Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “transcript abundance”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources
PubMed2003

Effect of oocyte quality on the relative abundance of specific gene transcripts in bovine mature oocytes and 16-cell embryos.

Although the developmental potential of oocytes is related to oocyte quality, whether the expression of specific genes is altered in oocytes of different quality and in resulting embryos is not known. Semi-quantitativereverse transcription-polymerase chain reaction was used to compare the relative abundance of 2 transcripts for housekeeping proteins (beta-actin and ribosomal protein L30) and 3 transcripts for growth factor ligand or receptors (platelet derived growth factor receptor alpha (PDGFRalpha), basic fibroblast growth factor (bFGF)), in mature bovine oocytes of high versus low developmental potential. The transcripts for L30, PDGFRalpha, and bFGF in 16-cell embryos originating from these oocytes were also examined. No significant effect of oocyte quality was detected for any of the transcripts examined from oocytes or 16-cell embryos. In conclusion, a lower developmental potential of oocytes with advanced signs of atresia, was not associated with a lower level of abundance of the transcripts examined.

Actins↗
PubMed1996

Three abundant germ line-specific transcripts in Volvox carteri encode photosynthetic proteins.

Volvox carteri is a multicellular eukaryotic green alga composed of about 2000 cells of only two differentiated types: somatic and germ line. To understand how embryonic cells are assigned either to somatic or germ line fates, we are investigating the regulation of transcripts that are abundant in only one cell type. Here we report the identity of three transcripts that are coordinately expressed at high levels in germ line cells but not in somatic cells. Surprisingly, all three transcripts encode photosynthetic chloroplast proteins (light-harvesting complex protein, oxygen-evolving enhancer protein 3, and ferredoxin-NADP+ reductase) that are transcribed from nuclear genes. We discuss why these mRNAs might be required at high levels in germ line cells and present a hypothesis, suggested by our results, on the evolution of cell specialization in the Volvocales.

Algal Proteins↗
PubMed2003

Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE.

Serial analysis of gene expression (SAGE) is a technology for quantifying gene expression in biological tissue that yields count data that can be modeled by a multinomial distribution with two characteristics: skewness in the relative frequencies and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample may fail to capture a large number of expressed mRNA species present in the tissue. Empirical estimators of mRNA species' relative abundance effectively ignore these missing species, and as a result tend to overestimate the abundance of the scarce observed species comprising a vast majority of the total. We have developed a new Bayesian estimation procedure that quantifies our prior information about these characteristics, yielding a nonlinear shrinkage estimator with efficiency advantages over the MLE. Our prior is mixture of Dirichlets, whereby species are stochastically partitioned into abundant and scarce classes, each with its own multivariate prior. Simulation studies reveal our estimator has lower integrated mean squared error (IMSE) than the MLE for the SAGE scenarios simulated, and yields relative abundance profiles closer in Euclidean distance to the truth for all samples simulated. We apply our method to a SAGE library of normal colon tissue, and discuss its implications for assessing differential expression.

Bayes Theorem↗
PubMed2002

Contribution of Kv4 channels toward the A-type potassium current in murine colonic myocytes.

A rapidly inactivating K(+) current (A-type current; I(A)) present in murine colonic myocytes is important in maintaining physiological patterns of slow wave electrical activity. The kinetic profile of colonic I(A) resembles that of Kv4-derived currents. We examined the contribution of Kv4 alpha-subunits to I(A) in the murine colon using pharmacological, molecular and immunohistochemical approaches. The divalent cation Cd(2+) decreased peak I(A) and shifted the voltage dependence of activation and inactivation to more depolarized potentials. Similar results were observed with La(3+). Colonic I(A) was sensitive to low micromolar concentrations of flecainide (IC(50) = 11 microM). Quantitative PCR indicated that in colonic and jejunal tissue, Kv4.3 transcripts demonstrate greater relative abundance than transcripts encoding Kv4.1 or Kv4.2. Antibodies revealed greater Kv4.3-like immunoreactivity than Kv4.2-like immunoreactivity in colonic myocytes. Kv4-like immunoreactivity was less evident in jejunal myocytes. To address this finding, we examined the expression of K(+) channel-interacting proteins (KChIPs), which act as positive modulators of Kv4-mediated currents. Qualitative PCR identified transcripts encoding the four known members of the KChIP family in isolated colonic and jejunal myocytes. However, the relative abundance of KChIP transcript was 2.6-fold greater in colon tissue than in jejunum, as assessed by quantitative PCR, with KChIP1 showing predominance. This observation is in accordance with the amplitude of the A-type current present in these two tissues, where colonic myocytes possess densities twice that of jejunal myocytes. From this we conclude that Kv4.3, in association with KChIP1, is the major molecular determinant of I(A) in murine colonic myocytes.

Animals↗
PubMed1978

Nucleotide sequence of the DNA encoding the 5'-terminal sequences of simian virus 40 late mRNA.

We have used a combination of techniques of DNA and RNA sequence analysis to determine the nucleotide sequence of the portion of simian virus 40 DNA preceding and encoding the 5' end of mRNA for the structural protein VP2 of simian virus 40. Comparison of the sequence with those found in polyadenylated RNA in the cytoplasm of infected cells RNA shows that the transcript of sequences preceding the structural gene is more abundant than the transcript containing the codons for the protein. Between the abundant transcript of sequences preceding the coding region and the less abundant transcript of the coding region there is a short sequence whose transcript is not detected.

Base Sequence↗
PubMed1999

Spatiotemporal expression of alternatively spliced IGF-I mRNA in the rat costochondral growth plate.

IGF-I acts as a local proliferation and maturation factor for chondrocytes in the growth plate. However, the expression of different alternative IGF-I mRNA classes in the growth plate has not been characterized. Using quantitative reverse transcription PCR, the abundance of each alternative IGF-I mRNA class in resting, proliferative and hypertrophic chondrocytes was measured in rat costochondral growth plates. Class 1Ea mRNA was the most abundant IGF-I transcript overall and was highly expressed in proliferative chondrocytes at 2 and 4 weeks of age; by 6 weeks, the majority of 1Ea mRNA expression had shifted to hypertrophic chondrocytes. Class 1Eb mRNA was the second most abundant transcript and its distribution was uniform across all the cell types at 2 weeks of age. The expression pattern changed with increasing age such that at 6 weeks a gradient existed with hypertrophic chondrocytes expressing higher levels of 1Eb than resting chondrocytes. Class 2Ea mRNA was constitutively expressed at low levels across the growth plate at all ages, while class 2Eb mRNA expression was negligible. The distribution of total IGF-I mRNA also shifted across growth plate cell types as the animals aged from 2 to 6 weeks. These findings suggest that IGF-I class 1 mRNA plays the predominant role in the maturation of the growth plate.

Alternative Splicing↗
PubMed1996

Sugar regulation of harvest-related genes in asparagus.

The signals controlling the abundance of transcripts up-regulated (pTIP27, pTIP31, and pTIP32) or down-regulated (pTIP20 and pTIP21) after harvest in asparagus (Asparagus officinalis L.) spears were examined. pTIP27 and pTIP31 are known to encode asparagine synthetase (AS) and a beta-galactosidase (beta-gal) homolog, respectively. The nucleotide sequences of pTIP20, pTIP21, and pTIP32 were determined, and they encode histone 3, histone 2B, and an unknown product, respectively. Changes in respiration, soluble sugars, and abundance of the five mRNAs were similar in the tips stored as 30-mm lengths or as part of 180-mm spears. We previously hypothesized that sugars may regulate the level of AS transcripts in asparagus tissue. Asparagus cell cultures were used to test the role of sugar status may regulate the level of AS transcripts in asparagus tissue. Asparagus cell cultures were used to test the role of sugar status in regulating gene expression. Transcript abundance for AS, beta-gal, and pTIP32 was low in cells in sugar-containing medium but increased within 12 h after transferring cells to a sugar-free medium. Histone 3 and histone 2B transcripts were, in general, abundant in cells on sugar-containing medium but declined in abundance when transferred to sugar-free medium. When cells were returned to sugar-containing medium the abundance of transcripts for histone 3 and histone 2B increased, whereas that for AS, beta-gal, and pTIP32 decreased. Soluble sugar levels are known to decline rapidly in the tips of harvested spears. Metabolic regulation by sugar status may have a major influence on gene expression in asparagus spears and other tissue after harvest.

Aspartate-Ammonia Ligase↗
PubMed1997

Abundance of BRCA1 transcripts in human cancer and lymphoblastoid cell lines carrying BRCA1 germ-line alterations.

A competitive polymerase chain reaction has been developed for quantitation of BRCA1 mRNA. In human cancer cell lines, the amount of BRCA1 mRNA is relatively low, ranging from 6 to 38 copies per cell. The decay rate of these transcripts in actinomycin-treated cells indicates that the half-life of these molecules is about 4 hr, suggesting that the low concentration of BRCA1 messages is not due to molecular unstability. In human lymphoblastoid cell lines derived from patients carrying germ-line alterations of BRCA1, the amount of BRCA1 mRNA per cell is lowered only in cell lines exhibiting alterations leading to specific loss of transcripts from the mutated allele. These data indicate that the amount of BRCA1 available in these cells can be related directly to the number of "active" allele.

Breast Neoplasms↗
PubMed1997

Luteinizing hormone increases the abundance of various transcripts, independently of the androgens, in the rat prostate.

Differential display analysis was carried out to find, in the rat prostate, genes that could be regulated by Luteinizing Hormone (LH), independently of the androgens. Hypophysectomized and castrated adult rats were treated with either LH, testosterone or saline. Regulated discrete bands have been eluted and reamplified. After Northern blotting, the levels of mRNA corresponding to 8 PCR fragments were significantly increased by LH treatment. None of these inserts were found to be induced by testosterone. One insert was subcloned, sequenced and identified as the ribosomial protein S 23. A competitive RT-PCR assay was carried out on the full length S 23 cDNA and confirmed that its mRNA levels were stimulated by LH but not by testosterone. These results strongly suggest that the LH membrane receptor, previously shown to be expressed in the rat prostate, has a physiological significance in this organ. Moreover, it appears that the effect of LH on the rat prostate are independent of the androgens.

Animals↗
PubMed2002

Global analysis of gene expression in yeast.

In the past decade, there has been an intense effort to comprehensively catalogue the expressed genes in the yeast Saccharomyces cerevisiae and to determine the absolute and relative abundance of transcript and protein levels under different cellular conditions. Several methods have been developed to monitor gene expression: DNA microarray analysis, Serial Analysis of Gene Expression (SAGE), kinetic RT-PCR and monitoring expression of beta-galactosidase fusion proteins. These techniques have been used to measure transcript and protein abundance in different developmental states and under different environmental stimuli. A wealth of expression data for yeast is now publicly available through several web sites. The expression information that exists has the obvious benefits of providing a better understanding of the gene expression patterns that accompany changes in a yeast cell's environmental and developmental states. This data has also, however, provided clues to unraveling the complicated questions surrounding gene regulation: why and how is gene expression controlled?

Gene Expression Regulation, Fungal↗
PubMed2001

Variant hepatocyte nuclear factor 1 expression in the mouse genital tract.

Variant Hepatocyte Nuclear Factor 1 (vHNF1/HNF1beta) is a homeodomain-containing transcription factor first expressed in the primitive endoderm and its derivatives, the visceral and parietal endoderm. It is subsequently expressed in epithelial cells of different organs, including the primitive gut and derivatives (liver, pancreas, lung), the kidney, and transiently, in the neural tube. We report here new data concerning vHnf1 expression in the mouse genital tract, using both RNA analyses and our vHnf1 heterozygous mutant mouse line, in which the first coding exon of the vHnf1 gene is replaced by the NLSLacZ reporter gene. Both beta-galactosidase activity and vHnf1 transcripts are detected in epididymus, vas deferens, seminal vesicle, prostate, uterus and oviduct. RNA analysis and in situ hybridization studies demonstrate that vHnf1 transcripts are restricted to the germinal cells of the testis. Unexpectedly, no beta-galactosidase activity is detected in the testis. We further show that, in addition to the somatic transcript, two more abundant vHnf1 transcript variants, which lack exons 1-4, appear in this organ after meiosis.

Animals↗
PubMed2002

Identification of low-abundance differentially expressed transcripts using arrayed cDNA clones.

Analysis of comparative gene expression by the use of DNA microarrays has become a widely used tool. However, this technique is only readily applied to organisms where sequence information is known. This paper describes the development of a low-cost method of gene discovery by enrichment of differentially expressed transcripts, which uses cDNA library arrays of bacterial clones on nylon membranes (macroarrays) coupled with a subtractive probe preparation method to discover differentially expressed genes. The method requires no prior knowledge of the organism's genome sequence and overcomes the inherent insensitivity of standard methods of macroarray hybridisation.

Animals↗
PubMed1999

Ialpha exon-replacement mice synthesize a spliced HPRT-C(alpha) transcript which may explain their ability to switch to IgA. Inhibition of switching to IgG in these mice.

Antibody class switching is regulated by transcription of unrearranged C(H) genes to produce germline (GL) transcripts which direct the choice of isotype and are required for switching. However, their role is unknown. GL transcripts are initiated at the I exons located upstream of each switch region. Although deletion of the I exon by gene targeting prevents switch recombination to that CH gene, the Ialpha exon can be replaced by an entirely different DNA segment, a minigene driven by the phosphoglycerate kinase (PGK) promoter and encoding hypoxanthine phosphoribosyl transferase (HPRT), oriented in the sense direction, without reducing antibody class switching to IgA. To understand why HPRT substitution of the Ialpha exon does not disrupt switch recombination, we have analyzed the structure of the transcript from the targeted allele in these mice. We identify a spliced transcript in which the HPRT exons are spliced to the C(alpha) gene segments, resulting in a structure similar to normal GL transcripts. The abundance of this transcript is similar to that of the normal alpha GL RNA. We also demonstrate that switching to the four IgG subclasses in B cells from these mice is reduced in comparison to wild-type mice. We discuss the possibility that the strong PGK promoter inserted at the Ig alpha locus may interfere with interaction of the promoters for gamma GL transcripts with the 3' IgH enhancer.

Animals↗
PubMed2002

Azoarcus grass endophytes contribute fixed nitrogen to the plant in an unculturable state.

The extent to which the N2-fixing bacterial endophyte Azoarcus sp. strain BH72 in the rhizosphere of Kallar grass can provide fixed nitrogen to the plant was assessed by evaluating inoculated plants grown in the greenhouse and uninoculated plants taken from the natural environment. The inoculum consisted of either wild-type bacteria or nifK- mutant strain BHNKD4. In N2-deficient conditions, plants inoculated with strain BH72 (N2-fixing test plants) grew better and accumulated more nitrogen with a lower delta15N signature after 8 months than did plants inoculated with the mutant strain (non-N2-fixing control plants). Polyadenylated or polymerase chain reaction-amplified BH72 nifH transcripts were retrieved from test but not from control plants. BH72 nifH transcripts were abundant. The inocula could not be reisolated. These results indicate that Azoarcus sp. BH72 can contribute combined N2 to the plant in an unculturable state. Abundant BH72 nifH transcripts were detected also in uninoculated plants taken from the natural environment, from which Azoarcus sp. BH72 also could not be isolated. Quantification of nitrogenase gene transcription indicated a high potential of strain BH72 for biological N2 fixation in association with roots. Phylogenetic analysis of nitrogenase sequences predicted that uncultured grass endophytes including Azoarcus spp. are ecologically dominant and play an important role in N2-fixation in natural grass ecosystems.

Azoarcus↗
PubMed1992

Plastid DNA in developing maize endosperm : genome structure, methylation, and transcript accumulation patterns.

Amyloplasts in storage organs such as maize (Zea mays L.) endosperm are plastid-derived, nonphotosynthetic, starch-accumulating organelles. This study was initiated to characterize the plastid genome in maize endosperm cells containing differentiated amyloplasts and to determine whether plastid genes are transcribed during the period of amyloplast biogenesis in endosperm development. Four cosmid clones representing the total sequence diversity of the maize plastid genome were hybridized to restriction digests of total cellular DNA from isolated 16-day-old endosperms. The hybridization patterns indicated that the plastid DNA present in endosperm tissue was indistinguishable from that in leaf total DNA. Methylation of maize endosperm amyloplast DNA or leaf chloroplast DNA was not detected with the methylation-sensitive enzymes HpaII and EcoRII. Transcripts homologous to the 17 specific plastid DNA BamHI fragments tested were detectable in total RNA prepared from 16-day-old endosperm tissue. Compared with leaf transcripts, the abundance of endosperm transcripts was substantially lower for transcripts detected by 12 different BamHI fragments and was similar or relatively higher for some transcripts homologous to five BamHi fragments. Transcripts homologous to genes for plastid ribosomal small subunit proteins 7 and 12 on fragments 10 and 23 and to an open reading frame on fragment 14 accumulated primarily as unprocessed or partially processed species in endosperm RNA. The demonstration that maize endosperm cells contain an intact, transcriptionally active plastid genome indicates that plastid genes could contribute to amyloplast biogenesis, although no transcripts unique to endosperm were identified.

Journal Article↗
PubMed1998

Premature polyadenylation at multiple sites within a Bacillus thuringiensis toxin gene-coding region.

Some foreign genes introduced into plants are poorly expressed, even when transcription is controlled by a strong promoter. Perhaps the best examples of this problem are the cry genes of Bacillus thuringiensis (B.t.), which encode the insecticidal proteins commonly referred to as B.t. toxins. As a step toward overcoming such problems most effectively, we sought to elucidate the mechanisms limiting the expression of a typical B.t.-toxin gene, cryIA(c), which accumulates very little mRNA in tobacco (Nicotiana tabacum) cells. Most cell lines transformed with the cryIA(c) B.t.-toxin gene accumulate short, polyadenylated transcripts. The abundance of these transcripts can be increased by treating the cells with cycloheximide, a translation inhibitor that can stabilize many unstable transcripts. Using a series of hybridizations, reverse-transcriptase polymerase chain reactions, and RNase-H-digestion experiments, poly(A+) addition sites were identified in the B.t.-toxin-coding region corresponding to the short transcripts. A fourth polyadenylation site was identified using a chimeric gene. These results demonstrate for the first time to our knowledge that premature polyadenylation can limit the expression of a foreign gene in plants. Moreover, this work emphasizes that further study of the fundamental principles governing polyadenylation in plants will have basic as well as applied significance.

Bacillus thuringiensis↗
PubMed1994

The molecular lesion in the alpha-N-acetylgalactosaminidase gene that causes angiokeratoma corporis diffusum with glycopeptiduria.

Angiokeratoma corporis diffusum with glycopeptiduria is a recently recognized inborn error of glycoprotein catabolism resulting from the deficient activity of human alpha-N-acetylgalactosaminidase (E.C. 3.2.1.49; alpha-GalNAc). The first patient with this autosomal recessive disorder, a 46-yr-old consanguineous Japanese woman, presented with diffuse angiokeratoma, mild intellectual impairment, and peripheral neuroaxonal degeneration. Deficient alpha-GalNAc activity also has been reported in consanguineous brothers with an infantile-onset form of neuroaxonal dystrophy resulting from a missense mutation (designated E325K) in the alpha-GalNAc gene. To identify the mutation causing the phenotypically distinct adult-onset disorder, Southern and Northern hybridization analyses of DNA and RNA from the affected homozygote were performed which revealed a grossly normal alpha-GalNAc gene structure and normal transcript size and abundancy. Reverse transcription, amplification, and sequencing of the alpha-GalNAc transcript identified a single C to T transition at nucleotide (nt) 985 that predicted an arginine to tryptophan substitution in residue 329 (designated R329W) of the alpha-GalNAc polypeptide. This base substitution was confirmed by hybridization of PCR-amplified genomic DNA from family members with allele-specific oligonucleotides. Transient expression of an alpha-GalNAc construct containing the R329W mutation resulted in the expression of an immunoreactive polypeptide which had no detectable alpha-GalNAc activity. Comparison of the biosynthesis and stabilities of the transiently expressed and radiolabeled normal, E325K (infantile-onset) and R329W (adult-onset) alpha-GalNAc polypeptides in COS-1 cells indicated that both the mutant precursors were processed to the mature form; however, the E325K mutant polypeptide was more rapidly degraded than the R329W subunit, thereby providing a basis for the distinctly different infantile- and adult-onset phenotypes.

Base Sequence↗