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At least 595 records · Page 33Linked to original sources
PubMed1997

A knowledge base for D. melanogaster gene interactions involved in pattern formation.

The understanding of pattern formation in Drosophila requires the handling of the many genetic and molecular interactions which occur between developmental genes. For that purpose, a knowledge base (KNIFE) has been developed in order to structure and manipulate the interaction data. KNIFE contains data about interactions published in the literature and gathered from various databases. These data are structured in an object knowledge representation system into various interrelated entities. KNIFE can be browsed through a WWW interface in order to select, classify and examine the objects and their references in other bases. It also provides specialised biological tools such as interaction network manipulation and diagnosis of missing interactions.

Animals↗
PubMed1998

Anterior specification of embryonic ectoderm: the role of the Xenopus cement gland-specific gene XAG-2.

In a search for novel developmental genes expressed in a spatially restricted pattern in dorsal ectoderm of Xenopus we have identified XAG-2, a cement gland-specific gene with a putative role in ectodermal patterning. XAG-2 encodes a secreted protein, which is expressed in the anterior region of dorsal ectoderm from late gastrula stages onwards. Activation of XAG-2 transcription is observed in response to organizer-secreted molecules including the noggin, chordin, follistatin and cerberus gene products. Overexpression of XAG-2 but not of the related cement gland marker XAG-1 induces both cement gland differentiation and expression of anterior neural marker genes in the absence of mesoderm formation. Further, we show that XAG-2 signaling depends on an intact fibroblast growth factor (FGF) signal transduction pathway and that XAG-2-induced anterior neural fate of ectodermal cells can be transformed to a more posterior character by retinoic acid. Based on these findings we propose a role for XAG-2 in the specification of dorsoanterior ectodermal fate, i.e. in the formation of cement gland and induction of forebrain fate of Xenopus.

Amino Acid Sequence↗
PubMed1997

A sex-influenced modifier in Drosophila that affects a broad spectrum of target loci including the histone repeats.

A second chromosomal trans-acting modifier, Lightener of white (Low), modulates the phenotypic expression of various alleles of the white eye color gene. This modifier has an unusually broad spectrum of affected genes including white, brown, scarlet and the eye developmental genes, Bar and Lobe. In addition, Low weakly suppresses position effect variegation. Northern blot hybridization with different X and autosomal probes reveals that Low modulates genes of independent expression patterns. Interestingly, many of the modulations of gene expression are developmentally restricted and differ in intensity between the sexes. Low also elevates the expression of the histone tandem repeats in three distinct developmental stages. A deficiency encompassing the histone cluster reduces their transcript levels and significantly alters the expression of some of the tested genes. Thus, Low is a modifier that plays a role in modulating the expression of genes governing various processes including pigment deposition, eye development, chromosomal proteins and position effect variegation.

Alleles↗
PubMed2003

Characterization of PTM5 in aspen trees: a MADS-box gene expressed during woody vascular development.

The vascular component of trees possesses some of the most specialized processes active in the formation of roots, stems, and branches, and its wood component continues to be of primary importance to our daily lives. The molecular mechanisms of wood development, however, remain poorly understood with few well-characterized regulatory genes. We have identified a vascular tissue-specific MADS-box gene, Populus tremuloides MADS-box 5 (PTM5) that is expressed in differentiating primary and secondary xylem and phloem. Phylogenetic analysis has shown that PTM5 is a member of the SOC1/TM3 class of MADS-box genes. Temporal expression analysis of PTM5 in staged vascular cambium and other tissues indicated that PTM5 expression is seasonal and is limited to spring wood formation and rapidly expanding floral catkins. Spatial expression analysis using in situ hybridization revealed that PTM5 expression is localized within a few layers of differentiating vascular cambium and xylem tissues as well as the vascular bundles of expanding catkins. Since many MADS-box genes are known to act as transcription factors, these results suggest that the coordinated expression of PTM5 with other vascular developmental genes may be a hallmark of the complex events that lead to the formation of the woody plant body.

Amino Acid Sequence↗
PubMed2003

Spatiotemporal patterns of gene expression during fetal monkey brain development.

Human DNA microarrays are used to study the spatiotemporal patterns of gene expression during the course of fetal monkey brain development. The 444 most dynamically expressed genes in four major brain areas are reported at five different fetal ages. The spatiotemporal profiles of gene expression show both regional specificity as well as waves of gene expression across the developing brain. These patterns of expression are used to identify statistically significant clusters of co-regulated genes. This study demonstrates for the first time in the primate the relevance, timing, and spatial locations of expression for many developmental genes identified in other animals and provides clues to the functions of many unknowns. Two different microarray platforms are used to provide high-throughput cross validation of the most important gene expression changes. These results may lead to new understanding of brain development and new strategies for treating and repairing disorders of brain function.

Animals↗
PubMed2001

Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis.

The duplication and divergence of developmental control genes is thought to have driven morphological diversification during the evolution of multicellular organisms. To examine the molecular basis of this process, we analyzed the functional relationship between two paralogous MYB transcription factor genes, WEREWOLF (WER) and GLABROUS1 (GL1), in Arabidopsis. The WER and GL1 genes specify distinct cell types and exhibit non-overlapping expression patterns during Arabidopsis development. Nevertheless, reciprocal complementation experiments with a series of gene fusions showed that WER and GL1 encode functionally equivalent proteins, and their unique roles in plant development are entirely due to differences in their cis-regulatory sequences. Similar experiments with a distantly related MYB gene (MYB2) showed that its product cannot functionally substitute for WER or GL1. Furthermore, an analysis of the WER and GL1 proteins shows that conserved sequences correspond to specific functional domains. These results provide new insights into the evolution of the MYB gene family in Arabidopsis, and, more generally, they demonstrate that novel developmental gene function may arise solely by the modification of cis-regulatory sequences.

Amino Acid Sequence↗
PubMed1995

An insertional mutation in the BTF3 transcription factor gene leads to an early postimplantation lethality in mice.

The gene that encodes the general transcription factor known as BTF3 was disrupted in mouse embryonic stem cells in a random mutagenesis screen for developmental genes with the ROSA beta-geo (Friedrich and Soriano, 1991) retroviral gene trap vector. The BTF3 mutation was transmitted through the germline of chimaeric mice. While the endogenous BTF3 gene is ubiquitously expressed, the expression pattern of the beta-galactosidase reporter gene present in the gene trap vector in BTF3 heterozygotes was restricted. Mice homozygous for the mutant allele died soon after implantation, around embryonic day 6.5. Thus, BTF3 is essential for postimplantation development. The isolation of the BTF3 sequences in this ROSA beta-geo insertion was facilitated by a relatively simple single lacZ primer reverse transcription PCR strategy.

Animals↗
PubMed2002

Regulation of alpha-fetoprotein expression by Nkx2.8.

The alpha-fetoprotein (AFP) gene is an important model of developmental gene silencing and neoplastic gene reactivation. Nkx2.8 is a divergent homeodomain factor originally cloned through its binding to the promoter-coupling element (PCE), a regulatory region upstream of the AFP promoter that mediates stimulation by distant enhancers. Nkx2.8 is the only developmentally regulated factor that has been associated with AFP gene expression. Fetoprotein transcription factor, an orphan nuclear receptor, has also been shown to bind the PCE but is not developmentally regulated. The binding specificities of both families of transcription factor were determined, and overlapping sites for each were defined in the PCE. After modification of nuclear extract and gel shift analysis procedures, Nkx2.8 was identified in six AFP-positive cell lines. Transient-transfection analysis did not show transcriptional stimulation by Nkx2.8 or other active NK2 factors, which only interfered with gene expression. However, two sets of analysis demonstrated the relationship of Nkx2.8 to AFP expression: chromatin immunoprecipitation demonstrated that Nkx2.8 bound to the active AFP promoter, and antisense inhibition of Nkx2.8 mRNA translation selectively reduced expression of both the endogenous human AFP gene and transfected reporters containing the rat AFP promoter.

Animals↗
PubMed2000

Conserved and divergent genes in apex and axis development of cnidarians.

Despite their radial organization and their sister group position in the life tree, cnidarian species express during morphogenesis a large number of genes that are related to bilaterian developmental genes. Among those, homologs to forkhead, emx, aristaless, goosecoid, brachyury, wnt and nanos genes are regulated during apical patterning in cnidarians, suggesting that key components of early organizer activity were conserved across evolution and recruited for either anterior, axial, or dorso-ventral patterning in bilaterians. In contrast, the expression patterns of the cnidarian Hox-related genes suggest that the apical-basal axis of the cnidarian polyp and the anterior-posterior axis of bilaterians do not differentiate following homologous processes.

Animals↗
PubMed1997

The hardwiring of development: organization and function of genomic regulatory systems.

The gene regulatory apparatus that directs development is encoded in the DNA, in the form of organized arrays of transcription factor target sites. Genes are regulated by interactions with multiple transcription factors and the target sites for the transcription factors required for the control of each gene constitute its cis-regulatory system. These systems are remarkably complex. Their hardwired internal organization enables them to behave as genomic information processing systems. Developmental gene regulatory networks consist of the cis-regulatory systems of all the relevant genes and the regulatory linkages amongst them. Though there is yet little explicit information, some general properties of genomic regulatory networks have become apparent. The key to understanding how genomic regulatory networks are organized, and how they work, lies in experimental analysis of cis-regulatory systems at all levels of the regulatory network.

Animals↗
PubMed2004

Targeted inactivation of serum response factor in the developing heart results in myocardial defects and embryonic lethality.

Serum response factor (SRF) is at the confluence of multiple signaling pathways controlling the transcription of immediate-early response genes and muscle-specific genes. There are active SRF target sequences in more than 50 genes expressed in the three muscle lineages including normal and diseased hearts. However, the role of SRF in heart formation has not been addressed in vivo thus far due to the early requirement of SRF for mesoderm formation. We have generated a conditional mutant of SRF by using Cre-LoxP strategy that will be extremely useful to study the role of SRF in embryonic and postnatal cardiac functions, as well as in other tissues. This report shows that heart-specific deletion of SRF in the embryo by using a new beta MHC-Cre transgenic mouse line results in lethal cardiac defects between embryonic day 10.5 (E10.5) and E13.5, as evidenced by abnormally thin myocardium, dilated cardiac chambers, poor trabeculation, and a disorganized interventricular septum. At E9.5, we found a marked reduction in the expression of essential regulators of heart development, including Nkx2.5, GATA4, myocardin, and the SRF target gene c-fos prior to overt maldevelopment. We conclude that SRF is crucial for cardiac differentiation and maturation, acting as a global regulator of multiple developmental genes.

Animals↗
PubMed1997

Evolutionary origins and maintenance of redundant gene expression during metazoan development.

Various levels of redundancy in developmental gene function appear common in complex metazoans. There might be no apparent phenotype at many, or even any, of a gene's specific expression sites in homozygous null mutant embryos. Here we ask what underlies the origin of such arrangements. The generation of families of genes by duplication has clearly been important. Additionally, however, selection might have driven molecularly unrelated genes, which encode proteins of similar physiological function, to become expressed during the same sets of developmental events (times and places), even though each such gene might initially have evolved in connection with just one of these events.

Animals↗
PubMed1984

Developmental expression of the rat somatostatin gene.

The developmental expression of the somatostatin (SRIF) gene was investigated in rat brain and stomach, two SRIF-rich tissues. The accumulation of mRNA encoding SRIF was determined in these organs during fetal and early (1-4 weeks) postnatal development using a sensitive radiodensitometric cDNA hybridization assay and a cloned preprosomatostatin cDNA. A single band of mRNA which hybridized specifically to the rat SRIF cDNA was detected in both tissues examined throughout ontogenesis, suggesting that the same SRIF gene is expressed in these tissues in the developing as well as in the adult rat. Whereas SRIF mRNA was undetectable in fetal stomach and rose gradually only after birth, brain SRIF mRNA was already detectable by day 7 of embryonic life and reached concentrations corresponding to those in the adult brain by embryonic day 20. These marked differences may reflect basic differences in the developmental regulation of SRIF gene expression in neural vs. nonneural tissues or may be related to the onset of functional activity in the organs studied.

Aging↗
PubMed2005

Transgenic models for studying expression and function of axonal adhesive glycoproteins.

In this study, by using two transgenic models, we address the general topic of the significance of axonal glycoproteins regulated expression in nervous tissue maturation. The immunoglobulin superfamily components F3/Contactin (F3) and TAG-1 are used as the molecular models in this respect. First, a minigene including the relevant regulatory sequences of the F3 gene, deduced by a previous in vitro study, has been fused to an EGFP (Enhanced Green Fluorescent Protein) reporter and expressed in transgenic mice, which provided information about the profile of F3 gene developmental activation. In a complementary model, transgenic mice have been generated which express the F3 cDNA under control of a selected regulatory region from the TAG-1 gene. While leading to ectopic expression of F3, this perturbed neuronal precursor proliferation and differentiation. The arising effects were even stronger than those coming from the overall suppression of the F3 or, respectively, TAG-1 genes, thus supporting the hypothesis that the mechanisms underlying axonal glycoprotein regulated expression are themselves endowed with a key significance in neural development.

Animals↗
PubMed2000

The molecular basis for developmental disorders of the pituitary gland in man.

The development of the anterior pituitary gland is dependent upon a cascade of signalling molecules and developmental genes that function as transcription factors. Many of these genes are homeobox genes which contain a DNA-binding region or homeobox. Animal models have given a valuable insight into human pituitary disease. For example, Pit-1 and Prop1 mutants are known to have deficiencies of growth hormone, prolactin and thyroid-stimulating hormone. Human phenotypes arising as a result of mutations in these genes are similar to the mouse mutants. Mutations in the novel homeobox gene Hesx1/HESX1 are associated with the highly variable phenotype of septo-optic dysplasia in mouse and man. The unravelling of this complex developmental cascade is just commencing.

Animals↗
PubMed1992

The homeodomain: a new face for the helix-turn-helix?

The discovery of conserved protein domains found in many Drosophila and mammalian developmental gene products suggests that fundamental developmental processes are conserved throughout evolution. Our understanding of development has been enhanced by the discovery of the widespread role of the homeodomain (HD). The action of HD-containing proteins as transcriptional regulators is mediated through a helix-turn-helix motif which confers sequence specific DNA binding. Unexpectedly, the well conserved structural homology between the HD and the prokaryotic helix-turn-helix proteins contrasts with their divergent types of physical interaction with DNA. A C-terminal extension of the HD recognition helix has assumed the role that the N-terminus of the prokaryotic helix plays for specification of DNA binding preference. However, the HD appears also capable of recognizing DNA in an alternative way and its specificity in vivo may be modified by regions outside the helix-turn-helix motif. We propose that this intrinsic complexity of the HD, as well as its frequent association with other DNA binding domains, explains the functional specificity achieved by genes encoding highly related HDs.

Amino Acid Sequence↗
PubMed1989

Chromosomal rearrangement generating a composite gene for a developmental transcription factor.

Differential gene expression in the mother cell chamber of sporulating cells of Bacillus subtilis is determined in part by an RNA polymerase sigma factor called sigma K (or sigma 27). The sigma K factor was assigned as the product of the sporulation gene spoIVCB on the basis of the partial aminoterminal amino acid sequence of the purified protein. The spoIVCB gene is now shown to be a truncated gene capable of specifying only the amino terminal half of sigma K. The carboxyl terminal half is specified by another sporulation gene, spoIIIC, to which spoIVCB becomes joined inframe at an intermediate stage of sporulation by site-specific recombination within a 5-base pair repeated sequence. Juxtaposition of spoIVCB and spoIIIC need not be reversible in that the mother cell and its chromosome are discarded at the end of the developmental cycle. The rearrangement of chromosomal DNA could account for the presence of sigma K selectively in the mother cell and may be a precedent for the generation of cell type-specific regulatory proteins in other developmental systems where cells undergo terminal differentiation.

Amino Acid Sequence↗
PubMed2006

Transcriptional profiling endometrial carcinomas microdissected from DES-treated mice identifies changes in gene expression associated with estrogenic tumor promotion.

Exposure to unopposed estrogen is a potent risk factor for developing human endometrial cancer. However, little is known about the transcriptional changes elicited by estrogens in endometrial carcinogenesis, in part, because of genetic and environmental heterogeneity of human tumors. We have begun to chart the expression signatures of endometrial tumors promoted with the synthetic estrogen, diethylstilbestrol (DES), in inbred mice. As expected, laser-capture-microdissected endometrial cancers from DES-treated mice displayed a large number of transcriptional changes when compared to uninvolved endometrial epithelium. Genes differentially expressed in carcinomas included cell adhesion and extracellular matrix genes (Decorin as 1 example), developmental genes (Hoxa11), and cytokine signaling genes (Socs3). The DES-promoted carcinomas appeared to fall into 2 distinct transcriptional classes, and expression of the tumor suppressor Pten was among the top discriminators between the 2 cancer groups. Pten was down regulated in the majority of the DES-promoted carcinomas, which is analogous to the frequent loss of PTEN expression in human endometrial tumors. Although preliminary, these observations suggest that the cancers that arise in the DES model bear similarities to human endometrial cancers and provide insights into transcriptional alterations that accompany estrogen-driven endometrial carcinogenesis.

Animals↗