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At least 19 recordsLinked to original sources

Control of bacteriophage P2 gene expression: analysis of transcription of the ogr gene.

The bacteriophage P2 ogr gene encodes an 8.3-kDa protein that is a positive effector of P2 late gene transcription. The ogr gene is preceded by a promoter sequence (Pogr) resembling a normal Escherichia coli promoter and is located just downstream of a late transcription unit. We analyzed the kinetics and regulation of ogr gene transcription by using an ogr-specific antisense RNA probe in an S1 mapping assay. During a normal P2 infection, ogr gene transcription starts from Pogr at an intermediate time between the onset of early and late transcription. At late times after infection the ogr gene is cotranscribed with the late FETUD operon; the ogr gene product thus positively regulates its own synthesis from the P2 late promoter PF. Expression of the P2 late genes also requires P2 DNA replication. Complementation experiments and transcriptional analysis show that a nonreplicating P2 phage expresses the ogr gene from Pogr but is unable to transcribe the late genes. A P2 ogr-defective phage makes an increased level of ogr mRNA, consistent with autogenous control from Pogr. Transcription of the ogr gene in the prophage of a P2 heteroimmune lysogen is stimulated after infection with P2, suggesting that Pogr is under indirect immunity control and is activated by a yet-unidentified P2 early gene product during infection.

Coliphages

Cytokine gene expression: analysis using northern blotting, polymerase chain reaction and in situ hybridization.

We describe here the use of northern blotting, PCR and in situ hybridization for the analysis of cytokine gene expression. These techniques, each with their advantages and disadvantages, have been used to monitor cytokine gene expression in sites of immune reactivity and in the developing thymus. Whilst expression of a gene usually correlates well with protein production from that gene, this may not always be the case. The development of methods to analyze protein production in situ, for instance by immunohistochemistry, together with analysis of mRNA expression will allow us to begin to understand the role of cytokines within the immune system of the intact animal.

Animals

Comprehensive Identification of WDR Gene Family in Panax ginseng: PgWDR Gene Expression Analysis with Ginsenosides Biosynthesis Under MeJA.

Panax ginseng (Panax ginseng C.A. Mey.) produces pharmacologically valuable ginsenosides. WD40-repeat (WDR) proteins act as versatile regulators of plant specialized metabolism, yet their biological roles under methyl jasmonate (MeJA) elicitation remain largely uncharacterized in ginseng. In this study, we identified 29 PgWDR family members at the whole-genome level, and systematically analyzed their phylogeny, gene structure, cis-acting promoter elements, as well as organ- and development-dependent expression patterns. Six candidate genes potentially associated with ginsenoside biosynthesis were screened through integrating gene-metabolite correlation analysis and gene co-expression analysis. Under MeJA treatment, three of these candidates showed statistically significant expression responses, while the other three exhibited variable expression fluctuations with no statistical significance. PgWDR24 displayed a positive correlation with key ginsenoside biosynthetic enzyme genes, and a negative correlation with protopanaxadiol-type ginsenoside accumulation. Combined with its predicted nuclear localization, we hypothesize that PgWDR24 participates in the negative modulation of protopanaxadiol-type ginsenoside accumulation, although further genetic functional validation is still required. This work provides valuable candidate genes for deciphering ginsenoside regulatory networks and offers support for molecular-assisted breeding of high-quality ginseng.

Panax ginseng C. A. Mey.

Multi-organ gene expression analysis and network modeling reveal regulatory control cascades during the development of hypertension in female spontaneously hypertensive rat.

Hypertension is a multifactorial disease with stage-specific gene expression changes occurring in multiple organs over time. The temporal sequence and the extent of gene regulatory network changes occurring across organs during the development of hypertension remain unresolved. In this study, female spontaneously hypertensive (SHR) and normotensive Wistar Kyoto (WKY) rats were used to analyze expression patterns of 96 genes spanning inflammatory, metabolic, sympathetic, fibrotic, and renin-angiotensin (RAS) pathways in five organs, at five time points from the onset to established hypertension. We analyzed this multi-dimensional dataset containing ~15,000 data points and developed a data-driven dynamic network model that accounts for gene regulatory influences within and across visceral organs and multiple brainstem autonomic control regions. We integrated the data from female SHR and WKY with published multiorgan gene expression data from male SHR and WKY. In female SHR, catecholaminergic processes in the adrenal gland showed the earliest gene expression changes prior to inflammation-related gene expression changes in the kidney and liver. Hypertension pathogenesis in male SHR instead manifested early as catecholaminergic gene expression changes in brainstem and kidney, followed by an upregulation of inflammation-related genes in liver. RAS-related gene expression from the kidney-liver-lung axis was downregulated and intra-adrenal RAS was upregulated in female SHR, whereas the opposite pattern of gene regulation was observed in male SHR. We identified disease-specific and sex-specific differences in regulatory interactions within and across organs. The inferred multi-organ network model suggests a diminished influence of central autonomic neural circuits over multi-organ gene expression changes in female SHR. Our results point to the gene regulatory influence of the adrenal gland on spleen in female SHR, as compared to brainstem influence on kidney in male SHR. Our integrated molecular profiling and network modeling identified a stage-specific, sex-dependent, multi-organ cascade of gene regulation during the development of hypertension.

Animals

Regulation of class II gene expression: analysis in B cell stimulatory factor 1-inducible murine pre-B cell lines.

We have analyzed the mechanism of action of BSF-1 on class II gene expression in two murine pre-B cell lines that are at different stages of differentiation. In vitro transcription assays demonstrated that BSF-1 induced rapid transcription of class II genes within 1 hr by a mechanism that was independent of protein synthesis. Although cell surface expression of class II was detectable by 2 hr after induction and persisted for up to 96 hr after removal of BSF-1, levels of class II-specific mRNA and density of cell surface class II increased to a maximum between 24 and 72 hr after induction. Furthermore, prostaglandin E2 prevented the induction of class II gene expression by BSF-1. The effects of BSF-1 are unlikely to be mediated through calcium fluxes or activation of protein kinase C, since treatment with agents such as PMA and the calcium ionophore A23187 did not result in expression of class II molecules. Other lymphokines, such as IFN-gamma, IL 1, IL 2, and IL 3, did not affect class II gene expression in these two cell lines. These data provide further insight into the mechanisms by which class II gene expression is regulated in B cells.

Animals

Baculovirus gp64 gene expression: analysis of sequences modulating early transcription and transactivation by IE1.

Expression of the baculovirus major envelope glycoprotein gene (gp64) is regulated by transcription from both early and late promoters. To characterize the early promoter and identify sequences involved in the regulation of gp64 early transcription, promoter-reporter gene fusions were generated from the Orygia pseudotsugata nuclear polyhedrosis virus gp64 promoter and were analyzed by transient expression in uninfected insect cells. For these analyses, 5' deletion mutations were constructed in the gp64 upstream regulatory region. Larger promoter constructs were functional in uninfected Lymantria dispar cells, indicating that transcription from the gp64 early promoter required no additional viral gene products. Deletion analysis of the gp64 upstream region revealed several regulatory regions. These included a putative negative regulatory element between -319 and -166 nucleotides (nt) and multiple positive regulatory elements between -166 and -77 nt. Deletion of the TATA box located between -77 and -62 nt resulted in the loss of transcriptional activity. Cotransfections of reporter constructs and a plasmid containing a baculovirus transcriptional transactivator gene (Autographa californica nuclear polyhedrosis virus IE1) resulted in transcriptional transactivation of all constructs containing an intact TATA box. These data demonstrate that sequences upstream of the gp64 TATA box are not essential for IE1 transactivation and that only 34 nt upstream of the early transcription start site were necessary for basal levels of transcription and for transactivation by IE1. Function of the gp64 early promoter was also examined in cell lines from Spodoptera frugiperda and Drosophila melanogaster.

Amino Acid Sequence

Control of cytochrome P1-450 gene expression: analysis of a dioxin-responsive enhancer system.

We analyzed the function and sequence of a dioxin-responsive genomic element flanking the 5' end of the cytochrome P1-450 gene in high-activity variant mouse hepatoma cells. The element can regulate the mouse mammary tumor virus promoter. The element retains responsiveness to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) when the distance, the 5' or 3' position, and/or the 5' or 3' orientation with respect to the promoter are varied. The function of the element requires TCDD-receptor complexes. The element remains responsive to TCDD when transfected into cells from either a heterologous mouse tissue or a heterologous species (human). The DNA element and TCDD receptors together constitute a dioxin-responsive enhancer system.

Acetyltransferases

T cell receptor variable gene expression: analysis in ragweed-sensitive patients during allergen exposure.

Four monoclonal antibodies (MAb) to V region determinants of the alpha/beta-chain of the T cell antigen receptor (TCR) were used, by cytofluorography, to detect discrete populations of peripheral blood T cells (PBT). Together they identify 10-15% of circulating CD3+ T cells. Each MAb is known to detect specific V regions of the beta-chain. Thus V beta 5 gene products are recognized by MAb C37, V beta 6 by OT145, V beta 8 by Ti3a, and V beta 12 by MAb S511. In previous studies, we found that the percentages of PBT detected by these MAb show little variation over time in normal individuals. In order to determine if there is a change in TCR V gene usage during an immune response to an environmental antigen, 12 atopic patients with known ragweed sensitivity by history and skin test were followed for a 6-month period encompassing the ragweed season. No shifts in V gene usage that could be correlated with the ragweed season were consistently observed. The patients could be arbitrarily divided into two groups: in group I little variation over time was observed in the T cell populations identified by the MAb used, while group II was characterized by marked variation of the same T cell populations over time. In group II individuals, the population of Ti3a+ T cells showed the most variation over time. Failure to observe shifts in PBT subpopulations, identified by expression of different TCR V regions, during exposure to an allergen to which an IgE response has been made may mean that such shifts do not occur or that they occur primarily at the tissue site of antigen exposure and not in the peripheral circulation or that they occur in T cell subpopulations not identified by the reagents used.

Adult

De novo transcriptome assembly and gene expression analysis of Cnidium officinale under high-temperature conditions.

BACKGROUND: The medicinal plant Cnidium officinale (CO) is widespread in Northeast Asia and vulnerable to heat stress. The naturally occurring composition of pharmacological ingredients of CO results in overall physiological consequences; therefore, it is crucial to have a comprehensive understanding of metabolic response to ambient heat in terms of acclimation to estimate how much CO is exposed to threatening environmental conditions. RESULTS: Transcriptome analysis is critical for understanding the consequences of long-term physiological adaptation of CO to abiotic stress. However, transcriptome analysis on this species, particularly under prolonged stress conditions, has remained limited. We employed a temperature gradient tunnel (TGT) to subject CO to high-temperature exposure for four months, enabling us to observe the cumulative effects of heat and assess its acclimation mechanisms. In the absence of genome sequencing data, we performed de novo transcriptome assembly and compared DEGs from temperature treatment plots of a TGT and a growth chamber (GC). Since interpreting transcriptomic data can be complex, we employed a sequential analytical approach, including DEG clustering, GO enrichment, KEGG pathway mapping, miRNA-target gene analysis, and multiple rounds of RNA sequencing validation. DEGs were classified into two categories: genes exhibiting significant fold changes and genes showing significant count changes rather than fold changes. Then, we analyzed the functional roles of DEGs to determine which pathways respond to ambient and stressful high temperatures and validated the findings through cross-comparison with GC. Additionally, we conducted miRNA analysis to investigate post-transcriptional regulation under high temperatures. CO grown under higher ambient temperatures exhibited slight upregulation of pathways related to protein stability and turnover, ABA biosynthesis, and energy production, such as photosynthesis and oxidative phosphorylation. However, under extreme heat stress, most metabolic pathways were downregulated except for those involved in transcription, translation, oxidative phosphorylation and the biosynthesis of cutin, suberin, and wax. CONCLUSION: This study demonstrated that proper clustering of genes based on expression levels and fold changes in two different experimental conditions, along with pathway mapping, may provide a comprehensive understanding of CO's response to heat stress. These insights could contribute to future research on heat tolerance and crop improvement.

Gene Expression Profiling

Complex regulation of class II gene expression: analysis with class II mutant cell lines.

Several Ia-negative variants of a homozygous Iad-expressing antigen-presenting B lymphoma cell line, M12, have been obtained by repeated cycles of negative immunoselection after mutagenesis with ethylmethane sulfonate or gamma-irradiation. Two such Iad-negative cell lines, selected with a mixture of alpha I-Ad and alpha I-Ed monoclonal antibodies, failed to present antigen to all cloned Iad-restricted T cells tested, whereas the third cell line, selected with alpha I-Ad reagents only, stimulated I-Ed but not I-Ad-restricted T cells. The mutations in all three cell lines resulted in the absence of RNA specific for the A beta d gene. In addition, two-dimensional gel electrophoresis of immunoprecipitates from one of the I-Ed-negative cell lines demonstrated the presence of intracytoplasmic Ed polypeptides that exhibited significantly decreased amounts of oligosaccharide-induced heterogeneity. The introduction of class II A beta b and A alpha b genes by DNA-mediated transfection resulted in the serologic and functional expression of a class II I-Ab molecule but not the reexpression of the endogenous class II molecules; thus a transacting regulatory element is unlikely to be the target of the mutagenic event. The analysis of these and other Ia variant cell lines may prove useful in understanding the molecular mechanisms that control the expression of class II molecules in B cells.

Animals

Optimized Hot Phenol-Based RNA Extraction from Mycobacteria: A Robust Approach for Reliable Gene Expression Analysis.

Mycobacterium tuberculosis (Mtb) remains a major global health threat, underscoring the need for reliable transcriptomic studies to understand its biology and drug resistance mechanisms. Such analyses depend on obtaining high-quality, high-yield RNA. Although several RNA extraction methods are available, many require expensive reagents, large culture volumes, or specialized equipment, limiting their suitability for large-scale studies, particularly in resource-constrained settings. Here, an optimized Hot Phenol based RNA extraction method specifically tailored for mycobacteria is presented. The method uses minimal culture volume and commonly available reagents to consistently yield high-quality RNA suitable for high-throughput transcriptomic applications. RNA quantity and integrity were assessed by gel electrophoresis and RNA integrity analysis (RIN), and its suitability for downstream applications was confirmed by qPCR and Qubit 4. To benchmark the performance of the optimized method, a parallel RNA extraction using TRIzol and RNeasy under identical experimental conditions was carried out, including the same Mycobacterium species, culture volume, growth phase (logarithmic and stationary), and lysis conditions. This allowed a direct comparison of yield, quality, feasibility, and cost. The optimized Hot Phenol method demonstrated comparable or improved RNA yield and quality while significantly reducing reagent cost and dependence on specialized equipment. Owing to its efficiency, reproducibility, and affordability, this protocol provides a practical alternative for large-scale gene expression and transcriptomic studies in Mtb and other mycobacterial species.

RNA, Bacterial

Three years' experience with neonatal screening for Duchenne/Becker muscular dystrophy: gene analysis, gene expression, and phenotype prediction.

Neonatal screening for Duchenne/Becker Muscular dystrophy (DMD/BMD) was begun as a pilot program on January 1, 1986. The aim of this program was to reduce the incidence of this X-linked recessive degenerative neuromuscular disease. The neonatal detection of a boy with DMD allows early identification of carriers and genetic counselling. This may avert the birth of other affected males born prior to clinical diagnosis of DMD in the propositus at about age 5 years. Between January 1, 1986, and December 31, 1988, we identified and characterized a cohort of 8 asymptomatic infant boys with grossly elevated levels of creatine kinase, an active primary dystrophic process of muscle and complete dystrophin deficiency. Five of 8 males have detectable DNA alterations involving the DMD/BMD locus. Based on current hypotheses, characterization of dystrophin expression of this cohort allows us to predict a DMD phenotype in all 8 boys. To date, no additional males with DMD have been born in these families. Prospective follow-up will allow us to test the validity of dystrophin testing in predicting the clinical course and impact of this program on reproductive decision making in these families.

Cohort Studies

Expression polymerase chain reaction: a sensitive method for analysis of gene expression in human tumours.

To analyse the expression of individual genes in small tumour samples, we have used the method of RNA polymerase chain reaction (PCR) to develop a technique which we have termed expression PCR. With this technique, specific cDNA sequences of a target gene are amplified, analysed by gel electrophoresis, and semi-quantitated using laser densitometry. Alpha-actin is amplified as a reference gene to control for template RNA and each target gene is analysed at several cycle numbers to optimize PCR dynamics. In this study, we have demonstrated expression PCR by analysing the levels of expression of tyrosine kinase genes in a panel of human tumours. We have compared expression PCR with Northern analysis to show that these techniques provide equivalent information on relative levels of gene transcription, with expression PCR requiring 100-fold less RNA. This technique is sufficiently sensitive to detect and compare the levels of expression of genes not seen on Northern analysis and is ideally suited for analysing the expression of multiple genes within the same portion of a tumour.

Base Sequence

Distinct periarticular muscle transcriptomes: inflammation in rheumatoid arthritis versus metabolic dysregulation in osteoarthritis.

OBJECTIVES: Periarticular skeletal muscle abnormalities are recognised in rheumatoid arthritis (RA) and osteoarthritis (OA), but their divergent molecular pathologies are poorly defined. This study aimed to elucidate and directly compare the transcriptomic profiles of periarticular muscle in patients with RA and OA. METHODS: We performed bulk RNA sequencing of periarticular skeletal muscle samples collected during total joint arthroplasty from RA (n=6) and OA (n=4) patients. Differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), pathway enrichment, and gene set variation analyses were conducted to identify disease-specific molecular features and their clinical associations. RESULTS: The two conditions showed fundamentally distinct profiles. RA muscle exhibited a pronounced inflammatory signature, characterised by upregulation of cytokine-responsive genes including FOS, EGR1, and CXCL2, and enrichment of tumour necrosis factor-α and interleukin-6 (IL-6)/JAK-STAT3 signalling. In contrast, OA muscle was characterised by metabolic dysregulation, with upregulation of genes linked to adipogenesis (PCK1, SFRP4) and significant enrichment of epithelial-to-mesenchymal transition (EMT) signalling. These divergent profiles were further supported by WGCNA, which identified distinct modules reflecting heightened innate immune and complement activation in RA, and disrupted metabolic processes in OA. Notably, in RA, the IL-2-STAT5 signalling pathway was unique among those tested in showing a strong positive correlation with DAS28-ESR (r=0.94, p=0.019). CONCLUSIONS: This study reveals distinct molecular pathologies in the periarticular muscle of RA and OA. RA muscle shows an intense inflammatory profile potentially linked to cachexia, whereas OA muscle displays features of metabolic disease and pro-fibrotic remodelling.

Humans

transfactor: transcription factor activity estimation via probabilistic gene expression deconvolution.

Gene expression is a primary modality being studied to differentiate between biological cells. Contemporary single-cell studies simultaneously measure genome-wide transcription levels for thousands of individual cells in a single experiment. While the characterization of cell population differences has often occurred through differential gene expression analysis, tiny effect sizes become statistically significant when thousands of cells are available for each population, compromising biological interpretation. Moreover, these large studies have spurred the development of methods to infer gene regulatory networks (GRNs) directly from the data, and GRN databases are becoming more comprehensive. In this work, we propose a statistical model for gene expression measures and an inference method that leverage GRNs to deconvolve transcription factor (TF) activity from gene expression, by probabilistically assigning mRNA molecules to TFs. This shifts the paradigm from investigating gene expression differences to regulatory differences at the level of TF activity, aiding interpretation and allowing prioritization of a limited number of TFs responsible for significant contributions to the observed gene expression differences. The inferred TF activities result in intuitive prioritization of TFs in terms of the (difference in) estimated number of molecules they produce, in contrast to other widely used methods relying on arbitrary enrichment scores. Our model allows the incorporation of prior information on the regulatory potential between each TF and target gene and is able to deal with both repressing and activating interactions. We compare our approach to other TF activity estimation methods using two simulation experiments and two case studies. Single-cell RNA-sequencing; TF activity; bioinformatics; GRN.

Transcription Factors

Cloning of GT box-binding proteins: a novel Sp1 multigene family regulating T-cell receptor gene expression.

Analysis of a T-cell antigen receptor (TCR) alpha promoter from a variable gene segment (V) revealed a critical GT box element which is also found in upstream regions of several V alpha genes, TCR enhancer, and regulatory elements of other genes. This element is necessary for TCR gene expression and binds several proteins. These GT box-binding proteins were identified as members of a novel Sp1 multigene family. Two of them, which we term Sp2 and Sp3, were cloned. Sp2 and Sp3 contain zinc fingers and transactivation domains similar to those of Sp1. Like Sp1, Sp2 and Sp3 are expressed ubiquitously, and their in vitro-translated products bind to the GT box in TCR V alpha promoters. Sp3, in particular, also binds to the Sp1 consensus sequence GC box and has binding activity similar to that of Sp1. As the GT box has also previously been shown to play a role in gene regulation of other genes, these newly isolated Sp2 and Sp3 proteins might regulate expression not only of the TCR gene but of other genes as well.

Amino Acid Sequence

Identification of radiation-sensitive genes as biomarkers for biodosimetry: an ex vivo analysis of TNFRSF10B, ZMAT3, POLH, and PLK2 in human blood samples.

BACKGROUND: Humans are exposed to ionizing radiation (IR), which causes direct and indirect DNA damage. Biodosimetry is a critical component of clinical care following radiation exposure, enabling accurate assessment and mitigation of health effects. The present study was conducted to investigate the ex vivo expression of the genes TNFRSF10B, ZMAT3, PLK2, and POLH in human peripheral blood samples exposed to X-radiation at doses of 0, 0.5, 2, and 4 Gy at 0, 4, 24, and 48 hours post-exposure. Investigating gene expression dynamics through biodosimetry is a novel approach that may provide insights into gene-specific responses, potentially enhancing the accuracy and sensitivity of radiation dose assessment. MATERIALS AND METHODS: Peripheral blood samples were collected from five healthy volunteers and exposed to 0, 0.5, 2, or 4 Gy radiation with a 6 MV linear accelerator. Following the extraction of RNA and cDNA synthesis, gene expression analysis via qRT&#x2012;PCR was performed. These genes were normalized against the housekeeping gene &#x3b2;-actin, and the &#x394;&#x394;Ct method was used for statistical analysis of gene expression. The data were subjected to statistical analysis, and the level of significance (p < 0.05) was determined to test the effects of dose and time on gene expression. RESULTS: The expression of the TNFRSF10B, ZMAT3, POLH, and PLK2 genes was markedly dose- and time-dependent in response to X-ray radiation in vitro. Whole-blood samples irradiated at doses of 0, 0.5, 2, and 4 Gy and analyzed at four time points, 0, 4, 24, and 48 hours, respectively, revealed marked changes in the expression levels of the genes studied, revealing the mechanisms of the response at the cellular level to ionizing radiation. Although minor inter-individual variation in gene expression was observed, it did not significantly affect the overall trends, and the results remained statistically robust. CONCLUSION: These findings highlight a robust biodosimetry framework: TNFRSF10B demonstrated the highest diagnostic performance (AUC = 0.94; sensitivity = 98%; specificity = 75%; cut-off = 1.11), making it a highly reliable biomarker for radiation exposure. PLK2 also exhibited strong discriminative capacity (AUC = 0.84; sensitivity = 90%; specificity = 80%; cut-off =2.5), particularly for minimizing false positives. ZMAT3 (AUC = 0.78; sensitivity/specificity = 75%; cut-off = 3.21) showed balanced early-phase performance, whilePOLH (AUC = 0.73; sensitivity = 80%; specificity = 60%; cut-off = 1.10) may serve as a complementary marker. Collectively, these findings support a multi-gene expression approach for accurate biodosimetric assessment and improved triage following radiation exposure.

Humans

Expression of housekeeping genes in Hodgkin's disease lymph nodes.

Housekeeping genes, particularly actin, tubulin, and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH), are widely used to estimate the amount and integrity of RNA in Northern blotting. In this work, the most reliable housekeeping gene for gene expression analysis of Hodgkin's disease (HD) lymph nodes was determined by comparing the conventional housekeeping genes, beta-actin, beta-tubulin, GAPDH, and the mouse gene LLRep3, that had been used previously in gene expression studies. It was found that the amounts of mRNA in these genes are very heterogeneous in HD lymph nodes. In contrast, their expression was relatively constant in tonsils undergoing a chronic inflammatory process. It is concluded that none of the housekeeping genes tested is suitable for the fine quantitative analysis of gene expression in HD lymph nodes.

Actins