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PubMed2001

Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S. cerevisiae: a word of caution when correlating cis-acting sequences with genome-wide expression analyses.

Correlating genome-wide expression profiles with sequence searches of promoter regions is being used as a technique to identify putative binding sites for transacting factors or to refine consensus sequences of those already known. To evaluate the limitations of such an approach in our studies of GATA-mediated transcription in Saccharomyces cerevisiae, we identified the relative contributions made to DAL1 and DAL4 expression by each of five Gln3p-, and/or Gat1p-, and three Dal82p-binding site homologous sequences situated in the 829-bp intergenic region separating these highly related, divergently transcribed genes. Our data suggest that although the correlation of repeated sequences or sequence homologies appearing within promoter regions with expression profiles obtained from genome-wide transcription analyses can provide useful starting points for analyses of cis-acting sites, significant limitations and possibilities for misinterpretation also abound.

Amidohydrolases↗

PubMed1999

Transcriptional regulation in the hyperthermophilic archaeon Pyrococcus furiosus: coordinated expression of divergently oriented genes in response to beta-linked glucose polymers.

The genetic organization, expression, and regulation of the celB locus of the hyperthermophilic archaeon Pyrococcus furiosus were analyzed. This locus includes the celB gene, which codes for an intracellular beta-glucosidase, and a divergently orientated gene cluster, adhA-adhB-lamA, which codes for two alcohol dehydrogenases and an extracellular beta-1,3-endoglucanase that is transcribed as a polycistronic messenger (the lamA operon). During growth of P. furiosus on either the beta-1,4-linked glucose dimer cellobiose or the beta-1,3-linked glucose polymer laminarin, the activities of both beta-glucosidase and endoglucanase were increased at least fivefold compared with levels during growth on maltose or pyruvate. Northern blot analysis revealed an enhanced transcription of both the celB gene and the lamA operon in the presence of these glucose-containing substrates. The in vivo and in vitro transcription initiation sites of both the celB gene and the lamA operon were identified 25 nucleotides downstream of conserved TATA box motifs. A number of repeating sequences have been recognized in the celB-adhA intergenic region, some of which might be part of a transcriptional regulator-binding site.

Alcohol Dehydrogenase↗

PubMed1991

Control of cAMP-induced gene expression by divergent signal transduction pathways.

A compilation of literature data and recent experiments led to the following conclusions regarding cyclic adenosine 3':5' monophosphate (cAMP) regulation of gene expression. Several classes of cAMP-induced gene expression can be discriminated by sensitivity to stimulation kinetics. The aggregation-related genes respond only to nanomolar cAMP pulses. The prestalk-related genes respond both to nanomolar pulses and persistent micromolar stimulation. The prespore specific genes respond only to persistent micromolar stimulation. The induction of the aggregation- and prestalk-related genes by nanomolar cAMP pulses may share a common transduction pathway, which does not involve cAMP, while involvement of the inositol 1,4,5-trisphosphate (IP3)/Ca2+ pathway is unlikely. Induction of the expression of prespore and prestalk-related genes by micromolar cAMP stimuli utilizes divergent signal processing mechanisms. cAMP-induced prespore gene expression does not involve cAMP and probably also not cyclic guanosine 3'.5' monophosphate (cGMP) as intracellular intermediate. Involvement of cAMP-induced phospholipase C (PLC) activation in this pathway is suggested by the observation that IP3 and 1,2-diacylglycerol (DAG) can induce prespore gene expression, albeit in a somewhat indirect manner and by the observation that Li+ and Ca2+ antagonists inhibit prespore gene expression. Cyclic AMP induction of prestalk-related gene expression is inhibited by IP3 and DAG and promoted by Li+, and is relatively insensitive to Ca2+ antagonists, which indicates that PLC activation does not mediate prestalk-related gene expression. Neither prespore nor prestalk-related gene expression utilizes the sustained cAMP-induced pHi increase as intracellular intermediate.

Cyclic AMP↗

PubMed2006

Non-diverging analytic expression for the on-axis sensitivity of converging collimators: analytic derivation.

The expressions for the sensitivity of converging collimators found in the literature diverge at points near the focal locus of the collimator. In this paper, an analytical formula that does not diverge is derived and compared to that available in the literature. An analysis is provided to predict the cases in which use of the new formula is advisable. Since the first expression derived is rather complex, approximations were made to reach simpler formulae. The formulae derived can be used to define and extend the realm of applicability of the literature expression in the cases identified in their derivation.

Computer Simulation↗

PubMed2003

Rapid evolution of male-biased gene expression in Drosophila.

A number of genes associated with sexual traits and reproduction evolve at the sequence level faster than the majority of genes coding for non-sex-related traits. Whole genome analyses allow this observation to be extended beyond the limited set of genes that have been studied thus far. We use cDNA microarrays to demonstrate that this pattern holds in Drosophila for the phenotype of gene expression as well, but in one sex only. Genes that are male-biased in their expression show more variation in relative expression levels between conspecific populations and two closely related species than do female-biased genes or genes with sexually monomorphic expression patterns. Additionally, elevated ratios of interspecific expression divergence to intraspecific expression variation among male-biased genes suggest that differences in rates of evolution may be due in part to natural selection. This finding has implications for our understanding of the importance of sexual dimorphism for speciation and rates of phenotypic evolution.

Animals↗

PubMed2003

Decreased CD154 expression by neonatal CD4+ T cells is due to limitations in both proximal and distal events of T cell activation.

Neonatal CD4(+) T cells express less CD154 protein and mRNA than adult CD4(+) T cells after activation by calcium ionophore and phorbol ester, but the mechanism for this reduced expression and its relevance to the primary immune response remain unclear. We compared expression of CD154 protein and mRNA and CD154 gene promoter activity by purified naive (CD45RA(high)CD45RO(low)) neonatal and adult CD4(+) T cells after activation by calcium ionophore (ionomycin) and phorbol myristate acetate (PMA) treatment or by engagement of alphabeta TCR-CD3 complex. Substantial and consistent reductions in expression by neonatal cells were found in all cases and were paralleled by decreased CD154-dependent activation of a B cell line. CD69 expression by neonatal CD4(+) T cells after alphabeta TCR-CD3 engagement was also reduced compared to adult cells, which suggested that limitations in activation-induced signaling by neonatal CD4(+) T cells occurred at a point upstream of where the signaling pathways leading to CD154 and CD69 expression diverge. Decreased CD154 expression by neonatal cells after alphabeta TCR-CD3 engagement was paralleled by a lower free intracellular calcium concentration, a key event for CD154 gene transcription. Reduced CD154 promoter activity by neonatal cells persisted when proximal signaling events were bypassed using ionomycin and PMA, suggesting an additional and more distal mechanism for decreased transcription. In contrast, CD154 mRNA stability was similar in neonatal and adult cells after either ionomycin and PMA stimulation or engagement of the alphabeta TCR-CD3 complex. We conclude that decreased CD154 production by neonatal CD4(+) T cells is due to limitations in both proximal and distal activation events, which together ultimately limit CD154 gene transcription.

Adult↗

PubMed1997

Human and murine osteocalcin gene expression: conserved tissue restricted expression and divergent responses to 1,25-dihydroxyvitamin D3 in vivo.

Human and murine osteocalcin genes demonstrate similar cell-specific expression patterns despite significant differences in gene locus organization and sequence variations in cis-acting regulatory elements. To investigate whether differences in these regulatory regions result in an altered response to 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3] in vivo, we compared the response of the endogenous mouse osteocalcin gene to a bacterial reporter gene directed by flanking regions of the human osteocalcin gene in transgenic mice. Transgene expression colocalized with endogenous osteocalcin expression in serial sections, being detected in osteoblasts, osteocytes and hypertrophic chondrocytes. In calvarial cell culture lysates from transgenic and nontransgenic mice, the endogenous mouse osteocalcin gene did not respond to 1,25-(OH)2D3 treatment. Despite this, transgene activity was significantly increased in the same cells. Similarly, Northern blots of total cellular RNA and in situ hybridization studies of transgenic animals demonstrated a maximal increase in transgene expression at 6 h after 1,25-(OH)2D3 injection (23.6+/-3.6-fold) with a return to levels equivalent to uninjected animals by 24 h (1.2+/-0.1-fold). This increase in transgene expression was also observed at 6 h after 1,25-(OH)2D3 treatment in animals on a low calcium diet (25.2+/-7.7-fold) as well as in transgenic mice fed a vitamin D-deficient diet containing strontium chloride to block endogenous 1,25-(OH)2D3 production (7.5+/-0.9-fold). In contrast to the increased transgene expression levels, neither endogenous mouse osteocalcin mRNA levels nor serum osteocalcin levels were significantly altered after 1,25-(OH)2D3 injection in transgenic or nontransgenic mice, regardless of dietary manipulations, supporting evidence for different mechanisms regulating the response of human and mouse osteocalcin genes to 1,25-(OH)2D3. Although the cis- and trans-acting mechanisms directing cell-specific gene expression appear to be conserved in the mouse and human osteocalcin genes, responsiveness to 1,25-(OH)2D3 is not. The mouse osteocalcin genes do not respond to 1,25-(OH)2D3 treatment, but the human osteocalcin-directed transgene is markedly upregulated under the same conditions and in the same cells. The divergent responses of these homologous genes to 1,25-(OH)2D3 are therefore likely to be due to differences in mouse and human osteocalcin-regulatory sequences rather than to variation in the complement of trans-acting factors present in mouse osteoblastic cells. Increased understanding of these murine-human differences in osteocalcin regulation may shed light on the function of osteocalcin and its regulation by vitamin D in bone physiology.

Animals↗

PubMed2005

Evolutionary conservation of expression profiles between human and mouse orthologous genes.

Mouse models are often used to study human genes because it is believed that the expression and function are similar for the majority of orthologous genes between the two species. However, recent comparisons of microarray data from thousands of orthologous human and mouse genes suggested rapid evolution of gene expression profiles under minimal or no selective constraint. These findings appear to contradict non-array-based observations from many individual genes and imply the uselessness of mouse models for studying human genes. Because absolute levels of gene expression are not comparable between species when the data are generated by species-specific microarrays, use of relative mRNA abundance among tissues (RA) is preferred to that of absolute expression signals. We thus reanalyze human and mouse genome-wide gene expression data generated by oligonucleotide microarrays. We show that the mean correlation coefficient among expression profiles detected by different probe sets of the same gene is only 0.38 for humans and 0.28 for mice, indicating that current measures of expression divergence are flawed because the large estimation error (discrepancy in expression signal detected by different probe sets of the same gene) is mistakenly included in the between-species divergence. When this error is subtracted, 84% of human-mouse orthologous gene pairs show significantly lower expression divergence than that of random gene pairs. In contrast to a previous finding, but consistent with the common sense, expression profiles of orthologous tissues between species are more similar to each other than to those of nonorthologous tissues. Furthermore, the evolutionary rate of expression divergence and that of coding sequence divergence are found to be weakly, but significantly positively correlated, when RA and the Euclidean distance are used to measure expression-profile divergence. These results highlight the importance of proper consideration of various estimation errors in comparing the microarray data between species.

Animals↗

PubMed1982

Ultrastructural and biochemical expressions of divergent differentiation in prostates of castrated dogs treated with estrogen and androgen.

To investigate the role of estrogen and androgen in prostatic differentiation and induction of epithelial hyperplasia, we studied ultrastructural and biochemical responses to estradiol-17 beta 17-cyclopentylpropionate (ECP) and 5 alpha-androstane-3 alpha, 17 beta-diol dipropionate (3 alpha-diol DP) in glands of castrated dogs. The hormones were injected individually or in combination. Organ cultures, incubated with 1.7 microM radioisotope-labeled testosterone in serum-free Trowell T8 medium, were used to compare capacities of key transforming enzymes in hormone-modified glands. High-affinity binding of labeled 8.5 nM estradiol-17 beta and 5 alpha-dihydrotestosterone (5 alpha-DHT) to 0.4 M KCl-extractable explant protein was also determined. Treatment with 1 mg. of ECP per week for 2 weeks produced basal cell mitosis and early squamous metaplasia. The glandular epithelium hypertrophied but was not repopulated. When compared with radiotestosterone disposition by explanted prostate from untreated castrates, increased formation and egress of 17-oxo C19O2 steroids, predominantly 4-androstene-3,17-dione, occurred at the expense of 5 alpha-reduced 17 beta-hydroxy C19O2-steroids and hydroxylated metabolites. Administration of 2 x 50 mg. of 3 alpha-diol DP per week for 2 weeks also induced basal cell proliferation. The glandular epithelium was repopulated, and atrophic glandular cells were partially restored. This treatment increased accumulation of radiotestosterone-derived 5 alpha-reduced C19O2-metabolites and C19O3-steroids in the explants. Joint administration of ECP and 3 alpha-diol DP yielded proliferating squamous and glandular cells within the same acinus. Each type of proliferating cell was identified by specific cytologic markers. Chromosomes were observed with tonofilament bundles in squamous cells and with secretory granules in glandular cells. However, most glandular cells were not dividing. They were characterized by co-existing tonofilament bundles and secretory granules. The dual hormone administration increased radiotestosterone metabolism. The separate effect of each hormone was notable since estrogen increased the ratio of 17-oxo C19O2 to 5 alpha-reduced 17 beta-hydroxy C19O2-metabolites, whereas androgen restored both terminal hydroxylations and high-affinity binding of 5 alpha-DHT. The levels of saturable binding of estradiol-17 beta were high but variable in explants of each treatment group. We conclude that estrogen and androgen act cooperatively and synergistically on basal cells of regressed canine prostate to induce divergently differentiated epithelial cells. Together with stromal components, these glandular and squamous cells express distinctive pathways of androgen disposition.

Androgens↗

PubMed2005

Evolution of myelin proteolipid proteins: gene duplication in teleosts and expression pattern divergence.

The coevolution of neurons and their supporting glia to the highly specialized axon-myelin unit included the recruitment of proteolipids as neuronal glycoproteins (DMbeta, DMgamma) or myelin proteins (DMalpha/PLP/DM20). Consistent with a genome duplication at the root of teleosts, we identified three proteolipid pairs in zebrafish, termed DMalpha1 and DMalpha2, DMbeta1 and DMbeta2, DMgamma1 and DMgamma2. The paralogous amino acid sequences diverged remarkably after gene duplication, indicating functional specialization. Each proteolipid has adopted a distinct spatio-temporal expression pattern in neural progenitors, neurons, and in glia. DMalpha2, the closest homolog to mammalian PLP/DM20, is coexpressed with P0 in oligodendrocytes and upregulated after optic nerve lesion. DMgamma2 is expressed in multipotential stem cells, and the other four proteolipids are confined to subsets of CNS neurons. Comparing protein sequences and gene structures from birds, teleosts, one urochordate species, and four invertebrates, we have reconstructed major steps in the evolution of proteolipids.

Amino Acid Sequence↗

PubMed1990

Tissue, developmental, and tumor-specific expression of divergent transcripts in Wilms tumor.

The Wilms tumor locus on chromosome 11p13 has been mapped to a region defined by overlapping, tumor-specific deletions. Complementary DNA clones representing transcripts of 2.5 (WIT-1) and 3.5 kb (WIT-2) mapping to this region were isolated from a kidney complementary DNA library. Expression of WIT-1 and WIT-2 was restricted to kidney and spleen. RNase protection revealed divergent transcription of WIT-1 and WIT-2, originating from a DNA region of less than 600 bp. Both transcripts were present at high concentrations in fetal kidney and at much reduced amounts in 5-year-old and adult kidneys. Eleven of 12 Wilms tumors classified as histopathologically heterogeneous exhibited absent or reduced expression of WIT-2, whereas only 4 of 14 histopathologically homogeneous tumors showed reduced expression. These data demonstrate a molecular basis for the pathogenetic heterogeneity in Wilms tumorigenesis.

Base Sequence↗

PubMed2006

Non-diverging analytic expression for the on-axis sensitivity of converging collimators: experimental verification.

The previous paper presented the derivation of an analytical formula for the sensitivity of converging collimators that does not diverge at the focal locus of the collimator. Its predictions, those from a simplified version, and those from the most commonly referenced formula are compared to Monte Carlo and experimental data. Agreement is excellent for all formulae far from the focal locus of the collimator, where it is markedly better for the new formula and its approximation. It is inferred that such formulae should be used in the cases identified by theory, namely around the focal locus of collimators of any focal length and over a substantial part of the field-of-view for short focal length collimators.

Calibration↗

PubMed2006

A genetic signature of interspecies variations in gene expression.

Phenotypic diversity is generated through changes in gene structure or gene regulation. The availability of full genomic sequences allows for the analysis of gene sequence evolution. In contrast, little is known about the principles driving the evolution of gene expression. Here we describe the differential transcriptional response of four closely related yeast species to a variety of environmental stresses. Genes containing a TATA box in their promoters show an increased interspecies variability in expression, independent of their functional association. Examining additional data sets, we find that this enhanced expression divergence of TATA-containing genes is consistent across all eukaryotes studied to date, including nematodes, fruit flies, plants and mammals. TATA-dependent regulation may enhance the sensitivity of gene expression to genetic perturbations, thus facilitating expression divergence at particular genetic loci.

DNA↗

PubMed1998

Highly divergent actin expressed in a Chlamydomonas mutant lacking the conventional actin gene.

The Chlamydomonas mutant ida5 is deficient in the conventional actin gene and its axoneme lacks a subset of inner dynein arms that contain actin as a subunit. However, this mutant retains some other inner dynein arms because a novel protein (NAP) is expressed as a substitute for actin. In this study, we show by sequence analysis that NAP is identical to a putative actin-related protein, the cDNA sequence of which has recently been reported and shown to have 64% amino acid identity with conventional actin. A polyclonal antibody raised against a synthetic polypeptide corresponding to the NH2-terminal sequence of this protein specifically reacted with the spot corresponding to NAP in two-dimensional electrophoresis patterns. NAP apparently can substitute for conventional actin in some, but not all, cellular functions, and therefore can be regarded as a highly divergent actin. This unconventional actin appears to be expressed only when conventional actin is absent.

Actins↗

PubMed2006

Sex-biased gene expression in a ZW sex determination system.

Studies of the transcriptome have shown that a substantial fraction of interspecific differences in gene expression is the result of sex-biased gene expression. These results suggest that sex-dependent selection may be an important force in generating differences between species but to date all studies have focused on Drosophila. We examined a sample of the transcriptome in the gonads of two species of Xenopus to provide an additional test of how sex-biased gene expression may contribute to differences in gene expression between species. In contrast to Drosophila, Xenopus provides an example of a ZW system with morphologically indistinguishable sex chromosomes. About 81% of the transcriptome was differentially expressed between X. laevis and X. muelleri and there were more genes that were male-biased compared to the number of genes that were female-biased or non-sex-biased. While there were more genes up-regulated in males of Xenopus, the largest magnitude difference in expression between species occurred in female-biased genes, and male-biased genes were proportionally more abundant for the smallest changes in expression between species. Our results suggest that more genes have a role in the function of the testis compared to the ovary and female-biased genes play a principle role in expression divergence between species. These results differ from those in the Drosophila XY system in that more female-biased genes had >4-fold difference of expression between species than male-biased genes, suggesting that ZW sex chromosomes may facilitate enhanced gene expression divergence between species.

Animals↗

PubMed2005

Rapid evolution of expression and regulatory divergences after yeast gene duplication.

Although gene duplication is widely believed to be the major source of genetic novelty, how the expression or regulatory network of duplicate genes evolves remains poorly understood. In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an approximately 20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9 x 10(-9) per year, whereas the baseline rate for very ancient gene duplication is 0.14 x 10(-9) per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network.

Evolution, Molecular↗

PubMed2026

A duplicated female pathway gene figla-like evolves as the male sex-determining gene in tilapia.

As the largest group of vertebrates, fish exhibit frequent turnover of sex-determining (SD) genes. Here, we assemble a chromosome-level YY red tilapia genome and identify figla-like (figlal) as the SD gene on tilapia linkage group (LG) 1. Integrative phylogenetic and genomic evidence suggests that figlal originated from a tilapia-specific duplication and transposition of the ancestral bHLH family gene figla from LG12 to LG1. Fluorescence in situ hybridization reveals expression divergence between figla and figlal, with figla expressed in female oocytes and figlal expressed in male gonadal somatic cells during early gonadal differentiation. The shift in expression after duplication might be driven by the insertion of cis-regulatory elements mediated by transposable elements. Knockout of figlal in XY fish results in male-to-female sex reversal as indicated by ovarian morphology, down-regulation of the male pathway gene dmrt1, and up-regulation of the female pathway gene cyp19a1a in the gonads. In contrast, overexpression of figlal in XX fish induces female-to-male sex reversal. These findings implicate figlal as an SD gene on tilapia LG1 and reveal the history of a unique evolutionary innovation in which a female oocyte gene evolved into a male SD gene via duplication, transposition, and cis-regulatory rewiring.

Animals↗

PubMed1994

Arabidopsis thaliana expresses three divergent Srp54 genes.

The Arabidopsis thaliana Srp54 gene family was determined to consist of three genes, all of which were cloned and sequenced. In addition, cDNAs corresponding to two of the genes were obtained. To our knowledge this is the first description of multiple Srp54 genes within an organism. In contrast to the situation in mammals, where there are only three amino acid differences between the mouse and canine sequences, there was significant amino acid sequence diversity among the genes, particularly in the methionine-rich region of the protein, which is the region responsible for binding to the 7S RNA of the signal recognition particle and to the signal sequence of newly synthesized proteins. The amino acid sequences of the GTP-binding domains of the three clones were 86% identical, whereas the methionine-rich domains were only 65% identical. RNA gel blots of various tissues and developmental stages hybridized with gene-specific probes revealed that all three genes were expressed in all the tissues investigated. There were, however, quantitative differences in expression levels.

Amino Acid Sequence↗