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PubMed1990

Molecular cloning of cDNAs for auxin-induced mRNAs and developmental expression of the auxin-inducible genes.

By differential hybridization, two auxin-inducible cDNA clones (lambda SAR1 and lambda SAR2) have been isolated from a cDNA library constructed to poly(A)+ mRNA from auxin-treated strawberry receptacles. Both the clones have been used as probes to study the expression of the auxin-induced genes in pollinated and unpollinated fruits of various stages of development and in different organs. A high level of auxin-induced mRNAs is found in pollinated fruits as compared to unpollinated fruits of the same age, suggesting that the expression of the auxin-induced genes is developmentally regulated and the level of auxin-induced mRNAs is regulated by endogenous auxin. Furthermore, our data on the expression of lambda SAR1 and lambda SAR2 genes in pollinated and unpollinated fruits revealed a positive correlation between growth of strawberry fruit and the induction of mRNA corresponding to the lambda SAR1 and lambda SAR2 clones. Ethylene has no effect on the expression of the auxin-induced mRNAs. lambda SAR1 mRNA is not detected in other parts of strawberry plants whereas lambda SAR2 mRNA is present in roots. Furthermore, mRNA corresponding to lambda SAR1 and lambda SAR2 is not detected in other auxin-responsive plant systems such as pea epicotyls and bean explants.

Cloning, Molecular↗
PubMed2003

DNA methylation and expression of major histocompatibility complex class I and class II transactivator genes in human developmental tumor cells and in T cell malignancies.

Major histocompatibility complex (MHC) class I and class II molecules play essential roles in the immune response by virtue of their ability to present peptides to T lymphocytes. Given their central role in adaptive immunity, the genes encoding these peptide-presenting molecules are regulated in a tight fashion to meet with local requirements for an adequate immune response. In contrast to MHC class I gene products, which are expressed on almost all nucleated cells, constitutive expression of MHC class II molecules is found in specialized antigen presenting cells of the immune system only. Transcription of both MHC class I and class II genes can be induced by immune regulators and upon cell activation. Transcription of MHC class I genes is mediated by a set of conserved cis acting regulatory elements in their promoters. Of these regulatory elements, MHC class II promoters share the SXY-module. Essential for activation of MHC class II promoters is the class II transactivator (CIITA), which acts through protein/protein interactions with regulatory factors bound to the SXY module. In this review, we discuss the role of DNA methylation in relation to altered expression of MHC class I and CIITA genes as observed in malignancies and in development.

Chromatin↗
PubMed1980

Molecular analysis of a gene in a developmentally regulated puff of Drosophila melanogaster.

An increase in the concentration of the steroid hormone ecdysone in late larval life triggers a profound change in the pattern of polytene chromosome puffs in the Drosophila melanogaster salivary gland. One of the preexisting puffs that regress as the ecdysone concentration increases is located at the 3C11-12 bands, the site of the Sgs-4 gene, which codes for the sgs-4 protein, one of the proteins in the salivary glue secretion. We have isolated cloned segments of chromosomal DNA that define a 60-kilobase region containing the 0.9-kilobase Sgs-4 gene, and we have determined its position and orientation within this region. Fine structure restriction endonuclease mapping shows that approximately 45% of this gene consists of tandemly repeated sequences of 21 base pairs that occupy most of its 5' half, indicating that most of the amino-terminal half of the sgs-4 protein consists of tandemly repeated amino acid sequences of seven residues. We also report on the amount of the Sgs-4 mRNA as a function of developmental stage and in nine different strains, four of which produce little or no sgs-4 protein. Three of the null strains produce minute amounts of the mRNA and one yields none, whereas the five sgs-4 producing strains yield abundant amounts. The mRNAs frm these strains exhibit different lengths, which correlate with different gene lengths that appear to result from different numbers of the repeated sequences in their tandem arrays.

Animals↗
PubMed2002

Identification of a hydrophobin gene that is developmentally regulated in the ectomycorrhizal fungus Tricholoma terreum.

The symbiosis between ectomycorrhizal fungi and trees is an essential part of forest ecology and depends entirely on the communication between the two partners for establishing and maintaining the relationship. The identification and characterization of differentially expressed genes is a step to identifying such signals and to understanding the regulation of this process. We determined the role of hydrophobins produced by Tricholoma terreum in mycorrhiza formation and hyphal development. A hydrophobin was purified from culture supernatant, and the corresponding gene was identified. The gene is expressed in aerial mycelium and in mycorrhiza. By using a heterologous antiserum directed against a hydrophobin found in the aerial mycelium of Schizophyllum commune, we detected a hydrophobin in the symbiosis between T. terreum and its native pine host Pinus sylvestris. The hydrophobin was found in aerial mycelium of the hyphal mantle and also in the Hartig net hyphae, which form the interface between both partners. Interestingly, this was not the case in the interaction of T. terreum with a host of low compatibility, the spruce Picea abies. The differential expression with respect to host was verified at the transcriptional level by competitive PCR. The differential protein accumulation pattern with respect to host compatibility seen by immunofluorescence staining can thus be attributed at least in part to transcriptional control of the hyd1 gene.

Basidiomycota↗
PubMed1993

The WT1 Wilms tumor gene product: a developmentally regulated transcription factor in the kidney that functions as a tumor suppressor.

Alteration of transcription factor function is becoming a common theme in molecular mechanisms of oncogenesis. A recent example of this trend is the isolation and characterization of the chromosome 11p13 Wilms tumor suppressor gene, WT1. The WT1 protein contains a DNA binding domain consisting of four zinc fingers of the Cys2-His2 class and a proline-glutamine rich region capable of regulating transcription. Deletions of the WT1 gene or point mutations which destroy the DNA binding activity of the protein are associated with the development of the pediatric nephroblastoma Wilms tumor and Denys-Drash syndrome. This article reviews the role of WT1 in normal kidney development processes, the known biochemical functions of the protein and the status of identifying target genes regulated by this potentially oncogenic transcription factor.

Amino Acid Sequence↗
PubMed1998

The M31 gene has a complex developmentally regulated expression profile and may encode alternative protein products that possess diverse subcellular localisation patterns.

HP1-like chromobox genes comprise an evolutionarily conserved family of genes that encode components of centromeric heterochromatin. In order to investigate the role of the murine HP1-like gene, M31, in heterochromatin formation we have isolated its gene and characterised its transcripts and protein products. PCR products that represent M31 transcripts were detected at the one-cell stage and were maternal in origin. Maternal provision of M31 transcripts may reflect a need for M31 in the formation of a functional centromere in order that there is proper segregation of chromosomes during the early cleavage divisions; studies in fission yeast and Drosophila have suggested a crucial role for HP1-like genes in centromere function. There are three protein products encoded by the M31 gene. Surprisingly, the two smaller products are found almost exclusively in the cytoplasm.

Alternative Splicing↗
PubMed1992

Identification of the gene for the developmentally expressed 70 kDa heat-shock protein (P70) of mouse spermatogenic cells.

Mouse spermatogenic cells synthesize a 70-kDa protein (P70) closely related to the major heat-shock protein (hsp70) of mammalian cells (R. L. Allen, D. A. O'Brien, and E. M. Eddy, Mol. Cell. Biol. 8, 828-832, 1988). Expression of P70 is developmentally regulated while hsp70 is induced in response to stress, suggesting that P70 is the product of a unique member of the Hsp70 multigene family transcribed in spermatogenic cells. A strong candidate for this gene was the Hsp70.2 gene (Z. F. Zakeri, D. J. Wolgemuth, and C. R. Hunt, Mol. Cell. Biol. 8, 2925-2932, 1988). A DNA segment from the 5' region of Hsp70.2 hybridized to a 2.7-kb transcript with a temporal pattern of expression in mouse spermatogenic cells similar to the P70 protein. We used a polyclonal antiserum generated against a synthetic peptide predicted from the Hsp70.2 sequence to characterize its protein product and to isolate cDNA clones from a pachytene spermatocyte expression library. The antiserum reacted specifically with meiotic and postmeiotic spermatogenic cells on sections of mouse testis. It recognized the P70 protein on Western blots of two-dimensional gels and did not bind to other heat-shock proteins of spermatogenic or somatic cells. The cDNAs hybridized to a 2.7-kb mRNA that was abundant in unstressed pachytene spermatocytes and round spermatids but was not detected in other cell types. Two cDNAs were sequenced and found to be 99% homologous to the 3' end of the Hsp70.2 gene. These data strongly supported the hypothesis that P70 is the expressed product of the Hsp70.2 gene in mouse spermatogenic cells.

Amino Acid Sequence↗
PubMed2002

Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development.

MOTIVATION: The DNA microarray technology can generate a large amount of data describing the time-course of gene expression. These data, when properly interpreted, can yield a great deal of information concerning differential gene expression during development. Much current effort in bioinformatics has been devoted to the analysis of gene expression data, usually via some 'clustering analysis' on the raw data in some abstract high dimensional space. Here, we describe a method where we first 'process' the raw time-course data using a simple biologically based kinetic model of gene expression. This allows us to reduce the vast data to a few vital attributes characterizing each expression profile, e.g. the times of the onset and cessation of the expression of the developmentally regulated genes. These vital attributes can then be trivially clustered by visual inspection to reveal biologically significant effects. RESULTS: We have applied this approach to microarray expression data from samples isolated every 2 h throughout the 24 h developmental program of Dictyostelium discoideum. mRNA accumulation patterns for 50 developmental genes were found to fit the kinetic model with a p-value of 0.05 or better. Transcription of these genes appears to be initiated in bursts at well-defined periods during development, in a manner suggestive of a dependent sequence. This approach can be applied to analyses of other temporal gene expression patterns, including those of the cell cycle.

Algorithms↗
PubMed1995

The PKD1 gene produces a developmentally regulated protein in mesenchyme and vasculature.

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common human genetic diseases. In addition to polycystic kidneys, the disease can cause cystic changes in liver and other organs, cardiac valvular insufficiency and cerebral arterial aneurysms. Using antibodies raised against the predicted gene product of PKD1, which is mutated in about 85% of ADPKD cases, we show that PKD1 is a 530-kD protein localized to the extracellular matrix of kidney, liver and cerebral blood vessels. We discovered that the PKD1 protein was highly expressed in the mesenchyme of developing kidney and liver, transiently localized in the developing glomerulus and juxtaglomerular apparatus and restricted to perivascular, extraglomerular areas in adult renal cortex. These data suggest that the PKD1 protein plays a role in renal and hepatic morphogenesis.

Adult↗
PubMed1999

Middle ear defects associated with the double knock out mutation of murine goosecoid and Msx1 genes.

A number of developmental regulatory genes, including homeobox genes, are dynamically expressed in the mammalian cephalic ectomesenchyme during craniofacial morphogenesis. Owing to the vast amount of gene knock out experiments, functions of such genes are now being revealed in the mammalian skeletal patterning process. The murine goosecoid (Gsc) and Msx1 genes are expressed during craniofacial development and each mutant mouse displays intriguing facial abnormalities including those of middle ear ossicles, suggesting that both genes play roles in spatial programming of craniofacial regions. In order to examine whether these genes could function in concert to direct particular craniofacial morphogenesis, double knock out mice were analyzed. The phenotype of the double mutant mice was restricted to the first arch derivatives and was apparently additive of the single gene mutant mice, implying region specific genetic interactions of these homeobox genes expressed in overlapping regions of middle ear forming ectomesenchyme. Our results also suggested that the patterning of distal portions of the malleus depends on the tympanic membrane, for which normal expressions of both the genes are prerequisite.

Animals↗
PubMed1999

A 3'-flanking NF-kappaB site mediates developmental silencing of the human zeta-globin gene.

The central developmental event in the human (h)alpha-globin gene cluster is selective silencing of the zeta-globin gene as erythropoiesis shifts from primitive erythroblasts in the embryonic yolk sac to definitive erythroblasts in the fetal liver. Previous studies have demonstrated that full developmental silencing of the hzeta-globin gene in transgenic mice requires the proximal 2.1 kb of its 3'-flanking region. In the current report, we localize this silencing activity to a 108 bp segment located 1.2 kb 3' to the zeta-globin gene. Protein(s) in nuclear extracts from cell lines representing the fetal/adult erythroid stage bind specifically to an NF-kappaB motif located at this site. In contrast, this binding activity is lacking in the nuclear extract of an embryonic-stage erythroid line expressing zeta-globin. This complex is quantitatively recognized by antisera to the NF-kappaB p50 and to a lesser extent to p65 subunits. A two-base substitution that disrupts NF-kappaB site protein binding in vitro also results in the loss of the developmental silencing activity in vivo. The data suggest that NF-kappaB complex formation is a crucial component of hzeta-globin gene silencing. This finding expands the roles of this widely distributed transcriptional complex to include negative regulation in mammalian development.

Adult↗
PubMed1990

Olfactory-specific cytochrome P-450 (P-450olf1; IIG1). Gene structure and developmental regulation.

The olfactory neuroepithelium is the principal site of interaction for airborne molecules, mainly odorants, in the organism. The presence of an active cytochrome P-450-dependent oxidative metabolism in this tissue has not yet been studied as well as the hepatic cytochrome P-450-dependent oxidations. In this report, we describe cytochrome P-450olf1 (IIG1), a P-450 gene expressed at high levels uniquely in the olfactory epithelium. By Southern analysis and genomic DNA cloning, we demonstrate that a single copy of the P-450olf1 gene is present in the rat genome and contains 9 exons. We conclude that rat P-450IIG1 is a single gene subfamily. P-450olf1 gene expression was activated after birth in both male and female Sprague-Dawley rats and remained active in adult olfactory epithelium. A first maximum level of expression was reached around postnatal day 21. The coincidence between the temporal gene activation of P-450olf1 and the postnatal increase in the sensitivity of olfactory response to odorants is consistent with a potential role of this enzyme in olfactory function.

Aging↗
PubMed1995

Narbonin, a novel 2S protein from Vicia narbonensis L. seeds: cDNA, gene structure and developmentally regulated formation.

cDNA and genomic clones encoding narbonin, a 2S globulin from the seed of narbon bean (Vicia narbonensis L.), were obtained using the polymerase chain reaction (PCR) and sequenced. The full-length cDNA as well as genomic clones contain a single open reading frame (ORF) of 873 bp that encodes a protein with 291 amino acids comprising the mature narbonin polypeptide (M(r) ca. 33 100) and an initiation methionine. The deduced amino acid sequence lacks a transient N-terminal signal peptide. The genomic clones do not contain any intron. No homology was found to nucleic acid and protein sequences so far registered in sequence data libraries. The biosynthesis of narbonin during embryogenesis is developmentally-regulated and its pattern of synthesis closely resembles that of typical seed storage globulins. However, during seed germination narbonin was degraded very slowly, indicating that it may have other function than storage protein. Southern analysis suggests the existence of a small narbonin gene family. Narbonin genes were also found in four different species of the genus Vicia as well as in other legumes such as Canavalia ensiformis and Glycine max. In Escherichia coli a recombinant narbonin was produced which yielded crystals like those prepared from narbonin purified from seeds.

Amino Acid Sequence↗
PubMed1987

A lineage-specific gene encoding a major matrix protein of the sea urchin embryo spicule. I. Authentication of the cloned gene and its developmental expression.

The developing sea urchin embryo forms endoskeletal CaCO3 containing spicules which are elaborated by the primary mesenchyme cells, descendants of the micromeres, beginning at gastrulation. In this and the accompanying paper [H. M. Sucov, S. Benson, J. J. Robinson, R. J. Britten, F. Wilt, and E. H. Davidson (1987) Dev. Biol. 120, 507-519] the isolation and characterization of a gene that encodes a 50-kDa spicule matrix glycoprotein that we call SM50 are described. A cloned cDNA isolated from a lambda gt11 library was used in hybrid-selected translation and hybrid arrest of translation experiments to verify that the cDNA encodes a spicule matrix protein. The cognate RNA transcript encodes a 50-kDa protein which is precipitated by polyclonal antisera against spicule matrix proteins and is present only in polyadenylated RNA at stages known to be making a spicule. The cloned cDNA sequence described in the accompanying paper was used to follow the time of expression of the cognate gene by RNA blotting analysis. The 2.2-kb mRNA is first detected at late cleavage stages and rapidly accumulates as the primary mesenchyme forms, reaching an apparent maximum concentration in the late gastrula and pluteus stages. The cDNA was also used to identify the cells that contain the transcripts by hybridization in situ. Hybridization to cellular transcripts is first detected in primary mesenchyme cells as they enter the blastocoel, and transcripts are confined to these cells during spicule formation and subsequent development.

Animals↗
PubMed1999

Aaknox1, a kn1-like homeobox gene in Acetabularia acetabulum, undergoes developmentally regulated subcellular localization.

Homeobox-containing genes play developmentally important roles in a wide variety of plants, animals and fungi. As a way of studying how development is controlled in the unicellular green macroalga Acetabularia acetabulum, we used degenerate PCR to clone a knotted1-like (kn1-like) homeobox gene, Aaknox1 (Acetabularia acetabulum kn1-like homeobox 1). Aaknorx1 is the first knotted1-like homeobox gene to be cloned from a non-vascular plant and shows strong conservation with kn1-like genes from the vascular plants (ca. 56% amino acid identity within the homeodomain). Sequencing of cDNA clones indicates that Aaknor1 possesses at least two distinct polyadenylation sites spaced ca. 600 bp apart. Southern analysis suggests that several other kn1-like homeobox genes exist in the Acetabularia genome. Northern analyses demonstrate that expression of Aaknox1 is developmentally regulated, with peak levels of expression during early reproductive phase. Northern analyses further demonstrate that Aaknox1 mRNA undergoes a change in its subcellular localization pattern during the progression from late vegetative to early reproductive phase. In late adult phase, Aaknox1 is distributed uniformly throughout the alga; in early reproductive phase, Aaknox1 is present in a gradient with the highest concentration of the mRNA at the base of the stalk, near the single nucleus. These data suggest that Aaknox1 may have a role during early reproductive development and that mRNA localization may be one mechanism by which A. acetabulum regulates gene expression posttranscriptionally.

Acetabularia↗
PubMed2006

MyoD, Myf5, and the calcineurin pathway activate the developmental myosin heavy chain genes.

Myogenesis is accompanied by the activation of two developmental myosin heavy chains (MyHCs), embryonic and perinatal, followed by a dramatic decrease in their expression during early postnatal life. The pathways that control the transcription of these genes have not been previously determined. In this study, we identified cis-acting elements and trans-acting factors that regulate the expression of these two developmental MyHCs in the mouse. Between 800 and 1000 bp of proximal promoter sequence is sufficient to drive muscle-specific expression in cell culture. Further, these same regions contain sequences that confer downregulation in postnatal life in vivo. For the embryonic MyHC gene, the region between -791 bp and -626 bp contains the majority of activating elements. In the proximal promoter regions of both genes, we identified two E-box elements that work in conjunction to activate transcription, but only the embryonic MyHC E-boxes bind a complex containing MyoD. In addition, our results reveal activation by calcineurin that is transduced only partially by its conventional downstream effectors, MEF2 and NFAT. Some common features are shared between the promoters of these two genes; however, the mechanisms of their regulation appear distinct.

Animals↗
PubMed2005

A Sordaria macrospora mutant lacking the leu1 gene shows a developmental arrest during fruiting body formation.

Developmental mutants with defects in fruiting body formation are excellent resources for the identification of genetic components that control cellular differentiation processes in filamentous fungi. The mutant pro4 of the ascomycete Sordaria macrospora is characterized by a developmental arrest during the sexual life cycle. This mutant generates only pre-fruiting bodies (protoperithecia), and is unable to form ascospores. Besides being sterile, pro4 is auxotrophic for leucine. Ascospore analysis revealed that the two phenotypes are genetically linked. After isolation of the wild-type leu1 gene from S. macrospora, complementation experiments demonstrated that the gene was able to restore both prototrophy and fertility in pro4. To investigate the control of leu1 expression, other genes involved in leucine biosynthesis specifically and in the general control of amino acid biosynthesis ("cross-pathway control") have been analysed using Northern hybridization and quantitative RT-PCR. These analyses demonstrated that genes of leucine biosynthesis are transcribed at higher levels under conditions of amino acid starvation. In addition, the expression data for the cpc1 and cpc2 genes indicate that cross-pathway control is superimposed on leucine-specific regulation of fruiting body development in the leu1 mutant. This was further substantiated by growth experiments in which the wild-type strain was found to show a sterile phenotype when grown on a medium containing the amino acid analogue 5-methyl-tryptophan. Taken together, these data show that pro4 represents a novel mutant type in S. macrospora, in which amino acid starvation acts as a signal that interrupts the development of the fruiting body.

3-Isopropylmalate Dehydrogenase↗
PubMed1987

Developmental regulation of somatostatin gene expression in the brain is region specific.

Developmental regulation of somatostatin (SRIF) gene expression was studied in five regions of rat brain and in rat stomach. Total RNA was isolated from hypothalamus, cortex, brainstem, cerebellum, and olfactory bulb, as well as stomach at eight stages of development from prenatal day 16 to postnatal day 82. Hybridization of a 32P-labeled rat SRIF cDNA probe to Northern blots of total RNA from the above tissues during development demonstrated a single hybridizing band approximately 670 base pairs in length. When SRIF mRNA levels from each stage of development were quantified and normalized by the amount of poly (A)+ RNA present at that stage of development, a unique pattern of SRIF gene expression was seen in each region. In brainstem and cerebellum, SRIF mRNA levels peaked early in development between prenatal day 21 and postnatal day 8 and then declined until postnatal day 82. Hypothalamus and cortex, on the other hand, showed a progressive increase during development with peak levels occurring between postnatal days 13 and 82. In contrast, stomach and olfactory bulb showed SRIF mRNA levels which were low during early development and which rose late in development (postnatal days 13 to 82). Marked differences in the amount of SRIF mRNA within each region were present as well. These data suggest that there is differential expression of the SRIF gene in different regions of the brain and in the stomach during development. Further study of this phenomenon may provide insight into the in vivo control of SRIF gene expression and the role of SRIF in the developing brain.

Animals↗