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Rodrigues, Paulo H., and Ann Progulske-Fox. "Gene Expression Profile Analysis of Porphyromonas gingivalis during Invasion of Human Coronary Artery Endothelial Cells." Infection and Immunity 73, no. 9 (September 2005): 6169–73. http://dx.doi.org/10.1128/iai.73.9.6169-6173.2005.
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ABSTRACT Microarrays were used to identify genes of Porphyromonas gingivalis W83 differentially expressed during invasion of primary human coronary artery endothelial cells. Analyses of microarray images indicated that 62 genes were differentially regulated. Of these, 11 genes were up-regulated and 51 were down-regulated. The differential expression of 16 selected genes was confirmed by real-time PCR.
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Jagoueix-Eveillard, Sandrine, Frank Tarendeau, Karine Guolter, Jean-Luc Danet, Joseph M. Bové, and Monique Garnier. "Catharanthus roseus Genes Regulated Differentially by Mollicute Infections." Molecular Plant-Microbe Interactions® 14, no. 2 (February 2001): 225–33. http://dx.doi.org/10.1094/mpmi.2001.14.2.225.
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A differential display of mRNAs was used to isolate periwinkle cDNAs differentially expressed following infection with one of three mollicutes: Spiroplasma citri, Candidatus Phytoplasma aurantifolia, and stolbur phytoplasma. Twenty-four differentially expressed cDNAs were characterized by Northern blots and sequence analysis. Eight of them had homologies with genes in databanks coding for proteins involved in photosynthesis, sugar transport, response to stress, or pathways of phytosterol synthesis. The regulation of these genes in periwinkle plants infected by additional phloem-restricted bacteria showed that they were not specific to a given mollicute, but correlations with particular symptoms could be established. Expression of transketolase was down regulated following infection with a pathogenic strain of S. citri. No down regulation was observed for the nonphytopathogenic mutant GMT553, which is deficient for fructose utilization.
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Jin, Long, Jian Ping Yu, Zai Jun Yang, Juha Merilä, and Wen Bo Liao. "Modulation of Gene Expression in Liver of Hibernating Asiatic Toads (Bufo gargarizans)." International Journal of Molecular Sciences 19, no. 8 (August 10, 2018): 2363. http://dx.doi.org/10.3390/ijms19082363.
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Hibernation is an effective energy conservation strategy that has been widely adopted by animals to cope with unpredictable environmental conditions. The liver, in particular, plays an important role in adaptive metabolic adjustment during hibernation. Mammalian studies have revealed that many genes involved in metabolism are differentially expressed during the hibernation period. However, the differentiation in global gene expression between active and torpid states in amphibians remains largely unknown. We analyzed gene expression in the liver of active and torpid Asiatic toads (Bufo gargarizans) using RNA-sequencing. In addition, we evaluated the differential expression of genes between females and males. A total of 1399 genes were identified as differentially expressed between active and torpid females. Of these, the expressions of 395 genes were significantly elevated in torpid females and involved genes responding to stresses, as well as contractile proteins. The expression of 1004 genes were significantly down-regulated in torpid females, most which were involved in metabolic depression and shifts in the energy utilization. Of the 715 differentially expressed genes between active and torpid males, 337 were up-regulated and 378 down-regulated. A total of 695 genes were differentially expressed between active females and males, of which 655 genes were significantly down-regulated in males. Similarly, 374 differentially expressed genes were identified between torpid females and males, with the expression of 252 genes (mostly contractile proteins) being significantly down-regulated in males. Our findings suggest that expression of many genes in the liver of B. gargarizans are down-regulated during hibernation. Furthermore, there are marked sex differences in the levels of gene expression, with females showing elevated levels of gene expression as compared to males, as well as more marked down-regulation of gene-expression in torpid males than females.
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Wan, Guoqiang, Wenyang Zhou, Yang Hu, Rui Ma, Shuilin Jin, Guiyou Liu, and Qinghua Jiang. "Transcriptional Regulation of lncRNA Genes by Histone Modification in Alzheimer’s Disease." BioMed Research International 2016 (2016): 1–4. http://dx.doi.org/10.1155/2016/3164238.
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Increasing studies have revealed that long noncoding RNAs (lncRNAs) are not transcriptional noise but play important roles in the regulation of a wide range of biological processes, and the dysregulation of lncRNA genes is associated with disease development. Alzheimer’s disease (AD) is a chronic neurodegenerative disease that usually starts slowly and gets worse over time. However, little is known about the roles of lncRNA genes in AD and how the lncRNA genes are transcriptionally regulated. Herein, we analyzed RNA-seq data and ChIP-seq histone modification data from CK-p25 AD model and control mice and identified 72 differentially expressed lncRNA genes, 4,917 differential peaks of H3K4me3, and 1,624 differential peaks of H3K27me3 between AD and control samples, respectively. Furthermore, we found 92 differential peaks of histone modification H3K4me3 are located in the promoter of 39 differentially expressed lncRNA genes and 8 differential peaks of histone modification H3K27me3 are located upstream of 7 differentially expressed lncRNA genes, which suggest that the majority of lncRNA genes may be transcriptionally regulated by histone modification in AD.
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Jefferies, D., M. Botman, C. Farquharson, D. Lester, C. C. Whitehead, B. H. Thorp, and B. Houston. "Cloning differentially regulated genes from chondrocytes using agarose gel differential display." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1396, no. 3 (March 1998): 237–41. http://dx.doi.org/10.1016/s0167-4781(97)00234-0.
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Arvidsson, Gustav, and Anthony Wright. "A Protein Intrinsic Disorder Approach for Characterising Differentially Expressed Genes in Transcriptome Data: Analysis of Cell-Adhesion Regulated Gene Expression in Lymphoma Cells." International Journal of Molecular Sciences 19, no. 10 (October 10, 2018): 3101. http://dx.doi.org/10.3390/ijms19103101.
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Conformational protein properties are coupled to protein functionality and could provide a useful parameter for functional annotation of differentially expressed genes in transcriptome studies. The aim was to determine whether predicted intrinsic protein disorder was differentially associated with proteins encoded by genes that are differentially regulated in lymphoma cells upon interaction with stromal cells, an interaction that occurs in microenvironments, such as lymph nodes that are protective for lymphoma cells during chemotherapy. Intrinsic disorder protein properties were extracted from the Database of Disordered Protein Prediction (D2P2), which contains data from nine intrinsic disorder predictors. Proteins encoded by differentially regulated cell-adhesion regulated genes were enriched in intrinsically disordered regions (IDRs) compared to other genes both with regard to IDR number and length. The enrichment was further ascribed to down-regulated genes. Consistently, a higher proportion of proteins encoded by down-regulated genes contained at least one IDR or were completely disordered. We conclude that down-regulated genes in stromal cell-adherent lymphoma cells encode proteins that are characterized by elevated levels of intrinsically disordered conformation, indicating the importance of down-regulating functional mechanisms associated with intrinsically disordered proteins in these cells. Further, the approach provides a generally applicable and complementary alternative to classification of differentially regulated genes using gene ontology or pathway enrichment analysis.
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Buzzio, Oscar L., Zhenxiao Lu, Curt D. Miller, Terry G. Unterman, and J. Julie Kim. "FOXO1A Differentially Regulates Genes of Decidualization." Endocrinology 147, no. 8 (August 1, 2006): 3870–76. http://dx.doi.org/10.1210/en.2006-0167.
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The forkhead box O1A (FOXO1A) has been identified as one gene that is up-regulated early in the decidualization process. To further investigate the role of FOXO1A during this process, six genes, IGFBP1, PRL, TIMP3, LAMB1, CNR1, and DCN, shown to be up-regulated during decidualization, were chosen as potential targets of FOXO1A action. Treatment of human endometrial stromal cells with hormones (estradiol and medroxyprogesterone acetate) plus dibutyryl cAMP (H+dbcAMP) for 48 h increased expression of IGFBP1, PRL, TIMP3, CNR1, and DCN but not LAMB1, as measured by real-time PCR. Silencing of FOXO1A using small interfering RNA oligonucleotides decreased IGFBP1 and DCN levels and increased CNR1, TIMP3, and PRL levels. LAMB1 was not affected. When FOXO1A was overexpressed in human endometrial stromal cells, expression of IGFBP1, DCN, and PRL increased, whereas levels of TIMP3 and CNR1 decreased. Addition of H+dbcAMP caused an increased expression of IGFBP1, PRL, and DCN beyond that of FOXO1A alone. TIMP3 and CNR1 levels decreased even further in response to H+dbcAMP compared with FOXO1A alone. LAMB1, which was unresponsive to FOXO1A, decreased when H+dbcAMP was added. Overexpressing FOXO1A also caused a change in cell shape, in that the stromal fibroblasts acquired a rounded, epithelioid appearance. Finally, reporter studies showed that cotransfection of FOXO1A significantly increased PRL promoter activity but not TIMP3 promoter activity. Addition of H+dbcAMP resulted in a significant increase in PRL promoter activity and a significant decrease in TIMP3 promoter activity. In summary, this study demonstrates the versatile nature of FOXO1A in the regulation of a number of decidualization-specific genes.
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Dedonder, A., R. Rethy, H. Fredericq, M. Van Montagu, and E. Krebbers. "Arabidopsis rbcS Genes Are Differentially Regulated by Light." Plant Physiology 101, no. 3 (March 1, 1993): 801–8. http://dx.doi.org/10.1104/pp.101.3.801.
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Elalfy, Mahmoud M., and Jürgen Borlak. "Exon Array Analysis to Identify Diethyl-nitrosamine Differentially Regulated and Alternately Spliced Genes in Early Liver Carcinogenesis in the Transgenic Mouse ATT-myc Model." SciMedicine Journal 3, no. 2 (June 1, 2021): 138–52. http://dx.doi.org/10.28991/scimedj-2021-0302-6.
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Objectives: To identify the regulated genes or the spliced genes of diethylnitorsamine (NDEA) in ATT-myc mice versus control group. Methods: We analysed the 9 hybridizations on the MouseExon10ST array of NDEA treatments and control non- transgenic by application of a mixed model analysis of variance. Results: The 907 genes had regulated significantly between the groups and 916 genes had regulated with a significant exon-group interaction among of them 150 genes had regulated with both gene and possible splicing differences (p<0.01). The 7,618 genes had tested for the alternative gene up-regulation and splicing and compared to the gene-classifications. The genes functions, pathways and gene-classifications in the current study had presented in the contingency table analysis of the set of the regulated genes and alternatively spliced that regulated significantly in the ATT-myc mice treated by diethylnitorsamine versus control non-transgenic. The GOMolFn of gene-classification had 321 groups that had significantly regulated in the set of the regulated genes or differentially spliced. While the GOProcess of gene-classification had 330 groups that had significantly regulated in the set of differentially regulated genes or spliced. Additionally, the CELlLoc of gene-classification had 70 groups that had significantly regulated in the set of differentially regulated genes spliced. Finally, the Pathway gene-classification had 8 groups that had significantly regulated in the set of differentially regulated genes or spliced (p<0.01) in diethylnitorsamine when compared to control group. Conclusion: we summarized the toxicogenomics induced by diethylnitrosamine in early liver carcinogenesis in ATT-myc transgenic mice of liver cancer. Doi: 10.28991/SciMedJ-2021-0302-6 Full Text: PDF
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Fuchun, Si, Yue Jingyu, and Si Gao. "Screening of differentially expressed genes of esophageal squamous cell carcinoma with cDNA microarray." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): e13005-e13005. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13005.
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e13005 Background: Esophageal Carcinoma (EC) is one of the most common malignant tumors in digestive system and is the sixth leading cause of cancer-related mortality worldwide. To find out the genes related with the occurrence and development of EC can help to elucidate the pathogenesis and molecular mechanism of it. The aim of the present study was to find out differentially expressed genes of EC in different stages(cancerous tissue, paraneoplastic tissue, normal mucosa tissue) by cDNA microarray technique, so that to provide new molecular biomarker and approach for the treatment and diagnosis of EC, and contribute to comprehensively knowing the mechanism of EC occurrence and development. Methods: The whole RNA of 21 cases of EC cancerous tissue, paraneoplastic tissue and normal mucosa tissue were extracted, then using agarose gel electrophoresis to make quality control, Agilent human genome 4*44K gene chip was applied to screen differentially expressed genes. Results: 2659 differential expression genes between cancerous tissue and normal mucosa tissue were screened, included 1328 up-regulated genes and 1331 down-regulated genes; 2505 differential expression genes between cancerous tissue and paraneoplastic tissue were screened, included 1286 up-regulated genes and 1218 down-regulated genes. 48 significant up-regulation genes and 11 significant down-regulation genes were reported in association with EC for the first time. Through GO classification, screened differentially expressed genes mainly were involved in the following function and process: catalytic activity, signal transduction, molecular transport and combination, enzymatic activity regulation, transcription activity regulation, protein transportation function, cell growth and apoptosis, and so on. Conclusions: The screened differential expression genes of EC in different stages may provide experimental basis for further illuminating the occurrence mechanism of esophageal squamous carcinoma.
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Egger, Boris, Ronny Leemans, Thomas Loop, Lars Kammermeier, Yun Fan, Tanja Radimerski, Martin C. Strahm, Ulrich Certa, and Heinrich Reichert. "Gliogenesis inDrosophila: genome-wide analysis of downstream genes ofglial cells missingin the embryonic nervous system." Development 129, no. 14 (July 15, 2002): 3295–309. http://dx.doi.org/10.1242/dev.129.14.3295.
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In Drosophila, the glial cells missing (gcm) gene encodes a transcription factor that controls the determination of glial versus neuronal fate. In gcm mutants, presumptive glial cells are transformed into neurons and, conversely, when gcm is ectopically misexpressed, presumptive neurons become glia. Although gcm is thought to initiate glial cell development through its action on downstream genes that execute the glial differentiation program, little is known about the identity of these genes. To identify gcm downstream genes in a comprehensive manner, we used genome-wide oligonucleotide arrays to analyze differential gene expression in wild-type embryos versus embryos in which gcm is misexpressed throughout the neuroectoderm. Transcripts were analyzed at two defined temporal windows during embryogenesis. During the first period of initial gcm action on determination of glial cell precursors, over 400 genes were differentially regulated. Among these are numerous genes that encode other transcription factors, which underscores the master regulatory role of gcm in gliogenesis. During a second later period, when glial cells had already differentiated, over 1200 genes were differentially regulated. Most of these genes, including many genes for chromatin remodeling factors and cell cycle regulators, were not differentially expressed at the early stage, indicating that the genetic control of glial fate determination is largely different from that involved in maintenance of differentiated cells. At both stages, glial-specific genes were upregulated and neuron-specific genes were downregulated, supporting a model whereby gcm promotes glial development by activating glial genes, while simultaneously repressing neuronal genes. In addition, at both stages, numerous genes that were not previously known to be involved in glial development were differentially regulated and, thus, identified as potential new downstream targets of gcm. For a subset of the differentially regulated genes, tissue-specific in vivo expression data were obtained that confirmed the transcript profiling results. This first genome-wide analysis of gene expression events downstream of a key developmental transcription factor presents a novel level of insight into the repertoire of genes that initiate and maintain cell fate choices in CNS development.
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Parikh, Pratik, Haiqing Bai, Michael F. Swartz, George M. Alfieris, and David A. Dean. "Identification of differentially regulated genes in human patent ductus arteriosus." Experimental Biology and Medicine 241, no. 18 (July 28, 2016): 2112–18. http://dx.doi.org/10.1177/1535370216661778.
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In order to identify differentially expressed genes that are specific to the ductus arteriosus, 18 candidate genes were evaluated in matched ductus arteriosus and aortic samples from infants with coarctation of the aorta. The cell specificity of the gene's promoters was assessed by performing transient transfection studies in primary cells derived from several patients. Segments of ductus arteriosus and aorta were isolated from infants requiring repair for coarctation of the aorta and used for mRNA quantitation and culturing of cells. Differences in expression were determined by quantitative PCR using the ΔΔCt method. Promoter regions of six of these genes were cloned into luciferase reporter plasmids for transient transfection studies in matched human ductus arteriosus and aorta cells. Transcription factor AP-2b and phospholipase A2 were significantly up-regulated in ductus arteriosus compared to aorta in whole tissues and cultured cells, respectively. In transient transfection experiments, Angiotensin II type 1 receptor and Prostaglandin E receptor 4 promoters consistently gave higher expression in matched ductus arteriosus versus aorta cells from multiple patients. Taken together, these results demonstrate that several genes are differentially expressed in ductus arteriosus and that their promoters may be used to drive ductus arteriosus-enriched transgene expression.
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De León, Diva D., Cyrus Farzad, Michael F. Crutchlow, John Brestelli, John Tobias, Klaus H. Kaestner, and Doris A. Stoffers. "Identification of transcriptional targets during pancreatic growth after partial pancreatectomy and exendin-4 treatment." Physiological Genomics 24, no. 2 (February 2006): 133–43. http://dx.doi.org/10.1152/physiolgenomics.00156.2005.
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After partial pancreatectomy (Ppx), substantial regeneration of the endocrine and exocrine pancreatic compartments has been shown in adult rodents. Exendin-4 (Ex-4) is a glucagon-like peptide-1 receptor agonist that augments endocrine β-cell mass by stimulating neogenesis, proliferation, and cell survival. After Ppx, treatment with Ex-4 ameliorates hyperglycemia by stimulating β-cell mass recovery. We utilized a cDNA microarray approach to identify genes differentially regulated during pancreatic regeneration after Ppx and/or Ex-4 administration. The pancreatic remnant after Ppx showed a large number of differentially regulated genes. In contrast, Ex-4 treatment resulted in a smaller number of differentially regulated genes. Of note, a common subset of genes regulated by Ex-4 and after Ppx was identified, including three members of the mitogenic Reg gene family, Reg2, -3γ, and -3β, as well as fragilis, a gene that maintains pluripotency during germ cell specification, and Serpin b1a, a member of an intracellular protease inhibitor family involved in cell survival. These observations were confirmed by real-time PCR. We determined that Reg3β protein is also induced in the acinar pancreas after Ppx, suggesting a novel role for this factor in pancreatic growth or response to injury. Finally, comparison of transcription factor-binding sites present in the proximal promoters of these genes identified potential common transcription factors that may regulate these genes. Chromatin immunoprecipitation analyses confirmed Reg3γ as a novel transcriptional target of Foxa2 (HNF3β). Our data suggest molecular pathways that may regulate pancreatic growth and offer a unique set of candidate genes to target in the development of therapies aimed at improving pancreatic growth and function.
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Chen, Xiaoxue, and Mindan Sun. "Identification of key genes, pathways and potential therapeutic agents for IgA nephropathy using an integrated bioinformatics analysis." Journal of the Renin-Angiotensin-Aldosterone System 21, no. 2 (April 2020): 147032032091963. http://dx.doi.org/10.1177/1470320320919635.
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Purpose: This study aims to identify immunoglobulin-A-nephropathy-related genes based on microarray data and to investigate novel potential gene targets for immunoglobulin-A-nephropathy treatment. Methods: Immunoglobulin-A-nephropathy chip data was obtained from the Gene Expression Omnibus database, which included 10 immunoglobulin-A-nephropathy and 22 normal samples. We used the limma package of R software to screen differentially expressed genes in immunoglobulin-A-nephropathy and normal glomerular compartment tissues. Functional enrichment (including cellular components, molecular functions, biological processes) and signal pathways were performed for the differentially expressed genes. The online analysis database (STRING) was used to construct the protein-protein interaction networks of differentially expressed genes, and Cytoscape software was used to identify the hub genes of the signal pathway. In addition, we used the Connectivity Map database to predict possible drugs for the treatment of immunoglobulin-A-nephropathy. Results: A total of 348 differentially expressed genes were screened including 107 up-regulated and 241 down-regulated genes. Functional analysis showed that up-regulated differentially expressed genes were mainly concentrated on leukocyte migration, and the down-regulated differentially expressed genes were significantly enriched in alpha-amino acid metabolic process. A total of six hub genes were obtained: JUN, C3AR1, FN1, AGT, FOS, and SUCNR1. The small-molecule drugs thapsigargin, ciclopirox and ikarugamycin were predicted therapeutic targets against immunoglobulin-A-nephropathy. Conclusion: Differentially expressed genes and hub genes can contribute to understanding the molecular mechanism of immunoglobulin-A-nephropathy and providing potential therapeutic targets and drugs for the diagnosis and treatment of immunoglobulin-A-nephropathy.
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Majed, Sevan Omer. "RNA Sequencing-Based Total RNA Profiling; The Oncogenic MiR-191 Identification as a Novel Biomarker for Breast Cancer." Cellular and Molecular Biology 68, no. 1 (May 22, 2022): 177–91. http://dx.doi.org/10.14715/cmb/2022.68.1.22.
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This study aims to screen the differential expression of total RNA transcripts in formalin-fixed paraffin-embedded tissues (FFPETs) in breast cancer (BRCA) and normal adjacent tissues (NATs) and identify miR-191 as a new biomarker for early diagnosing BRCA. Differentially expressed genes (DEGs) by MACE-Seq and differentially expressed ncRNAs (DEncRNAs) by the TrueQuant technique were examined in this study. The miR-191 expression level was measured by Real Time-qPCR. An average of 4,739 coding genes from 25,713 significantly down-regulated genes was identified, whereas 3,954 coding genes were significantly up-regulated in the BRCA against NAT. An average of 1450 ncRNAs, including up-regulated= 679 and down-regulated= 780, were differentially expressed in 7 paired samples of BRCA and NAT. Among the ncRNAs, 227 microRNAs, including unchanged= 152, down=53, and up=22, were differentially expressed. MiR-191 was one of the 22 significant up-regulation, with p=0.0001. RT-qPCR results confirmed that miR-191, p=0.003, was significantly over-expressed in 120 paired samples of BRCA and NAT. Furthermore, NextSeq 500 revealed that a single nucleotide polymorphism (C>T) newly occurred in the mature sequence of miR-191-5p seed region in BRCA samples. However, the putative target genes regulated by the miR-191-5p were recognized by the above ten computational programs for the prediction. MACE-Seq outcomes showed that the genes of CDK6(P=0.0001), DAPK1(P=0.02), MTC7(P=0.04), SETD1B(P=0.005), CALN1(P=0.01), and TMOD2(P=0.001) were significantly over-expressed in the BRCA against the NATs. The expression level of the targets was adversely related to the miR-191-5p.
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Merrell, D. Scott, Lucinda J. Thompson, Charles C. Kim, Hazel Mitchell, Lucy S. Tompkins, Adrian Lee, and Stanley Falkow. "Growth Phase-Dependent Response of Helicobacter pylori to Iron Starvation." Infection and Immunity 71, no. 11 (November 2003): 6510–25. http://dx.doi.org/10.1128/iai.71.11.6510-6525.2003.
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ABSTRACT Iron is an essential nutrient that is often found in extremely limited available quantities within eukaryotic hosts. Because of this, many pathogenic bacteria have developed regulated networks of genes important for iron uptake and storage. In addition, it has been shown that many bacteria use available iron concentrations as a signal to regulate virulence gene expression. We have utilized DNA microarray technology to identify genes of the human pathogen Helicobacter pylori that are differentially regulated on a growth-inhibiting shift to iron starvation conditions. In addition, the growth phase-dependent expression of these genes was investigated by examining both exponential and stationary growth phase cultures. We identified known iron-regulated genes, as well as a number of genes whose regulation by iron concentration was not previously appreciated. Included in the list of regulated factors were the known virulence genes cagA, vacA, and napA. We examined the effect of iron starvation on the motility of H. pylori and found that exponential- and stationary-phase cultures responded differently to the stress. We further found that while growing cells are rapidly killed by iron starvation, stationary-phase cells show a remarkable ability to survive iron depletion. Finally, bioinformatic analysis of the predicted promoter regions of the differentially regulated genes led to identification of several putative Fur boxes, suggesting a direct role for Fur in iron-dependent regulation of these genes.
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Bigsby, R. M., and A. Li. "Differentially regulated immediate early genes in the rat uterus." Endocrinology 134, no. 4 (April 1994): 1820–26. http://dx.doi.org/10.1210/endo.134.4.8137748.
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Kawasaki, Laura, and Jesús Aguirre. "Multiple Catalase Genes Are Differentially Regulated in Aspergillus nidulans." Journal of Bacteriology 183, no. 4 (February 15, 2001): 1434–40. http://dx.doi.org/10.1128/jb.183.4.1434-1440.2001.
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ABSTRACT Detoxification of hydrogen peroxide is a fundamental aspect of the cellular antioxidant responses in which catalases play a major role. Two differentially regulated catalase genes, catA andcatB, have been studied in Aspergillus nidulans. Here we have characterized a third catalase gene, designated catC, which predicts a 475-amino-acid polypeptide containing a peroxisome-targeting signal. With a molecular mass of 54 kDa, CatC shows high similarity to other small-subunit monofunctional catalases and is most closely related to catalases from other fungi, Archaea, and animals. In contrast, the CatA (∼84 kDa) and CatB (∼79 kDa) enzymes belong to a family of large-subunit catalases, constituting a unique fungal and bacterial group. The catC gene displayed a relatively constant pattern of expression, not being induced by oxidative or other types of stress. Targeted disruption of catC eliminated a constitutive catalase activity not detected previously in zymogram gels. However, a catalase activity detected in catA catBmutant strains during late stationary phase was still present incatC and catABC null mutants, thus demonstrating the presence of a fourth catalase, here named catalase D (CatD). Neither catC nor catABC triple mutants showed any developmental defect, and both mutants grew as well as wild-type strains in H2O2-generating substrates, such as fatty acids, and/or purines as the sole carbon and nitrogen sources, respectively. CatD activity was induced during late stationary phase by glucose starvation, high temperature, and, to a lesser extent, H2O2 treatment. The existence of at least four differentially regulated catalases indicates a large and regulated capability for H2O2detoxification in filamentous fungi.
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Khristi, Vincentaben, V. Praveen Chakravarthi, Prabhakar Singh, Subhra Ghosh, Archit Pramanik, Anamika Ratri, Shaon Borosha, Katherine F. Roby, Michael W. Wolfe, and M. A. Karim Rumi. "Differentially regulated genes in Esr2-mutant rat granulosa cells." Data in Brief 19 (August 2018): 1008–11. http://dx.doi.org/10.1016/j.dib.2018.05.098.
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Tseng, Hung, Weichin Chou, Junwen Wang, Xiaohong Zhang, Shengliang Zhang, and Richard M. Schultz. "Mouse Ribosomal RNA Genes Contain Multiple Differentially Regulated Variants." PLoS ONE 3, no. 3 (March 26, 2008): e1843. http://dx.doi.org/10.1371/journal.pone.0001843.
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Eastwood, Daniel C., Andrew Mead, Martin J. Sergeant, and Kerry S. Burton. "Statistical modelling of transcript profiles of differentially regulated genes." BMC Molecular Biology 9, no. 1 (2008): 66. http://dx.doi.org/10.1186/1471-2199-9-66.
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Quesada, A., J. Hidalgo, and E. Fernández. "Three Nrt2 genes are differentially regulated in Chlamydomonas reinhardtii." Molecular and General Genetics MGG 258, no. 4 (May 1998): 373–77. http://dx.doi.org/10.1007/s004380050743.
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Sindi, Samar, Norah Hamdi, Sabah Hassan, Magdah Ganash, Mona Alharbi, Najla Alburae, Sheren Azhari, et al. "Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer." Breast Cancer: Targets and Therapy Volume 15 (July 2023): 435–50. http://dx.doi.org/10.2147/bctt.s408711.
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Cho, Catherine Mee-Hie, Tingfen Yan, Xueduan Liu, Liyou Wu, Jizhong Zhou, and Lisa Y. Stein. "Transcriptome of a Nitrosomonas europaea Mutant with a Disrupted Nitrite Reductase Gene (nirK)." Applied and Environmental Microbiology 72, no. 6 (June 2006): 4450–54. http://dx.doi.org/10.1128/aem.02958-05.
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ABSTRACT Global gene expression was compared between the Nitrosomonas europaea wild type and a nitrite reductase-deficient mutant using a genomic microarray. Forty-one genes were differentially regulated between the wild type and the nirK mutant, including the nirK operon, genes for cytochrome c oxidase, and seven iron uptake genes. Relationships of differentially regulated genes to the nirK mutant phenotype are discussed.
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Kian Tee, Meng, Inez Rogatsky, Christina Tzagarakis-Foster, Aleksandra Cvoro, Jinping An, Robert J. Christy, Keith R. Yamamoto, and Dale C. Leitman. "Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors α and β." Molecular Biology of the Cell 15, no. 3 (March 2004): 1262–72. http://dx.doi.org/10.1091/mbc.e03-06-0360.
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Estrogens and selective estrogen receptor modulators (SERMs) interact with estrogen receptor (ER) α and β to activate or repress gene transcription. To understand how estrogens and SERMs exert tissue-specific effects, we performed microarray analysis to determine whether ERα or ERβ regulate different target genes in response to estrogens and SERMs. We prepared human U2OS osteosarcoma cells that are stably transfected with a tetracycline-inducible vector to express ERα or ERβ. Western blotting, immunohistochemistry, and immunoprecipitation studies confirmed that U2OS-ERα cells synthesized only ERα and that U2OS-ERβ cells expressed exclusively ERβ. U2OS-ERα and U2OS-ERβ cells were treated either with 17β-estradiol (E2), raloxifene, and tamoxifen for 18 h. Labeled cRNAs were hybridized with U95Av2 GeneChips (Affymetrix). A total of 228, 190, and 236 genes were significantly activated or repressed at least 1.74-fold in U2OS-ERα and U2OS-ERβ cells by E2, raloxifene, and tamoxifen, respectively. Most genes regulated in ERα cells in response to E2, raloxifene, and tamoxifen were distinct from those regulated in ERβ cells. Only 38 of the 228 (17%) genes were regulated by E2 in both U2OS-ERα and U2OS-ERβ cells. Raloxifene and tamoxifen regulated only 27% of the same genes in both the ERα and ERβ cells. A subset of genes involved in bone-related activities regulated by E2, raloxifene, and tamoxifen were also distinct. Our results demonstrate that most genes regulated by ERα are distinct from those regulated by ERβ in response to E2 and SERMs. These results indicate that estrogens and SERMs exert tissue-specific effects by regulating unique sets of targets genes through ERα and ERβ
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Yang, Qiang, Juncan Ding, Ziyue Luo, and Pengfei Hu. "A bioinformatics approach to the identification of hub genes of Huo Xin Pill (HXP) for the treatment of acute myocardial infarction." Tropical Journal of Pharmaceutical Research 21, no. 12 (February 4, 2023): 2651–58. http://dx.doi.org/10.4314/tjpr.v21i12.21.
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Purpose: To apply bioinformatics for the identification of potential genes associated with Huo Xin Pill (HXP), a traditional Chinese medicine (TCM) used for the treatment of acute myocardial infarction AMI).Methods: Mouse AMI expression profile dataset GSE153485 and HXP-treated mouse AMI expression profile dataset GSE147365 were downloaded from GEO database. Then, R software was used to screen differentially-expressed genes in AMI and differentially-expressed genes in HXP-treated AMI. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, Venn diagrams, and protein-protein interaction (PPI) analysis were carried out on the hub genes linked to the effect of HXP on AMI.Results: Six hub genes were identified. Based on the differential analysis of the sham and AMI groups, GSE153485 and GSE147365 had 840 and 2116 differentially-expressed genes, respectively (p < 0.05). The GO and KEGG analyses revealed enrichments in actin filament organization, membrane repolarization, and regulation of the actin cytoskeleton. Differential analysis of the use of HXP on AMI showed that GSE147365 had 380 differentially-expressed genes, comprising 96 up-regulated genes and 284 down-regulated genes (p < 0.05). Thirteen potential acting target genes were obtained using a enn diagram, while 6 key acting genes were obtained via final screening.Conclusion: Six (6) hub genes linked to HXP and AMI have been identified using bioinformatics: Egr2, Tubb2a, Col4a2, Cnn2, Lmna, and Col4a1. This study provides a partial experimental basis for the use of HXP in the treatment of AMI. In addition, it provides new potential targets for the treatment of AMI.
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Ventoso, Pablo, Antonio J. Pazos, Juan Blanco, M. Luz Pérez-Parallé, Juan C. Triviño, and José L. Sánchez. "Transcriptional Response in the Digestive Gland of the King Scallop (Pecten maximus) After the Injection of Domoic Acid." Toxins 13, no. 5 (May 7, 2021): 339. http://dx.doi.org/10.3390/toxins13050339.
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Some diatom species of the genus Pseudo-nitzschia produce the toxin domoic acid. The depuration rate of domoic acid in Pecten maximus is very low; for this reason, king scallops generally contain high levels of domoic acid in their tissues. A transcriptomic approach was used to identify the genes differentially expressed in the P. maximus digestive gland after the injection of domoic acid. The differential expression analysis found 535 differentially expressed genes (226 up-regulated and 309 down-regulated). Protein–protein interaction networks obtained with the up-regulated genes were enriched in gene ontology terms, such as vesicle-mediated transport, response to stress, signal transduction, immune system process, RNA metabolic process, and autophagy, while networks obtained with the down-regulated genes were enriched in gene ontology terms, such as response to stress, immune system process, ribosome biogenesis, signal transduction, and mRNA processing. Genes that code for cytochrome P450 enzymes, glutathione S-transferase theta-1, glutamine synthase, pyrroline-5-carboxylate reductase 2, and sodium- and chloride-dependent glycine transporter 1 were among the up-regulated genes. Therefore, a stress response at the level of gene expression, that could be caused by the domoic acid injection, was evidenced by the alteration of several biological, cellular, and molecular processes.
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Barman, Bandana, and Anirban Mukhopadhyay. "Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants." International Journal of System Dynamics Applications 4, no. 4 (October 2015): 35–51. http://dx.doi.org/10.4018/ijsda.2015100103.
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Identification of protein interaction network is very important to find the cell signaling pathway for a particular disease. The authors have found the differentially expressed genes between two sample groups of HIV-1. Samples are wild type HIV-1 Vpr and HIV-1 mutant Vpr. They did statistical t-test and found false discovery rate (FDR) to identify the genes increased in expression (up-regulated) or decreased in expression (down-regulated). In the test, the authors have computed q-values of test to identify minimum FDR which occurs. As a result they found 172 differentially expressed genes between their sample wild type HIV-1 Vpr and HIV-1 mutant Vpr, R80A. They found 68 up-regulated genes and 104 down-regulated genes. From the 172 differentially expressed genes the authors found protein-protein interaction network with string-db and then clustered (subnetworks) the PPI networks with cytoscape3.0. Lastly, the authors studied significance of subnetworks with performing gene ontology and also studied the KEGG pathway of those subnetworks.
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Campbell, Elsie L., Michael L. Summers, Harry Christman, Miriam E. Martin, and John C. Meeks. "Global Gene Expression Patterns of Nostoc punctiforme in Steady-State Dinitrogen-Grown Heterocyst-Containing Cultures and at Single Time Points during the Differentiation of Akinetes and Hormogonia." Journal of Bacteriology 189, no. 14 (May 4, 2007): 5247–56. http://dx.doi.org/10.1128/jb.00360-07.
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ABSTRACT The vegetative cells of the filamentous cyanobacterium Nostoc punctiforme can differentiate into three mutually exclusive cell types: nitrogen-fixing heterocysts, spore-like akinetes, and motile hormogomium filaments. A DNA microarray consisting of 6,893 N. punctiforme genes was used to identify the global transcription patterns at single time points in the three developmental states, compared to those in ammonium-grown time zero cultures. Analysis of ammonium-grown cultures yielded a transcriptome of 2,935 genes, which is nearly twice the size of a soluble proteome. The NH4 +-grown transcriptome was enriched in genes encoding core metabolic functions. A steady-state N2-grown (heterocyst-containing) culture showed differential transcription of 495 genes, 373 of which were up-regulated. The majority of the up-regulated genes were predicted from studies of heterocyst differentiation and N2 fixation; other genes are candidates for more detailed genetic analysis. Three days into the developmental process, akinetes showed a similar number of differentially expressed genes (497 genes), which were equally up- and down-regulated. The down-regulated genes were enriched in core metabolic functions, consistent with entry into a nongrowth state. There were relatively few adaptive genes up-regulated in 3-day akinetes, and there was little overlap with putative heterocyst developmental genes. There were 1,827 differentially transcribed genes in 24-h hormogonia, which was nearly fivefold greater than the number in akinete-forming or N2-fixing cultures. The majority of the up-regulated adaptive genes were genes encoding proteins for signal transduction and transcriptional regulation, which is characteristic of a motile filament that is poised to sense and respond to the environment. The greatest fraction of the 883 down-regulated genes was involved in core metabolism, also consistent with entry into a nongrowth state. The differentiation of heterocysts (steady state, N2 grown), akinetes, and hormogonia appears to involve the up-regulation of genes distinct for each state.
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Prakasa, Kalpana Rao, Lewis Becker, Nauder Faraday, Diane Becker, and Rehan Qayyum. "Platelet RNA-Seq Identifies Genes Expressed Differentially After Clopidogrel Treatment." Blood 122, no. 21 (November 15, 2013): 4817. http://dx.doi.org/10.1182/blood.v122.21.4817.4817.
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Background Clopidogrel is an antiplatelet agent that acts through direct inhibition of ADP-dependent platelet activation. Several studies have also found an inhibitory effect of clopidogrel on inflammation. Although platelets are known to participate in inflammatory processes, the mechanism(s) through which clopidogrel might modify platelet-mediated inflammation is unknown. We examined the platelet transcriptome to gain insight into the mechanism(s) through which clopidogrel modulates inflammation. Methods Three individuals with subclinical atherosclerosis and family history of early onset coronary artery disease were enrolled. Blood was collected for RNA-seq at baseline and one-week after clopidogrel 75mg daily. RNA was extracted from leukocyte-depleted platelet-rich plasma and approximately 70 million 100bp paired-end reads per sample were obtained using the Illumina HiSeq 2500. RNA-seq analysis was performed using Bowtie/TopHat/Cufflinks software pipeline. Genes with expression ≥ 0.3 fragments per kilobase of transcript per million reads (FPKM) were considered to be expressed. We set the threshold for significant differential expression as ≥ 2-fold change in gene expression after clopidogrel therapy with a false discovery rate of 0.05. Results The study sample consisted of 2 women and 1 man. Among the 12,297 expressed genes, the most highly expressed nonubiquitous genes included PPBP, PF4, and TUBB1, confirming platelets as the source of the RNA. Comparing samples before and after clopidogrel, treatment was associated with up-regulation of 733 genes and down-regulation of 387 genes. Pathway analyses found that genes related to platelet activation, degranulation, and aggregation were up-regulated, while genes related to immune system processes, such as B- and T-cell activation and innate immune response, were down-regulated. Examples of down-regulated genes include the toll-like receptor family genes, TLR2, TLR4, TLR7, and TLR8, the chemokine receptor genes CCR2, CCR5,CCR6, and CCR7, and the interleukin receptor genes, IL4R, IL7R, and IL13RA. Conclusion One week of clopidogrel therapy up-regulates transcription of pro-thrombotic platelet genes and down regulates transcription of inflammation-related platelet genes. These data suggest that clopidogrel may exert a direct anti-inflammatory action by inhibiting the ability of platelets to participate in inflammatory processes. The relationship of variability in clopidogrel-induced modulation of these pathways to clinical outcomes is unknown. Disclosures: No relevant conflicts of interest to declare.
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Kharadi, Roshni R., Kayla Selbmann, and George W. Sundin. "A complete twelve-gene deletion null mutant reveals that cyclic di-GMP is a global regulator of phase-transition and host colonization in Erwinia amylovora." PLOS Pathogens 18, no. 8 (August 1, 2022): e1010737. http://dx.doi.org/10.1371/journal.ppat.1010737.
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Cyclic-di-GMP (c-di-GMP) is an essential bacterial second messenger that regulates biofilm formation and pathogenicity. To study the global regulatory effect of individual components of the c-di-GMP metabolic system, we deleted all 12 diguanylate cyclase (dgc) and phosphodiesterase (pde)-encoding genes in E. amylovora Ea1189 (Ea1189Δ12). Ea1189Δ12 was impaired in surface attachment due to a transcriptional dysregulation of the type IV pilus and the flagellar filament. A transcriptomic analysis of surface-exposed WT Ea1189 and Ea1189Δ12 cells indicated that genes involved in metabolism, appendage generation and global transcriptional/post-transcriptional regulation were differentially regulated in Ea1189Δ12. Biofilm formation was regulated by all 5 Dgcs, whereas type III secretion and disease development were differentially regulated by specific Dgcs. A comparative transcriptomic analysis of Ea1189Δ8 (lacks all five enzymatically active dgc and 3 pde genes) against Ea1189Δ8 expressing specific dgcs, revealed the presence of a dual modality of spatial and global regulatory frameworks in the c-di-GMP signaling network.
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Abdel-Ghany, Salah E., Fahad Ullah, Asa Ben-Hur, and Anireddy S. N. Reddy. "Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress." International Journal of Molecular Sciences 21, no. 3 (January 24, 2020): 772. http://dx.doi.org/10.3390/ijms21030772.
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Drought is a major limiting factor of crop yields. In response to drought, plants reprogram their gene expression, which ultimately regulates a multitude of biochemical and physiological processes. The timing of this reprogramming and the nature of the drought-regulated genes in different genotypes are thought to confer differential tolerance to drought stress. Sorghum is a highly drought-tolerant crop and has been increasingly used as a model cereal to identify genes that confer tolerance. Also, there is considerable natural variation in resistance to drought in different sorghum genotypes. Here, we evaluated drought resistance in four genotypes to polyethylene glycol (PEG)-induced drought stress at the seedling stage and performed transcriptome analysis in seedlings of sorghum genotypes that are either drought-resistant or drought-sensitive to identify drought-regulated changes in gene expression that are unique to drought-resistant genotypes of sorghum. Our analysis revealed that about 180 genes are differentially regulated in response to drought stress only in drought-resistant genotypes and most of these (over 70%) are up-regulated in response to drought. Among these, about 70 genes are novel with no known function and the remaining are transcription factors, signaling and stress-related proteins implicated in drought tolerance in other crops. This study revealed a set of drought-regulated genes, including many genes encoding uncharacterized proteins that are associated with drought tolerance at the seedling stage.
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He, Pei, Xing-Bo Mo, Shu-Feng Lei, and Fei-Yan Deng. "Epigenetically regulated co-expression network of genes significant for rheumatoid arthritis." Epigenomics 11, no. 14 (November 2019): 1601–12. http://dx.doi.org/10.2217/epi-2019-0028.
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Aim: To identify epigenetically regulated network of genes in peripheral blood mononuclear cells significant for rheumatoid arthritis (RA). Methods: Differentially expressed genes (DEGs) and their associated differentially expressed miRNAs and differentially methylated positions (DMPs) were identified. Causal inference test (CIT) identified the causal regulation chains. The analyses, for example, weighted gene co-expression network (WGCNA), protein–protein interaction and functional enrichment, evaluated interaction patterns among the DEGs and the associated epigenetic factors. Results: A total of 181 DEGs were identified. The DEGs were significantly regulated by DMPs and/or differentially expressed miRNAs. Causal inference test analyses identified 18 causal chains of DMP-DEG-RA and 16 intermediate DEGs enriched in ‘protein kinase inhibitor activity’. BTN2A1 was co-expressed with other 9 intermediate genes and 11 known RA-associated genes and played a pivotal role in the co-expression network. Conclusion: Epigenetically regulated network of genes in peripheral blood mononuclear cells (PBMC) contributed to RA. The causal DMPs and key intermediate genes may serve as potential biomarkers for RA.
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Zhang, Wen-Qian, Miao Zhao, Ming-Yu Huang, and Ji-Long Liu. "Comparative Transcriptomic Analysis of Embryo Implantation in Mice and Rats." Cellular Physiology and Biochemistry 50, no. 2 (2018): 668–78. http://dx.doi.org/10.1159/000494187.
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Background/Aims: Embryo implantation is an essential process for eutherian pregnancy, but this process varies across eutherians. The genomic mechanisms that led to the emergence and diversification of embryo implantation are largely unknown. Methods: In this study, we analyzed transcriptomic changes during embryo implantation in mice and rats by using RNA-seq. Bioinformatics and evolutionary analyses were performed to characterize implantation-associated genes in these two species. Results: We identified a total of 518 differentially expressed genes in mouse uterus during implantation, of which 253 genes were up-regulated and 265 genes were down-regulated at the implantation sites compared with the inter-implantation sites. In rat uterus, there were 374 differentially expressed genes, of which 284 genes were up-regulated and 90 genes were down-regulated. A cross-species comparison revealed that 92 up-regulated genes and 20 down-regulated genes were shared. The differences and similarities between mice and rats were investigated further at the gene ontology, pathway, network, and causal transcription factor levels. Additionally, we found that embryo implantation might have evolved through the recruitment of ancient genes into uterine expression. The evolutionary rates of the differentially expressed genes in mouse and rat uterus were significantly lower than those of the non-changed genes, indicating that implantation-related genes are evolutionary conserved due to high selection pressure. Conclusion: Our study provides insights into the molecular mechanisms involved in the evolution of embryo implantation.
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Jolly, Emmitt R. "HSP70, HSP90A, and HSP90B are Differentially Regulated in Response to Thermal, Osmotic and Hypoxic Stressors." Annals of Experimental and Molecular Biology 1, no. 1 (2018): 1–9. http://dx.doi.org/10.23880/aemb-16000101.
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The Heat shock proteins, Hsp70 and Hsp90 are highly conserved and play a significant role in cellular response to a variety of stressors. In response to stressors, cellular expression levels of these heat shock proteins are increased to stabilize degrading proteins and to initiate thermotolerance among other complex functions. Maintenance of physiological temperature in all organisms is imperative to ensure that biological systems function normally. This is especially critical for cold-blooded organisms whose internal temperature is subject to their environmental conditions. High temperatures and other stressors can deleteriously affect animal motility, its ability to avoid predators, neuronal activity and affect neuropeptide populations. However, the effect of stressors on muscle and on neuronal activity are not always equal. Here we use the important commercially important Jonah crab, Cancer borealis as a model to assess the effect of different stressors on transcript levels of the major heat shock proteins, HSP70, HSP90A and HSP90B. Since these genes have not been identified or sequenced in C borealis, we cloned each gene and we demonstrate that a) these genes have different expression profiles in thermal, osmotic and hypoxic stresses and that b) these genes are differentially expressed in muscle and brain cells.
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Xu, Guangyu, Xu Liu, Chunmei Wang, He Li, Chengyi Zhang, Jianguang Chen, and Jinghui Sun. "The Mechanisms of Shcisandrol A in Immune Function Modulation in Immunosuppressed Mice." Natural Product Communications 13, no. 2 (February 2018): 1934578X1801300. http://dx.doi.org/10.1177/1934578x1801300216.
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The population of people with immunodeficiency is increasing due to the accelerating pace of life, increase in work pressure, and lack of exercise, irregularity of diet and rest, and problems of environmental pollution. Chinese herbal medicines have been shown to improve immunity, with little to no side effects. In recent years, studies have shown that Shcisandrol A (Sch A) regulates immune functioning and inhibits inflammation of the nervous system. The current study used gene expression profiling of spleen tissue to screen differentially expressed genes related to Sch A treatment on cyclophosphamide (Cy)-induced immunosuppressed mice. The differentially expressed gene-related pathways were analyzed by gene ontology function cluster analysis and qPCR. Five genes related to immune functioning were found to be regulated by Sch A treatment: Mapk3, Pik3r1, Pik3r5, Ikbkg, and Cd247. qPCR analysis showed that all five genes were significantly down-regulated in mice treated with Sch A compared to untreated immunosuppressed mice. These results suggest potential mechanisms through which Sch A regulates immune functioning.
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Pedersen, Connor J., and Shin-Yi Lee Marzano. "Characterization of Transcriptional Responses to Genomovirus Infection of the White Mold Fungus, Sclerotinia sclerotiorum." Viruses 14, no. 9 (August 27, 2022): 1892. http://dx.doi.org/10.3390/v14091892.
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Soybean leaf-associated gemygorvirus-1 (SlaGemV−1) is a CRESS-DNA virus classified in the family Genomoviridae, which causes hypovirulence and abolishes sclerotia formation in infected fungal pathogens under the family Sclerotiniaceae. To investigate the mechanisms involved in the induction of hypovirulence, RNA-Seq was compared between virus-free and SlaGemV−1-infected Sclerotinia sclerotiorum strain DK3. Overall, 4639 genes were differentially expressed, with 50.5% up regulated and 49.5% down regulated genes. GO enrichments suggest changes in integral membrane components and transmission electron microscopy images reveal virus-like particles localized near the inner cell membrane. Differential gene expression analysis focused on genes responsible for cell cycle and DNA replication and repair pathways, ubiquitin proteolysis, gene silencing, methylation, pathogenesis-related, sclerotial development, carbohydrate metabolism, and oxalic acid biosynthesis. Carbohydrate metabolism showed the most changes, with two glycoside hydrolase genes being the most down regulated by −2396.1- and −648.6-fold. Genes relating to pathogenesis showed consistent down regulation with the greatest being SsNep1, SsSSVP1, and Endo2 showing, −4555-, −14.7-, and −12.3-fold changes. The cell cycle and DNA replication/repair pathways were almost entirely up regulated including a putative cyclin and separase being up regulated 8.3- and 5.2-fold. The oxalate decarboxylase genes necessary for oxalic acid catabolism and oxalic acid precursor biosynthesis genes and its metabolism show down regulations of −17.2- and −12.1-fold changes. Sclerotial formation genes also appear differentially regulated including a melanin biosynthesis gene Pks1 and a sclerotia formation gene Sl2 with fold changes of 3.8 and −2.9.
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Fisher, Susan H., and Lewis V. Wray. "Bacillus subtilis 168 Contains Two Differentially Regulated Genes Encoding l-Asparaginase." Journal of Bacteriology 184, no. 8 (April 15, 2002): 2148–54. http://dx.doi.org/10.1128/jb.184.8.2148-2154.2002.
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ABSTRACT Expression of the two Bacillus subtilis genes encoding l-asparaginase is controlled by independent regulatory factors. The ansZ gene (formerly yccC) was shown by mutational analysis to encode a functional l-asparaginase, the expression of which is activated during nitrogen-limited growth by the TnrA transcription factor. Gel mobility shift and DNase I footprinting experiments indicate that TnrA regulates ansZ expression by binding to a DNA site located upstream of the ansZ promoter. The expression of the ansA gene, which encodes the second l-asparaginase, was found to be induced by asparagine. The ansA repressor, AnsR, was shown to negatively regulate its own expression.
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Pan, Xiaoying, Wei Yan, Zhenyi Chang, Yingchao Xu, Ming Luo, Chunjue Xu, Zhufeng Chen, Jianxin Wu, and Xiaoyan Tang. "OsMYB80 Regulates Anther Development and Pollen Fertility by Targeting Multiple Biological Pathways." Plant and Cell Physiology 61, no. 5 (March 6, 2020): 988–1004. http://dx.doi.org/10.1093/pcp/pcaa025.
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Abstract Pollen development is critical to the reproductive success of flowering plants, but how it is regulated is not well understood. Here, we isolated two allelic male-sterile mutants of OsMYB80 and investigated how OsMYB80 regulates male fertility in rice. OsMYB80 was barely expressed in tissues other than anthers, where it initiated the expression during meiosis, reached the peak at the tetrad-releasing stage and then quickly declined afterward. The osmyb80 mutants exhibited premature tapetum cell death, lack of Ubisch bodies, no exine and microspore degeneration. To understand how OsMYB80 regulates anther development, RNA-seq analysis was conducted to identify genes differentially regulated by OsMYB80 in rice anthers. In addition, DNA affinity purification sequencing (DAP-seq) analysis was performed to identify DNA fragments interacting with OsMYB80 in vitro. Overlap of the genes identified by RNA-seq and DAP-seq revealed 188 genes that were differentially regulated by OsMYB80 and also carried an OsMYB80-interacting DNA element in the promoter. Ten of these promoter elements were randomly selected for gel shift assay and yeast one-hybrid assay, and all showed OsMYB80 binding. The 10 promoters also showed OsMYB80-dependent induction when co-expressed in rice protoplast. Functional annotation of the 188 genes suggested that OsMYB80 regulates male fertility by directly targeting multiple biological processes. The identification of these genes significantly enriched the gene networks governing anther development and provided much new information for the understanding of pollen development and male fertility.
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Zhu, Ming-Xi, Tian-Yang Zhao, and Yan Li. "Insight into the mechanism of DNA methylation and miRNA-mRNA regulatory network in ischemic stroke." Mathematical Biosciences and Engineering 20, no. 6 (2023): 10264–83. http://dx.doi.org/10.3934/mbe.2023450.
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<abstract> <sec><title>Background</title><p>Epigenetic changes, such as DNA methylation and miRNA-target gene mechanisms, have recently emerged as key provokers in Ischemic stroke (IS) onset. However, cellular and molecular events harboring these epigenetic alterations are poorly understood. Therefore, the present study aimed to explore the potential biomarkers and therapeutic targets for IS.</p> </sec> <sec><title>Methods</title><p>miRNAs, mRNAs and DNA methylation datasets of IS were derived from the GEO database and normalized by PCA sample analysis. Differentially expressed genes (DEGs) were identified, and GO and KEGG enrichment analyses were performed. The overlapped genes were utilized to construct a protein-protein interaction network (PPI). Meanwhile, differentially expressed mRNAs and miRNAs interaction pairs were obtained from the miRDB, TargetScan, miRanda, miRMap and miTarBase databases. We constructed differential miRNA-target gene regulatory networks based on mRNA-miRNA interactions.</p> </sec> <sec><title>Results</title><p>A total of 27 up-regulated and 15 down-regulated differential miRNAs were identified. Dataset analysis identified 1053 and 132 up-regulated and 1294 and 9068 down-regulated differentially expressed genes in the GSE16561 and GSE140275 datasets, respectively. Moreover, 9301 hypermethylated and 3356 hypomethylated differentially methylated sites were also identified. Moreover, DEGs were enriched in terms related to translation, peptide biosynthesis, gene expression, autophagy, Th1 and Th2 cell differentiation, primary immunodeficiency, oxidative phosphorylation and T cell receptor signaling pathway. MRPS9, MRPL22, MRPL32 and RPS15 were identified as hub genes. Finally, a differential miRNA-target gene regulatory network was constructed.</p> </sec> <sec><title>Conclusions</title><p>RPS15, along with hsa-miR-363-3p and hsa-miR-320e have been identified in the differential DNA methylation protein interaction network and miRNA-target gene regulatory network, respectively. These findings strongly posit the differentially expressed miRNAs as potential biomarkers to improve ischemic stroke diagnosis and prognosis.</p> </sec> </abstract>
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Peplow, Andrew W., Andrew G. Tag, Gulnara F. Garifullina, and Marian N. Beremand. "Identification of New Genes Positively Regulated by Tri10 and a Regulatory Network for Trichothecene Mycotoxin Production." Applied and Environmental Microbiology 69, no. 5 (May 2003): 2731–36. http://dx.doi.org/10.1128/aem.69.5.2731-2736.2003.
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ABSTRACT Tri10, a regulatory gene in trichothecene mycotoxin-producing Fusarium species, is required for trichothecene biosynthesis and the coordinated expression of four trichothecene pathway-specific genes (Tri4, Tri5, Tri6, and Tri101) and the isoprenoid biosynthetic gene for farnesyl pyrophosphate synthetase (FPPS). We showed that six more trichothecene genes (Tri3, Tri7, Tri8, Tri9, Tri11, and Tri12) are regulated by Tri10. We also constructed a cDNA library from a strain of Fusarium sporotrichioides that overexpresses Tri10 (↑Tri10) and used cDNA derived from the ↑Tri10 strain and a non-Tri10-expressing strain (ΔTri10) to differentially screen macroarrays prepared from the cDNA library. This screen identified 15 additional Tri10-regulated transcripts. Four of these transcripts represent Tri1, Tri13, and Tri14 and a gene designated Tri15. Three other sequences are putative orthologs of genes for isoprenoid biosynthesis, the primary metabolic pathway preceding trichothecene biosynthesis. The remaining eight sequences have been designated Ibt (influenced by Tri10) genes. Of the 26 transcripts now known to be positively regulated by Tri10, 22 are positively coregulated by Tri6, a gene that encodes a previously characterized trichothecene pathway-specific transcription factor. These 22 Tri10- and Tri6-coregulated sequences include all of the known Tri genes (except for Tri10), the FPPS gene, and the other three putative isoprenoid biosynthetic genes. Tri6 also regulates a transcript that is not regulated by Tri10. Thus, Tri10 and Tri6 regulate overlapping sets of genes that include a common group of multiple genes for both primary and secondary metabolism.
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Li, Wei, Aiqin Nie, Qiang Li, He Cao, Yinwei Song, Yunzhi Ling, Ning Xie, and Gaohua Liang. "Bioinformatic Analysis of Differentially Expressed Genes and Screening of Hub Genes in Uveal Melanoma Cells with BRCA1-Associated Protein 1 Related Protein 1 Depletion." Journal of Biomedical Nanotechnology 16, no. 8 (August 1, 2020): 1205–18. http://dx.doi.org/10.1166/jbn.2020.2968.
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Recent studies have found that chromosome 3 is frequently mutated in metastatic uveal melanoma (UVM), which leads to the loss of BAP1 expression or the weakening of BRCA1-associated protein 1 (BAP1) function and promotes metastasis of uveal melanoma cells. However, the specific signaling pathways that are affected by BAP1 depletion in uveal melanoma remain unclear. Our aim in this study was to verify the effect and regulatory mechanism of BAP1 on uveal melanoma. RT-qPCR and western blotting results showed that BAP1 was significantly down-regulated in OCM-1A cells treated with a BAP1 shRNA vector. MTT, cell scratch and transwell migration assays showed that low expression of BAP1 significantly promoted the proliferation and migration of UVM cells. A total of 269 up-regulated and 807 down-regulated genes were identified from the combined GSE110193 and GSE48863 data sets. These differentially expressed genes are mainly involved in the composition of extracellular matrix and the regulation of the Wnt signaling pathway and are closely related to the cell adhesion pathway. CXCL8, COL5A3, COL11A1, and COL12A1 were among the differentially expressed genes and are closely related to the prognosis of UVM. Therefore, the deletion of BAP1 is closely related to poor prognosis of UVM and is a risk factor for UVM metastasis. The potential targets of BAP1 include CXCL8, COL5A3, COL11A1, and COL12A1. It is believed that BAP1 regulates UVM cell adhesion through these four genes and ultimately regulates tumor development and migration.
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Macharia, Teresia N., Daniel Bellieny-Rabelo, and Lucy N. Moleleki. "Transcriptome Profiling of Potato (Solanum tuberosum L.) Responses to Root-Knot Nematode (Meloidogyne javanica) Infestation during A Compatible Interaction." Microorganisms 8, no. 9 (September 21, 2020): 1443. http://dx.doi.org/10.3390/microorganisms8091443.
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Root-knot nematode (RKN) Meloidogyne javanica presents a great challenge to Solanaceae crops, including potato. In this study, we investigated transcriptional responses of potato roots during a compatible interaction with M. javanica. In this respect, differential gene expression of Solanum tuberosum cultivar (cv.) Mondial challenged with M. javanica at 0, 3 and 7 days post-inoculation (dpi) was profiled. In total, 4948 and 4484 genes were detected, respectively, as differentially expressed genes (DEGs) at 3 and 7 dpi. Functional annotation revealed that genes associated with metabolic processes were enriched, suggesting they might have an important role in M. javanica disease development. MapMan analysis revealed down-regulation of genes associated with pathogen perception and signaling suggesting interference with plant immunity system. Notably, delayed activation of pathogenesis-related genes, down-regulation of disease resistance genes, and activation of host antioxidant system contributed to a susceptible response. Nematode infestation suppressed ethylene (ET) and jasmonic acid (JA) signaling pathway hindering JA/ET responsive genes associated with defense. Genes related to cell wall modification were differentially regulated while transport-related genes were up-regulated, facilitating the formation of nematode feeding sites (NFSs). Several families of transcription factors (TFs) were differentially regulated by M. javanica infestation. Suggesting that TFs play an indispensable role in physiological adaptation for successful M. javanica disease development. This genome-wide analysis reveals the molecular regulatory networks in potato roots which are potentially manipulated by M. javanica. Being the first study analyzing transcriptome profiling of M. javanica-diseased potato, it provides unparalleled insight into the mechanism underlying disease development.
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Bhat-Nakshatri, Poornima, Guohua Wang, Hitesh Appaiah, Nikhil Luktuke, Jason S. Carroll, Tim R. Geistlinger, Myles Brown, Sunil Badve, Yunlong Liu, and Harikrishna Nakshatri. "AKT Alters Genome-Wide Estrogen Receptor α Binding and Impacts Estrogen Signaling in Breast Cancer." Molecular and Cellular Biology 28, no. 24 (October 6, 2008): 7487–503. http://dx.doi.org/10.1128/mcb.00799-08.
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ABSTRACT Estrogen regulates several biological processes through estrogen receptor α (ERα) and ERβ. ERα-estrogen signaling is additionally controlled by extracellular signal activated kinases such as AKT. In this study, we analyzed the effect of AKT on genome-wide ERα binding in MCF-7 breast cancer cells. Parental and AKT-overexpressing cells displayed 4,349 and 4,359 ERα binding sites, respectively, with ∼60% overlap. In both cell types, ∼40% of estrogen-regulated genes associate with ERα binding sites; a similar percentage of estrogen-regulated genes are differentially expressed in two cell types. Based on pathway analysis, these differentially estrogen-regulated genes are linked to transforming growth factor β (TGF-β), NF-κB, and E2F pathways. Consistent with this, the two cell types responded differently to TGF-β treatment: parental cells, but not AKT-overexpressing cells, required estrogen to overcome growth inhibition. Combining the ERα DNA-binding pattern with gene expression data from primary tumors revealed specific effects of AKT on ERα binding and estrogen-regulated expression of genes that define prognostic subgroups and tamoxifen sensitivity of ERα-positive breast cancer. These results suggest a unique role of AKT in modulating estrogen signaling in ERα-positive breast cancers and highlights how extracellular signal activated kinases can change the landscape of transcription factor binding to the genome.
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Akison, L., D. Russell, and R. Robker. "136. PROGESTERONE RECEPTOR-REGULATED GENES IN THE PREOVULATORY OVARIAN FOLLICLE AND OVIDUCT." Reproduction, Fertility and Development 22, no. 9 (2010): 54. http://dx.doi.org/10.1071/srb10abs136.
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Ovulation is a highly regulated and precisely timed reproductive process but the underlying molecular mechanisms are not well understood. Progesterone receptor (PGR) is a transcription factor highly yet transiently expressed in granulosa cells (GCs) of preovulatory follicles; has low expression in cumulus-oocyte-complexes (COCs); and is abundantly expressed in the oviduct. PR–/– mice validate its essential role in ovulation as they are anovulatory, despite normal growth and development of ovarian follicles and oocytes. Our aim was to use microarray to identify differentially expressed genes in GCs, COCs and oviducts from PR–/– and PR+/– mice, specifically genes potentially involved in oocyte release and transport. GCs, COCs and oviducts were collected from 21d-old mice (n = 5; 3 mice/replicate) at 8h post-hCG/44h post-eCG. Extracted RNA samples were hybridized to Affymetrix Mouse Gene 1.0 ST Arrays and post-experiment processing/analysis performed using Partek Genomics Suite. Gene ontology analysis was performed using Ingenuity Pathway Analysis (IPA). In GCs, 296 genes were differentially expressed (P < 0.05); 78% down-regulated in PR–/–. IPA identified genes involved in cancer migration/invasion, chemotaxis, and adhesion; the chemokine receptor Cxcr4, was >3-fold down-regulated in PR–/–. Proteases were also decreased; Adam8 (3.5-fold) and Adamts1 (2.6-fold) in PR–/–. In oviducts, 1003 genes were differentially expressed at P < 0.05 and 266 genes at P < 0.01; 93% were down-regulated in PR–/–. IPA identified genes involved in cell adhesion, movement/migration, invasion and chemotaxis as well as muscle contraction and vasoconstriction. The most highly down-regulated was Itga8 (>9-fold), one of 11 integrins, well known cellular adhesion receptors, differentially expressed. In COCs, 44 genes were differentially expressed (P < 0.05); 52% down-regulated in PR–/–. IPA identified 18 genes (41%) involved in cancer invasion/migration or adhesion. Thus, this study has identified novel gene targets for PGR regulation, which may have essential roles in the molecular control of oocyte release into the oviduct at ovulation.
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Fang, Xibi, Lihong Qin, Haibin Yu, Ping Jiang, Lixin Xia, Zhen Gao, Runjun Yang, Yumin Zhao, Xianzhong Yu, and Zhihui Zhao. "Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle." Animals 11, no. 11 (October 21, 2021): 3024. http://dx.doi.org/10.3390/ani11113024.
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This study aims to screen potential regulators and regulate fecundity networks between microRNAs (miRNAs) and target genes. The bovine testes of immature and mature Chinese Red Steppes were performed by genome-wide analysis of mRNAs and miRNAs. Compared with testicular tissues of newborns, 6051 upregulated genes and 7104 downregulated genes in adult cattle were identified as differentially expressed genes (DEGs). The DEGs were significantly enriched in 808 GO terms (p < 0.05) including male gonad development, male genitalia development, spermatogenesis, and sperm motility. Moreover, DEGs were also significantly enriched in 105 KEGG pathways (p < 0.05), including cGMP-PKG signaling pathway and calcium signaling pathway. To explore the expression of miRNA-regulated gene expression, 896 differentially expressed target genes negatively regulated with the expression levels of 31 differentially expressed miRNAs (DERs) were predicted and analyzed, and a network-integrated analysis was constructed. Furthermore, real-time PCR was performed to verify the expression levels of DEGs and DERs. Our results identified novel candidate DEGs and DERs correlated with male reproduction and intricate regulating networks between miRNAs and genes, which will be valuable for future genetic and epigenetic studies of sperm development and maturity, as well as providing valuable insights into the molecular mechanisms of male fertility and spermatogenesis in cattle.
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Kucknoor, Ashwini S., Vasanthakrishna Mundodi, and J. F. Alderete. "Adherence to Human Vaginal Epithelial Cells Signals for Increased Expression of Trichomonas vaginalis Genes." Infection and Immunity 73, no. 10 (October 2005): 6472–78. http://dx.doi.org/10.1128/iai.73.10.6472-6478.2005.
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ABSTRACT Host parasitism by Trichomonas vaginalis is complex, and the adhesion to vaginal epithelial cells (VECs) by trichomonads is preparatory to colonization of the vagina. Since we showed increased synthesis of adhesins after contact with VECs (A. F. Garcia, et al., Mol. Microbiol. 47:1207-1224, 2003) and more recently demonstrated up-regulated gene expression in VECs after parasite attachment (A. S. Kucknoor, et al., Cell. Microbiol. 7:887-897, 2005), we hypothesized that enhanced expression of adhesin and other genes would result from signaling of trichomonads following adherence. In order to identify the genes that are up-regulated, we constructed a subtraction cDNA library enriched for differentially expressed genes from the parasites that were in contact with the host cells. Thirty randomly selected cDNA clones representing the differentially regulated genes upon initial contact of parasites with host cells were sequenced. Several genes encoded functional proteins with specific functions known to be associated with colonization, such as adherence, change in morphology, and gene transcription and translation. Interestingly, genes unique to trichomonads with unknown functions were also up-regulated. Semiquantitative reverse transcription-PCR (RT-PCR) confirmed expression of select genes. An increased amount of protein was demonstrated by immunoblotting with monoclonal antibody. Finally, we showed the transcriptional regulation of some genes by iron by using RT-PCR. To our knowledge, this is the first report addressing the differential regulation of T. vaginalis genes immediately upon contact with VECs.
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Zhan, Ni, Liejian Huang, Zhen Wang, Yaojian Xie, Xiuhua Shang, Guo Liu, and Zhihua Wu. "Comparative transcriptomics and bioinformatics analysis of genes related to photosynthesis in Eucalyptus camaldulensis." PeerJ 10 (November 11, 2022): e14351. http://dx.doi.org/10.7717/peerj.14351.
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The timber species Eucalyptus camaldulensis is one of the most important in southern China. Therefore, it is essential to understand the photosynthetic pattern in eucalyptus leaves. In the present study, eighteen photosynthesis-related genes were analyzed using bioinformatics methods. The results indicated that there were ten differentially expressed ribose-5-phosphate isomerase genes (RPI), and six of them were up-regulated in the mature leaves compared to the young leaves, while others were down-regulated. The differential expression of four rubisco methyltransferase genes (RBCMT) were observed. Two of them were up-regulated, while two were down-regulated in mature leaves compared to young leaves. Furthermore, two ribulose-phosphate-3-epimerase genes (RPE) were up-regulated in the mature leaves compared to the young leaves. In contrast, two genes involved in triosephosphate isomerase (TIM) were down-regulated in mature leaves compared with young leaves. The current study provides basic information about the transcriptome of E. camaldulensis and lays a foundation for further research in developing and utilizing important photosynthetic genes.
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Martínez, Isidoro, Luis Lombardía, Blanca García-Barreno, Orlando Domínguez, and José A. Melero. "Distinct gene subsets are induced at different time points after human respiratory syncytial virus infection of A549 cells." Journal of General Virology 88, no. 2 (February 1, 2007): 570–81. http://dx.doi.org/10.1099/vir.0.82187-0.
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cDNA microarray technology was applied to time course analysis of differentially expressed genes in A549 cells following human respiratory syncytial virus (HRSV) infection. Both up- and down-regulation of cellular genes were observed in a time-dependent manner. However, gene up-regulation prevailed over gene down-regulation. Virus infectivity was required as UV-inactivated virus failed to up-regulate/down-regulate those genes. At early times post-infection (0–6 h p.i.) 85 genes were up-regulated. Some of those genes were involved in cell growth/proliferation, cellular protein metabolism and cytoskeleton organization. Among the most strongly up-regulated genes at that time were the urokinase plasminogen activator (PLAU) and its receptor (PLAUR), a pleiotropic system involved in many biological processes, including chemotaxis and inflammation. Functionally related genes encoding the α- and β-chains of several integrins were also up-regulated within the first 12 h of infection. Genes up-regulated between 6 and 12 h p.i. included interferon-stimulated genes (ISGs), genes related to oxidative stress and genes of the non-canonical NF-κB pathway. At later times, genes involved in the immune response became predominant among the up-regulated genes, most of them being ISGs. Different up-regulation kinetics of cytokine and cytokine-signalling-related genes were also observed. These results highlight the dynamic interplay between the virus and the host cell and provide a general picture of changes in cellular gene expression along the HRSV replicative cycle.
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Yan, Yue, Yifan Tao, Zheming Cao, Siqi Lu, Pao Xu, and Jun Qiang. "The Effect of Knocked-Down Anti-Müllerian Hormone mRNA on Reproductive Characters of Male Nile Tilapia (Oreochromis niloticus) through Inhibition of the TGF-Beta Signaling Pathway." Fishes 7, no. 5 (October 21, 2022): 299. http://dx.doi.org/10.3390/fishes7050299.
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Anti-Müllerian hormone (amh), an important regulator of gonad development in male teleosts, regulates the development and differentiation of germ cells. We performed transcriptional knock-down of amh in Nile tilapia (Oreochromis niloticus) using antisense RNA technology, resulting in down-regulation in the expression of amh transcription and Amh protein in males. Compared with the control groups, the fish in treatment groups with down-regulated amh had increased weight and an extremely significant decrease in the gonadosomatic index. Hematoxylin–eosin staining revealed impaired testis development and significant reductions in numbers of sperm. Serum estradiol levels were significantly increased, and the levels of testosterone, luteinizing hormone, and follicle-stimulating hormone were significantly decreased. RNA-sequencing analysis of the fish in the down-regulated amh and control groups identified 12,048 differentially expressed genes, of which 1281 were up-regulated and 10,767 were down-regulated. Kyoto Encyclopedia of Genes and Genomes analysis revealed that differentially expressed genes related to growth and development were mainly enriched in the Cell cycle, Endocytosis, TGF-beta signaling pathway, Wnt signaling pathway, FoxO signaling pathway, Insulin signaling pathway, and MAPK signaling pathway. The RNA-sequencing data accuracy was verified by qRT-PCR analysis of the expression levels of selected differentially expressed genes. The abnormal TGF-beta signaling pathway may cause fish weight gain, testis dysplasia, and abnormal spermatogenesis: smad5, smad3a, tgfb2, tgfbr1b, gsdf, and amh were significantly down-regulated. These findings indicated that antisense RNA technology has strong application prospects and can specifically knock down amh in Nile tilapia, resulting in an abnormal TGF-beta signaling pathway, inhibiting testis development and inducing weight gain.