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At least 1,639 records · Page 91Linked to original sources
PubMed2003

Plac8 and Plac9, novel placental-enriched genes identified through microarray analysis.

Microarray expression profiling of a collection of 15,000 mouse genes with placental and embryonic RNAs revealed candidates for placental-enriched genes, three of which we have confirmed and further characterized. One, Plac1, strongly expressed in all trophoblast-derived cells in the placenta, has been described earlier (Genomics 68 (2000) 305). Here we report that of the other two, Plac8 expression is restricted to the spongiotrophoblast layer during development, whereas Plac9 is weakly expressed though highly enriched in placenta. For both, cDNAs with complete open reading frames were recovered and exon-intron structures inferred from comparisons of mouse cDNA and genomic sequence. The predicted proteins (112 and 108 amino acids) both contain putative signal peptides, with a coiled-coil segment of mPLAC9 as the only other detected motif. Genomic sequence comparisons reveal that in addition to an apparent pseudogene on chromosome 1, Plac8 is expressed at mouse cytoband 5e3. It is tightly conserved in human in a syntenically equivalent ortholog at 4q21.23. Plac9 is present in a single copy on chromosome 14, with a syntenically equivalent human ortholog at 10q22.3. Putative promoter regions up to 10 kb 5' of the transcription units for Plac1, Plac8, and Plac9 contain sites for widely-expressed transcription factors which, by analogy to other instances, may be sufficient to explain placental enrichment.

Amino Acid Sequence↗
PubMed2001

Altered gene expression profile in chemically induced rat mammary adenocarcinomas and its modulation by an aromatase inhibitor.

In the present study, competitive cDNA library screening (CCLS) and cDNA microarray analyses were employed to identify differentially expressed genes in methylnitrosourea-induced rat mammary adenocarcinomas. The preliminary screening of 100 000 plaques by CCLS identified 1217 clones with differential expression. Dot-blot analysis of the isolated clones verified differential expression in 471 distinct genes. Confirmation of these 471 genes was conducted by performing reverse transcription-polymerase chain reactions, and a total of 160 genes were confirmed after comparing six rat mammary adenocarcinomas and three normal rat mammary glands. Fifty-nine of these showed lower expression in the adenocarcinomas while the remaining 101 were overexpressed in the tumors. Employing a cDNA microarray containing 588 known genes revealed an additional 33 differentially expressed genes in these tumors. Importantly, most of the identified genes demonstrated relatively reproducible overexpression or underexpression in individual tumors. Many of the altered genes determined by cDNA microarray analysis were oncogenes, tumor suppressor genes, or genes involved in cell cycle control and apoptosis. CCLS identified many others not previously associated with mammary carcinogenesis, including a novel gene named RMT-7. Preliminary studies to determine the applicability of this gene expression approach for detecting potential biomarkers for cancer chemoprevention was evaluated in rat mammary tumors obtained from animals treated with vorozole, a potent aromatase inhibitor. When genes exhibiting differential expression as determined by CCLS or cDNA microarray analysis were examined in control and vorozole-treated tumors, expression of 19 genes was found to be modulated significantly in tumors treated with vorozole. Further investigations into these identified genes should contribute significantly to our understanding of the molecular mechanisms of rat mammary tumorigenesis. In addition, the identified genes may become useful targets for drug development and potential biomarkers for monitoring treatment and prevention of breast cancer in humans.

Adenocarcinoma↗
PubMed2003

Sporangium-specific gene expression in the oomycete phytopathogen Phytophthora infestans.

The oomycete genus Phytophthora includes many of the world's most destructive plant pathogens, which are generally disseminated by asexual sporangia. To identify factors relevant to the biology of these propagules, genes induced in sporangia of the potato late blight pathogen Phytophthora infestans were isolated using cDNA macroarrays. Of approximately 1,900 genes known to be expressed in sporangia, 61 were up-regulated >5-fold in sporangia versus hyphae based on the arrays, including 17 that were induced >100-fold. A subset were also activated by starvation and in a nonsporulating mutant. mRNAs of some genes declined in abundance after germination, while others persisted through the germinated zoospore cyst stage. Functions were predicted for about three-quarters of the genes, including potential regulators (protein kinases and phosphatases, transcription factors, and G-protein subunits), transporters, and metabolic enzymes. Predominant among the last were several dehydrogenases, especially a highly expressed sorbitol dehydrogenase that accounted for 3% of the mRNA. Sorbitol dehydrogenase activity also rose during sporulation and several stress treatments, paralleling the expression of the gene. Another interesting metabolic enzyme resembled creatine kinases, which previously were reported only in animals and trypanosomes. These results provide insight into the transcriptional and cellular processes occurring in sporangia and identify potential targets for crop protection strategies.

Amino Acid Sequence↗
PubMed2003

Mucosal pentraxin (Mptx), a novel rat gene 10-fold down-regulated in colon by dietary heme.

Consumption of red meat is associated with increased colon cancer risk. Our previous work indicated that this association might be due to the heme content of red meat. In rat studies, dietary heme increased colonic cytotoxicity and epithelial cell turnover, carcinogenesis biomarkers. Here we apply DNA microarray technology to examine effects of heme on colonic gene expression. A rat colon-specific microarray was constructed and hybridized in duplicate to RNA extracts from colon scrapings of rats fed diets with or without heme (n=6-7). We were able to reproducibly identify changes in colonic mRNA abundance in response to heme. Most striking was a >10-fold down-regulation of a single rat gene, an unprecedented gene-modulating effect of a dietary component. Based on homology, the novel gene encodes a pentraxin, the first identified in colon. Pentraxins are postulated to be involved in dealing with dying cells. Quantitative PCR confirmed the strong heme-induced down-regulation of this gene, which we named mucosal pentraxin (Mptx). Overall, our data support the efficacy of cDNA array expression profiling to investigate effects of specific nutrients in an in vivo system and may provide an approach to establishing markers for diet-induced stress of mammalian colonic mucosa.

Acute-Phase Proteins↗
PubMed2005

Approaches to bacterial RNA isolation and purification for microarray analysis of Escherichia coli K1 interaction with human brain microvascular endothelial cells.

We established a protocol for isolation of microarray-grade bacterial RNA from Escherichia coli K1 interacting with human brain microvascular endothelial cells. The extracted RNA was free of human RNA contamination. More importantly, microarray analysis demonstrated that no bias was introduced in the gene expression pattern during the RNA isolation procedure.

Brain↗
PubMed1995

Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA.

Sequence analysis of 236 promoters recognized by the Bacillus subtilis sigma A-RNA polymerase reveals an extended promoter structure. The most highly conserved bases include the -35 and -10 hexanucleotide core elements and a TG dinucleotide at position -15, -14. In addition, several weakly conserved A and T residues are present upstream of the -35 region. Analysis of dinucleotide composition reveals A2- and T2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNA helix: An tracts are common near -43, -54 and -65; Tn tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of An and Tn sequences for n > 4. These data indicate that an RNA polymerase binding site affects DNA sequence as far upstream as -70. This sequence conservation is discussed in light of recent evidence that the alpha subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.

Adenine↗
PubMed2006

Introduction of silencing-inducing transgenes does not affect expression of known transcripts.

While the RNA interference (RNAi) mechanism has only been discovered a decade ago, RNAi is now often used to study gene function by sequence-specific knockdown of gene expression. However, it is still unknown whether introduction of silencing-inducing transgenes alters the transcriptome. To address this question, genome-wide transcriptional changes in silenced and non-silenced backgrounds were monitored through microarray analysis. No significant transcriptional changes were detected when compared to the non-silenced control. This result was confirmed by real-time polymerase chain reaction analysis of genes known to be involved in RNA silencing. In conclusion, introduction of silencing-inducing constructs does not affect expression of known transcripts in other genes than in those homologous to the targeted ones. Consequently, when gene function is studied by RNAi, the transcriptional changes detected will specifically be the result of knockout of the gene of interest, at least for the genes present on the array used in our study.

Arabidopsis↗
PubMed2005

Global effects on gene expression in fission yeast by silencing and RNA interference machineries.

Histone modifications influence gene expression in complex ways. The RNA interference (RNAi) machinery can repress transcription by recruiting histone-modifying enzymes to chromatin, although it is not clear whether this is a general mechanism for gene silencing or whether it requires repeated sequences such as long terminal repeats (LTRs). We analyzed the global effects of the Clr3 and Clr6 histone deacetylases, the Clr4 methyltransferase, the zinc finger protein Clr1, and the RNAi proteins Dicer, RdRP, and Argonaute on the transcriptome of Schizosaccharomyces pombe (fission yeast). The clr mutants derepressed similar subsets of genes, many of which also became transcriptionally activated in cells that were exposed to environmental stresses such as nitrogen starvation. Many genes that were repressed by the Clr proteins clustered in extended regions close to the telomeres. Surprisingly few genes were repressed by both the silencing and RNAi machineries, with transcripts from centromeric repeats and Tf2 retrotransposons being notable exceptions. We found no correlation between repression by RNAi and proximity to LTRs, and the wtf family of repeated sequences seems to be repressed by histone deacetylation independent of RNAi. Our data indicate that the RNAi and Clr proteins show only a limited functional overlap and that the Clr proteins play more global roles in gene silencing.

Cell Cycle Proteins↗
PubMed2007

Real time PCR profiling of 330 human micro-RNAs.

The small size of miRNAs makes profiling of all the 462 known human miRNAs difficult using single cell samples. Recently, we showed that judicious sequence partitioning between RT primers and second strand synthesis primers permitted multiplexed RT-PCR amplification of miRNA in very small samples to allow individual real time PCR quantification. Here, we show that zip coding the primers and TaqMan probes with sequences specific to each miRNA greatly improves reaction specificity, which permits the profiling of all miRNAs in a single multiplexed RT-PCR reaction.

Base Sequence↗
PubMed2026

Whole-transcriptome RNA sequencing and ceRNA network analyses provide novel insights into the antibacterial immune response of Hippocampus abdominalis against Vibrio harveyi.

Long non-coding RNAs (lncRNAs) stand as newly-arisen molecular types that exert regulatory effects, able to operate as competitive endogenous RNAs (ceRNAs) to engage microRNAs (miRNAs) in interaction, resulting in the recovery of target mRNA expression and activity. Increasing evidences indicate that the ceRNA network affects various biological processes in mammals, including development, cellular differentiation, metabolism, immune response, and disease pathogenesis. In teleost fish, the lncRNA-miRNA-mRNA regulatory networks have been reported occasionally. However, up to now, the roles of lncRNAs in the big-belly seahorse (Hippocampus abdominalis) remains unclear. In this study, we reported for the first time, via whole-transcriptome RNA sequencing, the lncRNA mediated ceRNA regulatory network in Vibrio harveyi-infected H. abdominalis. A total of 4197 differentially expressed mRNAs (DE-mRNAs), 1317 DE-lncRNAs, and 183 DE-miRNAs were identified. Furthermore, the crosstalk between miRNAs and lncRNAs as well as between miRNAs and mRNAs was inferred based on the negative correlations between miRNAs and their target lncRNAs/mRNAs. A core immune associated lncRNA-miRNA-mRNA putative regulatory network was thus constructed, comprising 211 lncRNA-miRNA and 224 mRNA-miRNA pairs. In conclusion, our findings provide an integrative overview of the ceRNA regulatory networks on the underlying immune responses to V. harveyi infection in the big-belly seahorse, and offer a solid theoretical foundation for the comparative immunological research of teleost fish.

Animals↗
PubMed2001

Proposed secondary structure of eukaryote specific expansion segment 15 in 28S rRNA from mice, rats, and rabbits.

The expansion segments in eukaryotic ribosomal RNAs are additional RNA sequences not found in the RNA core common to both prokaryotes and eukaryotes. These regions show large species-dependent variations in sequence and size. This makes it difficult to create secondary structure models for the expansion segments exclusively based on phylogenetic sequence comparison. Here we have used a combination of experimental data and computational methods to generate secondary structure models for expansion segment 15 in 28S rRNA in mice, rats, and rabbits. The experimental data were collected using the structure sensitive reagents DMS, CMCT, kethoxal, micrococcal nuclease, RNase T(1), RNase CL3, RNase V(1), and lead(II) acetate. ES15 was folded with the computer program RNAStructure 3.5 using modification data and phylogenetic similarities between different ES15 sequences. This program uses energy minimization to find the most stable secondary structure of an RNA sequence. The presented secondary structure models include several common structural motifs, but they also have characteristics unique to each organism. Overall, the secondary structure models showed indications of an energetically stable but dynamic structure, easily accessible from the solution by the modification reagents, suggesting that the expansion segment is located on the ribosomal surface.

Aldehydes↗
PubMed2025

The offonome reveals on and off states of gene expression near the detection limit of RNA-seq.

RNA-seq, widely used for gene expression profiling, provides nucleotide level genome coverage and summary gene expression values. Generally, low-expressed genes are ignored due to their unfavorable signal-to-noise ratio, however, these genes may offer crucial information, such as detecting rare cells in bulk tissues. In this study, we applied an approach that transforms the expression levels of low-expressed genes into a robust dichotomized on/off state by leveraging similarities in transcript coverage shape. Applied to three human cancer cohorts from the Cancer Genome Atlas (TCGA), chosen based on tissue morphology and anatomic site, we identified genes, the "offonome" near the detection limit, consistently or occasionally off across samples. Genes in the offonome spectrum proved useful for supervised and unsupervised applications, including characterizing oncogenic pathways, and identifying rare populations of cells in bulk tissue. Interrogating the offonome is relevant to bulk tumor analyses like TCGA, potentially expediting gene investigation in low-input situations like single cell RNA-seq.

Humans↗
PubMed2006

The homeobox HOXB13 is expressed in human minor salivary gland.

BACKGROUND: Homeobox are a family of developmental genes involved in morphogenesis and cellular differentiation. Participation of homeobox within normal and malignant tissue has been recently discussed in the literature. OBJECTIVE: To analyze the presence of HOXB13 transcript expression in human minor salivary gland. MATERIAL AND METHODS: Ten-micrometer sections from frozen samples were evaluated employing non-radioactive in situ hybridization technique and HOXB13 mRNA probes. RESULTS: HOXB13 was found to be expressed in ducts and mucous acini but not in serous acini. CONCLUSIONS: RESULTS suggest that HOXB13 transcripts are differently expressed in normal mucous and serous acini, and it may possibly reflect a different role in salivary gland carcinogenesis.

Carcinoma, Squamous Cell↗
PubMed2003

The mRNA expression of insulin receptor isoforms (IR-A and IR-B) and IGFR-2 in the bovine corpus luteum during the estrous cycle, pregnancy, and induced luteolysis.

Isoform A of the human insulin receptor and the IGF-receptor type 2 (IGFR-2) are both receptors for insulin- like growth factor II (IGF II), which plays a major role in luteal development and function in bovine species. The objective of this study was to determine if both insulin receptor isoforms and IGFR-2 were expressed in the bovine corpus luteum (CL) and if they were regulated during the estrous cycle, pregnancy, and induced luteolysis. CL were collected at the slaughterhouse. For induced luteolysis, CL were obtained by transvaginal ovariectomy at 2, 4, 12, 48, and 64 h after prostaglandin (PG) F2alpha-injection. Real-time RT-PCR was applied to investigate mRNA expression. Two alternatively spliced transcripts encoding the insulin receptor were detected in bovine CL. These two isoforms corresponded to the known isoforms A (IR-A) and B (IR-B) in humans. IR-A mRNA predominated in bovine CL and was significantly down-regulated on d 5-7. IR-B mRNA was significantly up-regulated in the late luteal stage and during early pregnancy. IR-A showed a significant down-regulation at 48 h after PGF2. IGFR-2 mRNA was significantly up-regulated in mid and late luteal stages (d 8-18). It is proposed that the differential mRNA expression of IR-A and IGFR-2, both binding IGF II, may play a role in the development and function of the bovine corpus luteum.

Animals↗
PubMed1998

Molecular analysis of Ewing's sarcoma: another fusion gene, EWS-E1AF, available for diagnosis.

Ewing's sarcoma, one of the most malignant tumors of children and young adults, expresses specific chimeric genes, e.g. EWS-FLI-1, EWS-ERG, EWS-ETV1 and EWS-FEV. In this paper, we extensively characterized a new fusion gene, EWS-EIAF by means of whole cDNA sequencing, RNA blot analysis, DNA blot analysis and chromosomal analysis, and showed it to be available for the diagnosis of Ewing's sarcoma and to participate in the oncogenesis of Ewing's sarcoma. Furthermore, we conducted a genetic analysis of Ewing family tumors in conjunction with immunohistochemical analysis and ultrastructural analysis. Our results demonstrate some limitations of both genetic analysis and histopathological analysis, and establish the relationship between neurogenic phenotypes and chimera genes.

Adenovirus E1A Proteins↗
PubMed2000

Mouse cathepsin F: cDNA cloning, genomic organization and chromosomal assignment of the gene.

A murine cysteine protease of the papain family was identified by dbEST-database search. A 1.87kb full-length cDNA encoding a predicted polypeptide of 462 amino acids was sequenced. Since the encoded polypeptide shows more than 80% sequence identity with human cathepsin F, it is most likely that this cDNA represents the murine homologue of cathepsin F, and it was therefore named accordingly. Murine cathepsin F exhibits a domain structure typical for papain-like cysteine proteases, a 20 amino acid N-terminal hydrophobic signal sequence followed by an extraordinarily long propeptide of 228 amino acids and the domain of the mature protease comprising 214 amino acids. The mature region contains all features characteristic of a papain-like cysteine protease, including the highly conserved cysteine, histidine and asparagine residues of the 'catalytic triad'. Genomic clones covering the murine cathepsin F gene were isolated. The mouse cathepsin F gene consists of 14 exons and 13 introns and spans 5.8kb. Murine cathepsin F was mapped to chromosome 19, a region with synteny homology to a region of human chromosome 11 to which human cathepsin F has been mapped previously. Northern blot analysis of RNA from multiple tissues revealed a ubiquitous expression of cathepsin F in mouse and man.

Amino Acid Sequence↗
PubMed2006

Nucleotide sequence analysis of the ORF0 region of Potato leafroll virus isolates from Tunisia.

Potato leafroll virus (PLRV) isolates from potato plants from different regions of Tunisia were investigated for the ORF0 variable region of genomic RNA using PCR, nucleotide sequencing and sequence analysis. Based on the ORF0 variable region nucleotide sequence, individual Tunisian isolates were more homologous as a group compared to the isolates originating from other parts of the world. There was no correlation between bioclimatic origin of the isolates and their ORF0 sequence. Alignment of the deduced amino acid sequences showed that the P0 protein was not much conserved. Unexpectedly, Tunisian isolates were found to be most homologous to Peruvian ones both at nucleotide and amino acid level. A phylogenetic tree, based on the P0 amino acid sequence, showed that all the PLRV isolates were located in two major clusters regardless of their geographic origin. In the second cluster, three sub-clusters could be distinguished. These results provide valuable information for molecular characterization of the PLRV isolates occurring in Tunisia.

Base Sequence↗
PubMed1993

An Arabidopsis thaliana lipoxygenase gene can be induced by pathogens, abscisic acid, and methyl jasmonate.

We isolated and characterized a 2.8-kb, full-length, Arabidopsis thaliana cDNA clone encoding a lipoxygenase. DNA sequence analysis showed that the deduced amino acid sequence of the Arabidopsis protein is 72 to 78% similar to that of legume seed lipoxygenases. DNA blot analysis indicated that Arabidopsis contains a single gene, LOX1, with appreciable homology to the cDNA clone. RNA blot analysis showed that the LOX1 gene is expressed in Arabidopsis leaves, roots, inflorescences, and young seedlings. LOX1 expression levels were highest in roots and young seedlings. In mature plants, LOX1 mRNA levels increased upon treatment with the stress-related hormones abscisic acid and methyl jasmonate and remained high for at least 96 h. Expression of the LOX1 gene was examined following infiltration of leaves with virulent (Psm ES4326) and avirulent (Pst MM1065) strains of Pseudomonas syringae. LOX1 mRNA levels were induced approximately 6-fold by both virulent and avirulent strains; however, the response to avirulent strains was much more rapid. Infiltration of leaves with Pst MM1065 resulted in maximal induction within 12 h, whereas maximal induction by Psm ES4326 did not occur until 48 h. When a cloned avr gene, avrRpt2, was transferred to Psm ES4326, LOX1 mRNA accumulated in a pattern similar to that observed for the avirulent strain Pst MM1065.

Abscisic Acid↗