the hormonal milieu of the ovary may affect its transcription. Using a semi-quantitative single-cell-sensitive reverse transcription-polymerase chain reaction (RT-PCR) assay, we investigated the pattern of Oct-4 expression during mouse oocyte growth in females intraperitoneally injected with pregnant mare serum gonadotropin (PMSG) alone or PMSG followed by human chorionic gonadotropin (hCG). The results of this study show that gonadotropins induced two major increases in Oct-4 expression during folliculogenesis: (1) 48 hr after PMSG injection, in oocytes isolated from primordial follicles; and (2) following a surge of hCG, in preovulatory antral oocytes. These results suggest a potential twofold role for this gene in the recruitment of oocytes for initiating growth and in the selection of oocytes for ovulation. Also, they may contribute to our knowledge of the molecular bases of oocyte growth, meiosis resumption, and acquisition of a developmental competence.

Animals↗

Mutation of the SPS1-encoded protein kinase of Saccharomyces cerevisiae leads to defects in transcription and morphology during spore formation.

During sporulation of Saccharomyces cerevisiae, meiosis is followed by encapsulation of haploid nuclei within multilayered spore walls. Completion of the late events of the sporulation program requires the SPS1 gene. This developmentally regulated gene, which is expressed as cells are nearing the end of meiosis, encodes a protein with homology to serine/threonine protein kinases. The catalytic domain of Sps1 is 44% identical to the kinase domain of yeast Ste20, a protein involved in the pheromone-induced signal transduction pathway. Cells of a MATa/MAT alpha sps1/sps1 strain arrest after meiosis and fail to activate genes that are normally expressed at a late time of sporulation. The mutant cells do not form refractile spores as assessed by phase-contrast microscopy and do not display the natural fluorescence and ether resistance that is characteristic of mature spores. Examination by electron microscopy reveals, however, that prospore-like compartments form in some of the mutant cells. These immature spores lack the cross-linked surface layer that surrounds wild-type spores and are more variable in size and number than are the spores of wild-type cells. Despite their inability to complete spore formation, sps1-arrested cells are able to resume mitotic growth on transfer to rich medium, generating haploid progeny. Our results suggest that the developmentally regulated Sps1 kinase is required for normal progression of transcriptional, biochemical, and morphological events during the later portion of the sporulation program.

Amino Acid Sequence↗

Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics.

A model was built to examine the kinetics of regulatory cascades such as occur in developmental gene networks. The model relates occupancy of cis-regulatory target sites to transcriptional initiation rate, and thence to RNA and protein output. The model was used to simulate regulatory cascades in which genes encoding transcription factors are successively activated. Using realistic parameter ranges based on extensive earlier measurements in sea urchin embryos, we find that transitions of regulatory states occur sharply in these simulations, with respect to time or changing transcription factor concentrations. As is often observed in developing systems, the simulated regulatory cascades display a succession of gene activations separated by delays of some hours. The most important causes of this behavior are cooperativity in the assembly of cis-regulatory complexes and the high specificity of transcription factors for their target sites. Successive transitions in state occur long in advance of the approach to steady-state levels of the molecules that drive the process. The kinetics of such developmental systems thus depend mainly on the initial output rates of genes activated in response to the advent of new transcription factors.

Animals↗

Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks.

The Spdeadringer (Spdri) gene encodes an ARID-class transcription factor not previously known in sea urchin embryos. We show that Spdri is a key player in two separate developmental gene regulatory networks (GRNs). Spdri is expressed in a biphasic manner, first, after 12 h and until ingression in the skeletogenic descendants of the large micromeres; second, after about 20 h in the oral ectoderm, where its transcripts remain present at 30-50 mRNA molecules/cell far into development. In both territories, the periods of Spdri expression follow prior territorial specification events. The functional significance of each phase of expression was assessed by determining the effect of an alphaSpdri morpholino antisense oligonucleotide (MASO) on expression of 17 different mesodermal genes, 8 different oral ectoderm genes, and 18 other genes expressed specifically during endomesoderm specification. These effects were measured by quantitative PCR, supplemented by whole-mount in situ hybridization and morphological observations. Spdri is shown to act in the micromere descendants in the pathways that result in the expression of batteries of terminal skeletogenic genes. But, in the oral ectoderm, the same gene participates in the central GRN controlling oral ectoderm identity. Spdri is linked in the oral ectoderm GRN with several other genes encoding transcriptional regulators that are expressed specifically in various regions of the oral ectoderm. If its expression is blocked by treatment with alphaSpdri MASO, oral-specific features disappear and expression of the aboral ectoderm marker spec1 encompasses the whole of the ectoderm. In addition to disappearance of the oral ectoderm, morphological consequences of alphaSpdri MASO treatment include failure of spiculogenesis and of correct primary mesenchyme cell (pmc) patterning in the postgastrular embryo, and also failure of gastrulation. To further analyze these phenotypes, chimeric embryos were constructed consisting of two labeled micromeres combined with micromereless 4th cleavage host embryos; either the micromeres or the hosts contained alphaSpdri MASO. These experiments showed that, while Spdri expression is required autonomously for expression of skeletogenic genes prior to ingression, complete skeletogenesis also requires the expression of oral ectoderm patterning information. Presentation of this information on the oral side of the blastocoel in turn depends on Spdri expression in the oral ectoderm. Failure of gastrulation is not due to indirect interference with endomesodermal specification per se, since all endomesodermal genes tested function normally in alphaSpdri MASO embryos. Part of its cause is interference by alphaSpdri MASO with a late signaling function on the part of the micromere descendants that is needed to complete clearance of the Soxb1 repressor of gastrulation from the prospective endoderm, but in addition there is a nonautonomous oral ectoderm effect.

Amino Acid Sequence↗

Galpha3 and protein kinase A represent cross-talking pathways for gene expression in Dictyostelium discoideum.

Heterotrimeric G proteins and protein kinase A (PKA) are regulators of development in Dictyostelium discoideum. It has been reported that disruption of the Dictyostelium Galpha3 gene (galpha3-) blocks development and expression of several early development genes, characteristics that are reminiscent of mutants lacking the catalytic subunit of PKA (pkac-). The hypothesis that Galpha3 and PKA signaling pathways may interact to control developmental gene expression was tested by comparing the regulation of seven genes expressed early in development in the wild-type and in galpha3- and pkac- mutants, and comparing PKA activity in the wild-type and in a galpha3- mutant. The expression patterns of six genes were affected similarly by the Galpha3 and PKA mutations, while the expression of only one gene, the cAMP receptor 1 (cAR1), differed between the mutants. PKA activity, measured by phosphorylation of the PKA-specific substrate Kemptide, was higher in galpha3- cells than in wild-type cells, suggesting that Galpha3 normally exerts an inhibitory effect on PKA activity. Although some early development genes appear to require both Galpha3 and PKA for expression, the differing response of cAR1 expression and the inhibitory effect of Galpha3 on PKA activity suggest that Galpha3 and PKA are members of interacting pathways controlling gene expression early in development.

Animals↗

Characterization of genes that are developmentally regulated during Dictyostelium discoideum spore germination.

Similar to other stages in Dictyostelium development, spore germination is a particularly suitable model for studying the regulation of gene expression, because developmentally regulated changes in both protein and mRNA synthesis occur during the transition from dormant spore to amoeba. Spores are constitutively dormant and must be activated to germinate. Under the proper environmental conditions, spores germinate in a highly synchronous manner to give rise to individual amoebae that can then enter the vegetative growth phase. Protein synthesis is developmentally regulated during this process. Because protein synthesis is transcriptionally controlled during spore germination, the respective genes must be developmentally transcribed, and these can be isolated and analyzed. Three cDNA clones specific for mRNA developmentally regulated during spore germination have been characterized and used as probes to study mRNA accumulation and decay during spore germination. Because we are interested in defining the sequences of developmentally regulated genes that may relate to their regulation of transcription, we have sequenced the cDNAs and have isolated and sequenced their respective genomic clones. The sequences of the three gene families, their genomic organization, and their special structural features are described.

Amino Acid Sequence↗

Expression of natriuretic peptide system during embryonic stem cell vasculogenesis.

The natriuretic peptide family consists of atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and C-type natriuretic peptide (CNP). We have elucidated that CNP is synthesized by endothelial cells. We have also shown that CNP secretion is potently suppressed by vascular endothelial growth factor (VEGF). In the present study, we examined the developmental gene expression of the natriuretic peptide system with the expression of VEGF and endothelial cell-specific receptor tyrosine kinases (RTKs), which expression is necessary for vasculogenesis, using embryoid bodies (EB) as an in vitro model for vascular development. When mouse embryonic stem (ES) cells were cultured in suspension culture, ES cells spontaneously differentiated into EB on day 4 and then into cystic EB (day 10). The VEGF gene transcript was detected early, on day 4. The expression of Flk-1, and flt-1 (the two VEGF receptors) and also of tie-2, which is crucial for blood island formation, was detected as early as day 4, and also on days 8 and 21. In contrast, the expression of flt-4, the receptor for VEGF-C, and tie-1, was first detected on day 21. Along with the developmental expression of these markers of differentiation for endothelial cells, the gene expression of CNP and its specific receptor, ANP-B receptor, was detected on days 4, 8, and 21. In contrast, the gene expression of BNP, which acts as a cardiac hormone, and the gene expression of the ANP-A receptor, which is specific to ANP and BNP, was first detected on days 8 and 21, respectively. These results indicate the distinct role of CNP in the natriuretic peptide family and the close linkage of CNP expression and endothelial cell differentiation, suggesting a possible role of CNP in vasculogenesis.

Animals↗

Molecular determinants of mammmalian sex.

Mammalian male sex determination is controlled by a complex hierarchy of gene regulatory proteins and hormones, which promote male gonadal development and regression of the female primordia. At the core of this pathway lies the SRY protein, the master developmental switch for testicular differentiation and hence, the male sex. The three-dimensional structure of the SRY-DNA complex suggests a model of developmental gene regulation in which proteins that alter DNA structure and promote the assembly of higher-order nucleoprotein complexes play an essential role in the timing of cell specialization events.

Animals↗

Antisense attenuation of Wnt-1 and Wnt-3a expression in whole embryo culture reveals roles for these genes in craniofacial, spinal cord, and cardiac morphogenesis.

Wnt-1 and Wnt-3a proto-oncogenes have been implicated in the development of midbrain and hindbrain structures. Evidence for such a role has been derived from in situ hybridization studies showing Wnt-1 and -3a expression in developing cranial and spinal cord regions and from studies of mutant mice whose Wnt-1 genes have undergone targeted disruption by homologous recombination. Wnt-1 null mutants exhibit cranial defects but no spinal cord abnormalities, despite expression of the gene in these regions. The absence of spinal cord abnormalities is thought to be due to a functional compensation of the Wnt-1 deficiency by related genes, a problem that has complicated the analysis of null mutants of other developmental genes as well. Herein, we describe the attenuation of Wnt-1 expression using antisense oligonucleotide inhibition in mouse embryos grown in culture. We induce similar mid- and hindbrain abnormalities as those seen in the Wnt-1 null mutant mice. Attenuation of Wnt-1 expression was also associated with cardiomegaly resulting in hemostasis. These findings are consistent with the possibility that a subset of Wnt-1 expressing cells include neural crest cells known to contribute to septation of the truncus arteriosus and to formation of the visceral arches. Antisense knockout of Wnt-3a, a gene structurally related to Wnt-1, targeted the forebrain and midbrain region, which were hypoplastic and failed to expand, and the spinal cord, which exhibited lateral outpocketings at the level of the forelimb buds. Dual antisense knockouts of Wnt-1 and Wnt-3a targeted all brain regions leading to incomplete closure of the cranial neural folds, and an increase in the number and severity of outpocketings along the spinal cord, suggesting that these genes complement one another to produce normal patterning of the spinal cord. The short time required to assess the mutant phenotype (2 days) and the need for limited sequence information of the target gene (20-25 nucleotides) make this antisense oligonucleotide/whole embryo culture system ideal for testing the importance of specific genes and their interactions in murine embryonic development.

Animals↗

Role of phospholipase C in Dictyostelium: formation of inositol 1,4,5-trisphosphate and normal development in cells lacking phospholipase C activity.

The micro-organism Dictyostelium uses extracellular cAMP to induce chemotaxis and cell differentiation. Signals are transduced via surface receptors, which activate G proteins, to effector enzymes. The deduced protein sequence of Dictyostelium discoideum phosphatidylinositol-specific phospholipase C (PLC) shows strong homology with the mammalian PLC-delta isoforms. To study the role of PLC in Dictyostelium, a plc- mutant was constructed by disruption of the PLC gene. No basal or stimulated PLC activity could be measured during the whole developmental programme of the plc- cells. Loss of PLC activity did not result in a visible alteration of growth or development. Further analysis showed that developmental gene regulation, cAMP-mediated chemotaxis and activation of guanylyl and adenylyl cyclase were normal. Although the cells lack PLC activity, inositol 1,4,5-trisphosphate [Ins(1,4,5)P3] was present at only slightly lower concentrations compared with control cells. Mass analysis of inositol phosphates demonstrated the presence of a broad spectrum of inositol phosphates in Dictyostelium, which was unaltered in the plc- mutant. Cell labelling experiments with [3H]inositol indicated that [3H]Ins(1,4,5)P3 was formed in a different manner in the mutant than in control cells.

Animals↗

Plant development: the benefits of a change of scene.

Multicellular organisms are composed of groups of different cell types. The importance in the evolution of cellular diversity of regulatory changes in genes that control cell specification has been revealed by a recent study of developmental genes in Arabidopsis.

Animals↗

Interaction of an embryo DNA binding protein with a soybean lectin gene upstream region.

Seed protein genes are highly regulated during the soybean life cycle. These genes encode prevalent mRNAs that accumulate and decay during embryogenesis, and are either undetectable or present at low levels in mature plant organ systems. Transcriptional activation and repression processes are important in regulating seed protein gene developmental expression programs. We started DNA binding protein studies with the soybean lectin gene to begin to identify trans-acting proteins and cis-regulatory sequences required for seed protein gene expression. We have identified an embryo DNA binding protein that interacts with specific sequences in the lectin gene 5' region. The DNA binding protein is undetectable in mature plant organ systems and its concentration parallels the lectin gene transcription rate during embryogenesis. The DNA binding protein activity corresponds to a 60,000 Mr (60K) nuclear protein, and a protein of similar size interacts with at least one other seed protein gene but not with a gene inactive during embryogenesis. Our data suggest that the 60K protein, and the DNA sequences that it interacts with, may be involved in regulating lectin gene expression.

Base Sequence↗

Identification of potential genes regulated by DNA methyltransferase 3B in a hepatocellular carcinoma cell line by RNA interference and microarray analysis.

Whether DNA methyltransferase 3B (DNMT3B) is deregulated in hepatocellular carcinoma cell lines is still unclear. The expression levels of DNMT3B protein in normal liver cell line, pericacinoma cell line and hepatocellular carcinoma cell lines were compared by both Western blotting and immunocytochemistry. Long-term downregulated DNMT3B in a hepatocellular carcinoma cell line SMMC-7721 was achieved using a RNAi recombinant plasmid. The suppression of DNMT3B induced by RNA interference was confirmed using semi-quantitative RT-PCR and Western blotting. High throughput cDNA microarray was used to analyze the expression profiling of downstream genes of DNMT3B displayed in the treated cell lines and control. In the result,DNMT3B in hepatocellular carcinoma cell lines was expressed at a significantly higher level compared to those in pericacinoma cell line and normal liver cell line. A specific DNMT3B siRNA stably expressed from a plasmid vector effectively suppressed the expression of DNMT3B in SMMC-7721 cell line. By microarray analysis,26 downregulated genes and 115 upregulated genes have been identified in the DNMT3B knockdown cell line,including some important developmental genes and tumor-related genes such as SNCG, NOTCH1, MBD3, WNT11, MAOA and FACL4. The discovery showed DNMT3B was over-expressed in most hepatocellular carcinoma cell lines examined and may be linked to the carcinogenesis of hepatocytes. An array of candidate genes that are involved in the action of DNMT3B have been identified,including those related to development.

Carcinoma, Hepatocellular↗

Gene expression in Dictyostelium discoidium: mutually antagonistic roles of cyclic-AMP and ammonia.

Cyclic-AMP and ammonia have been previously identified as extracellular signals during Dictyostelium development. Both are important in controlling morphological movements and cyclic-AMP also in inducing gene expression. The work in tis paper is concerned with their effects on developmental gene expression. Cyclic-AMP was found to act as an inducer during the aggregative (as exemplified by phosphodiesterase) and the post-aggregative (glycogen phosphorylase, UDP-galactose polysaccharide transferase, prespore vacuoles and stalk cells) phases of gene expression. Ammonia inhibited the appearance of each of the above markers and antagonized the inductive effects of cyclic-AMP on them. This inhibition by ammonia of cyclic-AMP inducible gene expression may involve a step linking elevated intracellular cyclic-AMP levels to gene activation. It has been suggested that the specification of cells within the aggregate into the stalk and spore pathways of differentiation might be controlled by cyclic-AMP and ammonia. In this model for pattern formation cyclic-AMP would induce stalk cell differentiation and ammonia spore formation. The present results argue against this idea since cyclic-AMP induces and ammonia inhibits differentiation along both pathways. The function of these agents may rather be to coordinate the rates of biochemical differentiation of individual cells and link them to the overall morphological changes occurring during development.

3',5'-Cyclic-AMP Phosphodiesterases↗