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Results for “transcript abundance”

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At least 667 records · Page 37Linked to original sources
PubMed1999

The human multidrug resistance protein 2 gene: functional characterization of the 5'-flanking region and expression in hepatic cells.

The human multidrug resistance protein 2 (MRP2), also termed as the canalicular multispecific organic anion transporter (cMOAT), is a member of the adenosine triphosphate-binding cassette transporter superfamily. In the liver, MRP2 mediates the multispecific efflux of various types of organic anions, including glucuronate, sulfate, and glutathione conjugates, across the canalicular hepatocyte membrane to the bile. To investigate how the MRP2 gene is expressed in liver cells, the 5'-flanking region of the human MRP2 gene was isolated from a human placental genomic library. Sequence analysis of the MRP2 promoter showed a number of consensus binding sites for both ubiquitous and liver-enriched transcription factors. Transfection of human hepatic HepG2 cells with a series of 5'-deleted promoter luciferase constructs identified a putative silencer element localized in the -1,659/-491 region and a liver-specific positive regulatory element localized in the -491/-258 region. This latter region contained the liver-abundant transcription factor CCAAT-enhancer binding protein beta (C/EBPbeta). The transcriptional activity of the promoter construct containing a mutation in the C/EBPbeta binding site was significantly decreased in HepG2 cells. This study suggests that C/EBPbeta (-356 to -343) may regulate the liver expression of the MRP2 gene.

ATP Binding Cassette Transporter, Subfamily B↗
PubMed1988

[Transcription-active locus of the human genome from a gene family].

Previously described genomic sequences, related to viral oncogene mos (human mos pseudogene gp5 and main c-mos gene), are either totally silent or show highly limited degree of expression in some specialized tissues. The mos-related clone K51 isolated previously from rat genome was used here to study expression of the gene comprised. We have demonstrated the presence of abundant transcripts in rat and human brain, lung, skin and muscle. The pattern of transcription changes after the birth and is shown to depend on the presence of higher molecular weight transcripts in adult tissues. With the help of hybridization to K51 probe, we have isolated three clones from human embryonic cDNA library. One of these (son3) also hybridizes to the viral mos gene. These results evidence strongly in favour of the hypothesis that K51 recombinant contains a new member (son) of mos-related family of oncogenes, with the broad spectrum of tissue specificity.

Animals↗
PubMed2006

Adiponectin induces periovulatory changes in ovarian follicular cells.

Adiponectin, the most abundantly synthesized protein in adipose tissue, has plieotropic effects on liver, muscle, endothelium, placenta, and other tissues. We examined direct effects of recombinant porcine adiponectin on porcine ovarian granulosa cells in vitro. We demonstrate that adiponectin, at physiologically relevant levels (10-25 microg/ml), provokes expression of genes associated with periovulatory remodeling of the ovarian follicle over a time frame of 6-24 h. These include cyclooxygenase-2, prostaglandin E synthase, and vascular endothelial growth factor. Adiponectin modulates steroid synthetic protein gene expression, increasing steroidogenic acute regulatory protein transcript abundance and reducing cytochrome P450aromatase. Adiponectin has antidiabetic properties and sensitizes tissues to insulin. We show that it interacts with both LH and insulin in inducing expression of cyclooxygenase-2 transcripts in granulosa cells. We determined that the MAPK pathway, via phosphorylation of ERK1/2, is involved in mediation of the adiponectin signal in ovarian granulosa cells, rather than protein kinase A or the classic adiponectin transducer, AMP-activated protein kinase. Adiponectin synthesis is reduced in obesity, and our findings suggest that this reduction plays a role in obesity-related ovarian dysfunction.

Adiponectin↗
PubMed1999

Sp1 and CTF/NF-1 transcription factors are involved in the basal expression of the Hmgi-c proximal promoter.

HMGI-C is a nuclear architectural factor which is expressed during embryogenesis but not in adult tissues while it becomes re-expressed following neoplastic transformation. In this paper we identify the promoter region of the mouse Hmgi-c gene and by stepwise deletion of the 5' sequences we map the promoter activity of the most abundant transcript to a very short fragment containing a long polypyrimidine/polypurine (ppyr/ppur) tract. We demonstrate that this tract is a multiple binding site for the transcription factors Sp1 and Sp3 and that in Drosophila SL2 cells, Sp1 activates the Hmgi-c promoter. In addition, another transcription factor, CTF/NF-1, binds the proximal promoter immediately downstream of this region and its mutation decreases transcription in NIH-3T3 cells. This study identifies factors responsible for the basal activity of Hmgi-c gene and provides a foundation for further analysis of the mechanism of its regulation.

Animals↗
PubMed2004

Age-associated alteration of gene expression patterns in mouse oocytes.

Decreasing oocyte competence with maternal aging is a major factor in human infertility. To investigate the age-dependent molecular changes in a mouse model, we compared the expression profiles of metaphase II oocytes collected from 5- to 6-week-old mice with those collected from 42- to 45-week-old mice using the NIA 22K 60-mer oligo microarray. Among approximately 11,000 genes whose transcripts were detected in oocytes, about 5% (530) showed statistically significant expression changes, excluding the possibility of global decline in transcript abundance. Consistent with the generally accepted view of aging, the differentially expressed genes included ones involved in mitochondrial function and oxidative stress. However, the expression of other genes involved in chromatin structure, DNA methylation, genome stability and RNA helicases was also altered, suggesting the existence of additional mechanisms for aging. Among the transcripts decreased with aging, we identified and characterized a group of new oocyte-specific genes, members of the human NACHT, leucine-rich repeat and PYD-containing (NALP) gene family. These results have implications for aging research as well as for clinical ooplasmic donation to rejuvenate aging oocytes.

Aging↗
PubMed1996

A control system for cDNA enrichment reactions.

Most cDNA enrichment techniques involve technically complicated subtractive and hybridization reactions whose kinetics have not been characterized. We describe a control for cDNA enrichment procedures based on commercially available reagents, and we use this control to optimize a commonly used subtractive hybridization reaction. Using this control, we show that high-abundance transcripts can be efficiently removed following very short hybridization reactions. With the addition of unlabeled rat liver cDNA, we develop a system that mimics the reaction kinetics of complex cDNA pools. Because this system enables the measurement of specific vs. nonspecific hybridization and subtraction in the same tube and is an effective control for all steps in the cDNA enrichment procedure, it facilitates the development and optimization of novel cloning techniques for a desired abundance level of differentially expressed cDNAs.

Animals↗
PubMed1995

Identification of new Schistosoma mansoni genes by the EST strategy using a directional cDNA library.

A directional size-selected cDNA library constructed from Schistosoma mansoni (Sm) adult worm RNA was used for the generation of expressed sequence tags (EST). From one or both ends of 429 distinct cDNA clones 607 EST were obtained. Of these, only 16% were previously known Sm genes. More than 22% of the clones had matches with entries for other organisms in the databases. These new Sm genes constituted a broad range of transcripts distributed among cytoplasmic structural and regulatory proteins, enzymes, membrane, nuclear and secretory proteins, and proteins with other functions. Almost 33% of the clones had no significant database matches and thus potentially represent Sm-specific genes. Among the latter, several clones, as judged by their redundancy in the library, appear to represent abundant transcripts. The data, taken as a whole, more than double the number of Sm genes identified by nucleotide sequencing and indicate the potential value of the adoption of genome sequencing strategies for the rapid increase in knowledge of complex disease-causing organisms.

Animals↗
PubMed2004

Simulated annealing of microarray data reduces noise and enables cross-experimental comparisons.

Microarrays are a powerful tool for assessing the genome-wide induction of a transcriptional response to internal or external stimuli, but are not considered quantitatively rigorous (i.e., the signal intensity of hybridized probe is normally used to quantify relative transcript abundance). Thus, it is difficult, if not impossible, to accurately compare separate microarray experiments without a reference standard. However, even among replicated microarray experiments, each gene varies significantly in the amount of signal detected, suggesting no single gene would be appropriate as a standard. We propose and test a method to "align" experimental transcription profiles to a set of reference experiments using simulated annealing (SA), essentially using the relative positions of all genes as a reference standard. SA attempts to find a globally optimal adjustment factor for the relative expression level of each experimental gene expression signal, given a previously observed range of gene expression measurements. By defining a relative dynamic range of gene expression under control conditions for all genes, we can more accurately compare transcription profiles between separate experiments and, potentially, between species--enabling comparative transcriptomics. Testing SA on a published dataset, we find that it significantly reduces interexperimental variation, suggesting it holds promise to accomplish this goal.

Oligonucleotide Array Sequence Analysis↗
PubMed1999

Signaling events leading to crassulacean acid metabolism induction in the common ice plant

A rapid, semiquantitative reverse transcriptase-polymerase chain reaction assay was developed to investigate signal transduction events involved in the induction of Crassulacean acid metabolism (CAM) in detached common ice plant (Mesembryanthemum crystallinum) leaves. Transcript abundance of Ppc1, a gene encoding the CAM-specific isoform of phosphoenolpyruvate carboxylase, increased rapidly in response to osmotic stress (dehydration and mannitol), ionic stress (NaCl), and exogenous abscisic acid treatment, but failed to accumulate in response to exogenous cytokinin or methyl jasmonate. Stress-induced accumulation of Ppc1, GapC1, and Mdh1 transcripts was inhibited by pretreating leaves with the calcium chelator ethyleneglycol-bis(aminoethyl ether)-N,N'-tetraacetic acid, suggesting that extracellular calcium participates in signaling events leading to CAM induction. Treatment of unstressed detached leaves with ionomycin, a Ca(2+) ionophore, and thapsigargin, a Ca(2+)-ATPase inhibitor, enhanced Ppc1 transcript accumulation, indicating that elevations in cytosolic [Ca(2+)] are likely to participate in signaling CAM induction. Inhibitors of Ca(2+)- or calmodulin-dependent protein kinases (N-[6-aminohexyl]-5-chloro-1-napthalenesulfonamide, Lavendustin C) and protein phosphatase 1 and 2A (okadaic acid) activity suppressed Ppc1 transcript accumulation in response to ionic and osmotic stresses, as well as abscisic acid treatment. These results suggest that both protein phosphorylation and dephosphorylation events participate in signaling during CAM induction. In contrast, pretreatment with cyclosporin A or ascomycin, inhibitors of protein phosphatase 2B activity, stimulated Ppc1 gene expression either directly or indirectly through promoting water loss.

Journal Article↗
PubMed2006

Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana.

We examined the Leishmania mexicana transcriptome to identify differentially regulated mRNAs using high-density whole-genome oligonucleotide microarrays designed from the genome data of a closely related species, Leishmania major. Statistical analysis on array hybridization data representing 8156 predicted coding regions revealed 288 genes (3.5% of all genes) whose steady-state mRNA levels meet criteria for differential regulation between promastigotes and lesion-derived amastigotes. Interestingly, sample comparison of promastigotes to axenic amastigotes resulted in only 17 genes (0.2%) that meet the same statistical criteria for differential regulation. The reduced number of regulated genes is a consequence of an increase in the magnitude of the transcript levels in cells under axenic conditions. The expression data for a subset of genes was validated by quantitative PCR. Our studies show that interspecies hybridization on microarrays can be used to analyze closely related protozoan parasites, that axenic culture conditions may alter amastigote transcript abundance, and that there is only a relatively modest change in abundance of a few mRNAs between morphologically distinct promastigote and amastigote cultured cells. Leishmania may represent an alternative paradigm for eukaryotic differentiation with minimal contributions from changes in mRNA abundance.

Animals↗
PubMed2004

Immune-responsive lysozymes from hemocytes of the American dog tick, Dermacentor variabilis and an embryonic cell line of the Rocky Mountain wood tick, D. andersoni.

Immune-responsive lysozyme encoding cDNAs were identified from two medically important tick species by an expressed sequence tag approach of D. variabilis hemocytes (Dv Lys) and a D. andersoni embryonic derived cell line, DAE100. Comparative sequence analyses indicated the Dermacentor molecules to be products of orthologous genes and to be most similar to arthropod c-type lysozymes. Northern blotting analyses demonstrated that Dv Lys expression levels were most abundant in tick hemocytes and to a much lesser degree in the midgut while barely detectable in ovary, salivary gland, and Malpighian tubule tissues. Involvement of the Dermacentor c-type lysozymes in innate immunity was demonstrated by Escherichia coli challenges of D. variabilis ticks by injection resulting in a temporal profile of significantly elevated transcript abundances above those of naive controls that was similarly observed of the D. andersoni cells co-cultured with E. coli. In contrast to that reported of the digestive gut lysozyme of the soft tick Ornithodoros moubata, Dv Lys levels were not statistically differentially regulated by blood meal digestion. Additionally, given the differences in tissue distribution, sequence characteristics and phylogenetic placements between the Dermacentor and Ornithodoros lysozymes demonstrates that ticks possess differently adapted c-type lysozymes that are spatially and temporally differentially expressed.

Amino Acid Sequence↗
PubMed1983

Cloning of abundant mRNA species present during conjugation of Tetrahymena thermophila: identification of mRNA species present exclusively during meiosis.

A cDNA library was constructed by using as a template the RNA present during the meiotic prophase of Tetrahymena thermophila. Clones containing cDNA sequences homologous to moderately abundant to abundant transcripts were detected by colony hybridization and confirmed by hybridizing purified cDNA plasmids on filters with labeled RNA probes. Eighteen clones were isolated, and the sizes of their cDNA inserts were determined. Cross-hybridization of individual cDNA plasmid pairs showed that each of these clones contained cDNA that was homologous to one of eight different RNA transcripts. The sizes of the eight RNA transcripts and the stages of the T. thermophila life cycle during which they were present were determined by hybridizing nick-translated cDNA probes against denatured, electrophoresed RNA from various stages. Clones were identified that contained sequences homologous to RNAs present only in early conjugation (meiosis); other clones contained sequences homologous to RNAs which were abundant during conjugation but present at other stages as well. One clone contained a sequence homologous to an RNA that was abundantly present only in nongrowing cells.

Animals↗
PubMed1992

Characterization of the Expression of the Photosystem II-Oxygen Evolving Complex in C(4) Species of Flaveria.

We have determined the levels of photosystem II activity and polypeptide abundance in whole leaves and isolated bundle sheath and mesophyll cells of C(4), "C(4)-like," and C(3) species of the genus Flaveria (Asteraceae). On a chlorophyll basis, the whole leaf levels of the D1, D2, and 34-kilodalton photosystem II polypeptides were similar for each Flaveria species. Photosystem II activity varied twofold, but was not correlated with photosynthetic type (C(3) or C(4)). The bundle sheath cell levels of photosystem II activity and associated polypeptides in C(4)-like and C(4)Flaveria species were approximately one-half those observed in mesophyll cells but equivalent to those in bundle sheath cells of the C(3) species, Flaveria cronquistii. Analyses of the steady-state levels of transcripts encoding photosystem II polypeptides indicated that there were no differences in transcript abundance between mesophyll and bundle sheath cells of the C(4)Flaveria species. This pattern was in contrast to the three- to tenfold higher levels of transcripts encoding photosystem II polypeptides in mesophyll versus bundle sheath cells of maize. It is apparent that the higher mesophyll cell to bundle sheath ratio of photosystem II polypeptides in C(4)- and C(4)-like species of Flaveria is the result of higher levels of photosystem II expression in mesophyll cells rather than lower levels of expression in bundle sheath cells.

Journal Article↗
PubMed2001

Immediate/early response to Trypanosoma cruzi infection involves minimal modulation of host cell transcription.

Host cell infection by the intracellular pathogen, Trypanosoma cruzi, involves activation of signaling pathways, cytoskeletal reorganization, and targeted recruitment of host cell lysosomes. To determine the consequences of T. cruzi invasion on host cell gene expression, high density microarrays consisting of approximately 27,000 human cDNAs were hybridized with fluorescent probes generated from T. cruzi-infected human fibroblasts (HFF) at early time points following infection (2-24 h). Surprisingly, no genes were induced > or =2-fold in HFF between 2 and 6 h post-infection (hpi) in repeated experiments while immediate repression of six host cell transcripts was observed. A significant increase in transcript abundance for 106 host cell genes was observed at 24 hpi. Among the most highly induced is a set of interferon-stimulated genes, indicative of a type I interferon (IFN) response to T. cruzi. In support of this, T. cruzi-infected fibroblasts begin to secrete IFNbeta at 18 hpi following the induction of IFNbeta transcripts. As compared with global transcriptional responses evoked by other intracellular pathogens, T. cruzi is a stealth parasite that elicits few changes in host cell transcription during the initiation of infection.

Animals↗
PubMed2003

Transcriptional regulation of sorghum defense determinants against a phloem-feeding aphid.

When attacked by a phloem-feeding greenbug aphid (Schizaphis graminum), sorghum (Sorghum bicolor) activates jasmonic acid (JA)- and salicylic acid (SA)-regulated genes, as well as genes outside known wounding and SA signaling pathways. A collection of 672 cDNAs was obtained by differential subtraction with cDNAs prepared from sorghum seedlings infested by greenbug aphids and those from uninfested seedlings. Subsequent expression profiling using DNA microarray and northern-blot analyses identified 82 transcript types from this collection responsive to greenbug feeding, methyl jasmonate (MeJA), or SA application. DNA sequencing analyses indicated that these encoded proteins functioning in direct defense, defense signaling, oxidative burst, secondary metabolism, abiotic stress, cell maintenance, and photosynthesis, as well as proteins of unknown function. In response to insect feeding, sorghum increased transcript abundance of numerous defense genes, with some SA-dependent pathogenesis-related genes responding to greenbug more strongly than to SA. In contrast, only weak induction of MeJA-regulated defense genes was observed after greenbug treatment. However, infestation tests confirmed that JA-regulated pathways were effective in plant defense against greenbugs. Activation of certain transcripts exclusively by greenbug infestation was observed, and may represent unique signal transduction events independent of JA- and SA-regulated pathways. Results indicate that plants coordinately regulate defense gene expression when attacked by phloem-feeding aphids, but also suggest that aphids are able to avoid triggering activation of some otherwise potentially effective plant defensive machinery, possibly through their particular mode of feeding.

Animals↗
PubMed2001

Phytochrome A mediates blue light and UV-A-dependent chloroplast gene transcription in green leaves.

We characterized the photobiology of light-activated chloroplast transcription and transcript abundance in mature primary leaves by using the following two systems: transplastomic promoter-reporter gene fusions in tobacco (Nicotiana tabacum), and phytochrome (phyA, phyB, and hy2) and cryptochrome (cry1) mutants of Arabidopsis. In both dicots, blue light and UV-A radiation were the major signals that activated total chloroplast and psbA, rbcL, and 16S rrn transcription. In contrast, transcription activities in plants exposed to red and far-red light were 30% to 85% less than in blue light/UV-A, depending on the gene and plant species. Total chloroplast, psbA, and 16S rrn transcription were 60% to 80% less in the Arabidopsis phyA mutant exposed to blue light/UV-A relative to wild type, thus definitively linking phyA signaling to these photoresponses. To our knowledge, the major role of phyA in mediating the blue light/UV-A photoresponses is a new function for phyA in chloroplast biogenesis at this stage of leaf development. Although rbcL expression in plants exposed to UV-A was 50% less in the phyA mutant relative to wild type, blue light-induced rbcL expression was not significantly affected in the phyA, phyB, and cry1 mutants. However, rbcL expression in blue light was 60% less in the phytochrome chromophore mutant, hy2, relative to wild type, indicating that another phytochrome species (phyC, D, or E) was involved in blue light-induced rbcL transcription. Therefore, at least two different phytochromes, as well as phytochrome-independent photosensory pathways, mediated blue light/UV-A-induced transcription of chloroplast genes in mature leaves.

Arabidopsis↗
PubMed2003

Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome.

Temporal profiles of transcript abundance during embryonic development were obtained by whole-genome expression analysis from precisely staged C. elegans embryos. The result is a highly resolved time course that commences with the zygote and extends into mid-gastrulation, spanning the transition from maternal to embryonic control of development and including the presumptive specification of most major cell fates. Transcripts for nearly half (8890) of the predicted open reading frames are detected and expression levels for the majority of them (>70%) change over time. The transcriptome is stable up to the four-cell stage where it begins rapidly changing until the rate of change plateaus before gastrulation. At gastrulation temporal patterns of maternal degradation and embryonic expression intersect indicating a mid-blastula transition from maternal to embryonic control of development. In addition, we find that embryonic genes tend to be expressed transiently on a time scale consistent with developmental decisions being made with each cell cycle. Furthermore, overall rates of synthesis and degradation are matched such that the transcriptome maintains a steady-state frequency distribution. Finally, a versatile analytical platform based on cluster analysis and developmental classification of genes is provided.

Animals↗
PubMed1992

Mouse submandibular glands express an androgen-regulated transcript encoding an acidic epididymal glycoprotein-like molecule.

Acidic epididymal glycoprotein (AEG) is an androgen-regulated, epididymal secretory protein assumed to be involved in sperm maturation. In the present study, we show that the mouse submandibular gland (SMG) expresses two genes designated Aeg-1 and Aeg-2. The nucleotide sequence of Aeg-1 cDNA clones was identical to that of epididymis-expressed Aeg cDNA clones, indicating that Aeg-1 is expressed in both epididymides and SMGs. The second, more abundant transcript, Aeg-2, had a sequence similar to, but distinct from, that of Aeg-1, and was not detectable in the epididymis. The level of Aeg-1 and Aeg-2 transcripts in the SMG was androgen-regulated and showed sexual dimorphism. In situ hybridization of SMG sections showed that Aeg-1 and Aeg-2 transcripts are produced by the cells of granular convoluted tubules. The C-terminal cysteine-rich region of the mouse AEG-2 molecule appears to have diverged faster than that of the mouse AEG-1 molecule, consistent with the idea that this region may play a role unique to the protein of the male reproductive system.

Amino Acid Sequence↗