scholarly journals Host Response to the Attenuated Poxvirus Vector NYVAC: Upregulation of Apoptotic Genes and NF-κB-Responsive Genes in Infected HeLa Cells

2006 ◽  
Vol 80 (2) ◽  
pp. 985-998 ◽  
Author(s):  
Susana Guerra ◽  
Luis A. López-Fernández ◽  
Alberto Pascual-Montano ◽  
José Luis Nájera ◽  
Angel Zaballos ◽  
...  
Keyword(s):  
Hela Cells ◽  
Host Response ◽  
Target Genes ◽  
Interleukin 1 ◽  
Expression Patterns ◽  
Gene Activation ◽  
Gene Clusters ◽  
Current Phase ◽  
Pcr Analysis ◽  
Altered Expression

ABSTRACT NYVAC has been engineered as a safe, attenuated vaccinia virus (VV) vector for use in vaccination against a broad spectrum of pathogens and tumors. Due to the interest in NYVAC-based vectors as vaccines and current phase I/II clinical trials with this vector, there is a need to analyze the human host response to NYVAC infection. Using high-density cDNA microarrays, we found 368 differentially regulated genes after NYVAC infection of HeLa cells. Clustering of the regulated genes identified six discrete gene clusters with altered expression patterns. Clusters 1 to 3 represented 47.5% of the regulated genes, with three patterns of gene activation kinetics, whereas clusters 4 to 6 showed distinct repression kinetics. Quantitative real-time reverse transcription-PCR analysis of selected genes validated the array data. Upregulated transcripts correlated with genes implicated in immune responses, including those encoding interleukin-1 receptor 2 (IL-1R2), IL-6, ISG-15, CD-80, and TNFSF7. NYVAC upregulated several intermediates of apoptotic cascades, including caspase-9, correlating with its ability to induce apoptosis. NYVAC infection also stimulated the expression of NF-κB1 and NF-κB2 as well as that of NF-κB target genes. Expression of the VV host range K1L gene during NYVAC infection prevented NF-κB activation, but not the induction of apoptosis. This study is the first overall analysis of the transcriptional response of human cells to NYVAC infection and provides a framework for future functional studies to evaluate this vector and its derivatives as human vaccines.

Discovery and Characterization of Differentially Expressed Soybean MiRNAs and Their Targets During Soybean Mosaic Virus Infection Unveils Novel Insight Into Soybean-SMV Interaction

2021 ◽  
Author(s):  
Bowen Li ◽  
Adhimoolam Karthikeyan ◽  
Liqun Wang ◽  
Jinlong Yin ◽  
Tongtong Jin ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Target Genes ◽  
Soybean Mosaic Virus ◽  
Expression Patterns ◽  
Defense Responses ◽  
Pcr Analysis ◽  
Functional Annotations ◽  
Additional Information ◽  
Insight Into

Abstract Background: Soybean mosaic virus (SMV) is the most devastating pathogen of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) and play important roles in regulating defense responses against pathogens. However, miRNA's response to SMV in soybean is not as well documented. Result: In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1× Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi, and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs responded during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. Eventually, the expression patterns of several miRNAs validated by quantitative real-time PCR analysis are consistent with sequencing results. Conclusion: We have identified a large number of miRNAs and their target genes and also functional annotations. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

scholarly journals Key Regulatory Pathways, MicroRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

Identifying targets of the rough homeobox gene of Drosophila: evidence that rhomboid functions in eye development

Development ◽  
1992 ◽  
Vol 116 (2) ◽  
pp. 335-346 ◽  
Author(s):  
M. Freeman ◽  
B.E. Kimmel ◽  
G.M. Rubin
Keyword(s):  
Cell Fate ◽  
Target Genes ◽  
Eye Development ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Homeobox Gene ◽  
Homeodomain Protein ◽  
Dorsoventral Patterning ◽  
Altered Expression ◽  
Enhancer Trap Lines

In order to identify potential target genes of the rough homeodomain protein, which is known to specify some aspects of the R2/R5 photoreceptor subtype in the Drosophila eye, we have carried out a search for enhancer trap lines whose expression is rough-dependent. We crossed 101 enhancer traps that are expressed in the developing eye into a rough mutant background, and have identified seven lines that have altered expression patterns. One of these putative rough target genes is rhomboid, a gene known to be required for dorsoventral patterning and development of some of the nervous system in the embryo. We have examined the role of rhomboid in eye development and find that, while mutant clones have only a subtle phenotype, ectopic expression of the gene causes the non-neuronal mystery cells to be transformed into photoreceptors. We propose that rhomboid is a part of a partially redundant network of genes that specify photoreceptor cell fate.

scholarly journals Key Regulatory Pathways, microRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L.

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2019 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Abstract Backgrounds Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown. Results In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
Lin Fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis ◽  
Mature Seeds

Abstract Backgrounds: Paphiopedilum is an important genus of orchid family (Orchidaceae) with high horticultural value. The wild populations are under the threat of extinction because of over collection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts the germplasm resources protection and commercial production. The germination inhibition factors are largely unknown.Results: In this study, we found large amounts of non-methylated lignin were accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. We then further compared the transcriptome profiles of P. armeniacum seed at different development stages to explore molecular clues for the non-methylated lignin synthesis. KEGG enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism as the seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathways displayed different expression patterns during the lignification process. PAL, 4CL, HCT and CSE were up-regulated to accelerate the C and H lignin accumulation. The expression of CCoAOMT, F5H and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes among seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed, and provided a better understanding of the molecular mechanism of seed-specific lignification process.

scholarly journals Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed

2020 ◽  
Author(s):  
lin fang ◽  
Xin Xu ◽  
Ji Li ◽  
Feng Zheng ◽  
Mingzhi Li ◽  
...  
Keyword(s):  
Germination Rate ◽  
Expression Patterns ◽  
Germplasm Conservation ◽  
Enrichment Analysis ◽  
Habitat Destruction ◽  
Seed Maturation ◽  
Pcr Analysis ◽  
Altered Expression ◽  
Lignin Synthesis ◽  
Phenylpropanoid Biosynthesis

Abstract Backgrounds: Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature seeds of most Paphiopedilum species are difficult to germinate, which severely restricts their germplasm conservation and commercial production. The factors inhibiting germination are largely unknown.Results: In this study, large amounts of non-methylated lignin accumulated during seed maturation of Paphiopedilum armeniacum (P. armeniacum), which negatively correlates with the germination rate. The transcriptome profiles of P. armeniacum seed at different development stages were compared to explore the molecular clues for non-methylated lignin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that a large number of genes associated with phenylpropanoid biosynthesis and phenylalanine metabolism during seed maturation were differentially expressed. Several key genes in the lignin biosynthetic pathway displayed different expression patterns during the lignification process. PAL, 4CL, HCT, and CSE upregulation was associated with C and H lignin accumulation. The expression of CCoAOMT, F5H, and COMT were maintained at a low level or down-regulated to inhibit the conversion to the typical G and S lignin. Quantitative real-time RT-PCR analysis confirmed the altered expression levels of these genes in seeds and vegetative tissues. Conclusions: This work demonstrated the plasticity of natural lignin polymer assembly in seed and provided a better understanding of the molecular mechanism of seed-specific lignification process.

Identification and Expression of Two microRNA Primary Transcripts, pri-miR-223 and pri-miR-10a, in Hematopoietic Cell Lines during Cytokine-Stimulated Differentiation.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1747-1747
Author(s):  
Nobuyoshi Kosaka ◽  
Keiichi Sugiura ◽  
Nami Nogawa ◽  
Norio Komatsu ◽  
Takashi Kato
Keyword(s):  
Bone Marrow ◽  
Cell Lines ◽  
Target Genes ◽  
Cell Lineage ◽  
Gene Clusters ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Protein Coding ◽  
Splicing Variants ◽  
Cytokine Stimulation

Abstract MicroRNAs (miRNAs) are small RNA molecules involved in various biological processes including cell differentiation, apoptosis, and oncogenesis. MiRNAs are generated from non-protein coding transcripts that are known as primary miRNA (pri-miRNA). Recently, some miRNAs were identified in hematopoietic cells. However, the relationship between pri-miRNA/miRNA expression and cytokine-induced cell proliferation/differentiation remains unclear. It has been reported that miR-223 is one of the miRNAs specifically expressed in murine myeloid lineages. We identified two splicing variants (672-nt and 437-nt) originated from its precursor pri-miR-223 (3256-nt). RT-PCR analysis by using oligo-dT primer and splice specific primer pair was performed to detect their expressions, and it revealed that pri-miR-223 was expressed in lung, brain, spleen and bone marrow but not in heart, liver or muscle. Notably each splicing variant displayed different tissue-specific expressions. Pri-miR-223 was more broadly expressed compared to the mature miR-223 expressed in bone marrow, spleen and thymus (Chen et al, Science, 2004), indicating that the generation of miR-223 is partly regulated by the miRNA processing pathway. In mouse promyelocytic NFS-60 cells, both pri-miR-223 splicing variants were expressed substantially when the cells were maintained in G-CSF (1ng/mL) exhibited granulocytic phenotype with myeloperoxidase expression, but the expression of the variants decreased on IL-3 (1ng/mL) stimulation: while the addition of G-CSF (10ng/mL) did not increase the expression of pri-miR-223. In other hematopoietic lineages, erythrocytic and megakaryocytic cells, the expressions of miRNAs had not been examined yet. As a first step to detect the miRNAs specific to erythrocytic and megakaryocytic cells, pri-miR-10a located within Hox gene clusters, was examined in the human cell lines established from the parent UT-7 cells, UT-7/GM, UT-7/EPO and UT-7/TPO. Their survival, growth and differentiation are known to be dependent on specific cytokine stimulations. Firstly, we identified the full-length sequence of human pri-miR-10a (482-nt) from EST database. RT-PCR analysis as with that for pri-miR-223 was then performed in each UT-7 cell line. Interestingly, pri-miR-10a was highly expressed in UT-7/EPO cells stimulated with erythropoietin but not in UT-7/TPO and UT-7/GM cells; though the expression of pri-miR-10a did not elevate by respective stimulation of erythropoietin (10U/mL), thrombopoietin (100ng/mL), or GM-CSF (10ng/mL) in UT-7/EPO, UT-7/TPO and UT-7/GM cells. These results showed that miR-223 and miR-10a expression was not regulated directly by cytokine stimulation, while their expression levels were altered by cytokine-dependent cell lineage commitment. The observations prompted us the hypothesis that lineage-specific miRNAs suppress the expression of their target genes that inhibit master transcription factors to direct gene silencing processes critical for differentiation. Since little information is available on transcription and processing of miRNAs specific to hematopoetic prolifiration and differentiation, our results provide a new approach to understand vital issues unsolved.

Gene expression profiling reveals the profound upregulation of hypoxia-responsive genes in primary human astrocytes

2006 ◽  
Vol 25 (3) ◽  
pp. 435-449 ◽  
Author(s):  
S. M. Mense ◽  
A. Sengupta ◽  
M. Zhou ◽  
C. Lan ◽  
G. Bentsman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Hela Cells ◽  
Expression Profiling ◽  
Target Genes ◽  
Expression Patterns ◽  
Angiogenic Growth Factors ◽  
Microarray Gene Expression ◽  
Human Astrocytes ◽  
The Brain

Oxygen is vital for the development and survival of mammals. In response to hypoxia, the brain initiates numerous adaptive responses at the organ level as well as at the molecular and cellular levels, including the alteration of gene expression. Astrocytes play critical roles in the proper functioning of the brain; thus the manner in which astrocytes respond to hypoxia is likely important in determining the outcome of brain hypoxia. Here, we used microarray gene expression profiling and data-analysis algorithms to identify and analyze hypoxia-responsive genes in primary human astrocytes. We also compared gene expression patterns in astrocytes with those in human HeLa cells and pulmonary artery endothelial cells (ECs). Remarkably, in astrocytes, five times as many genes were induced as suppressed, whereas in HeLa and pulmonary ECs, as many as or more genes were suppressed than induced. More genes encoding hypoxia-inducible functions, such as glycolytic enzymes and angiogenic growth factors, were strongly induced in astrocytes compared with HeLa cells. Furthermore, gene ontology and computational algorithms revealed that many target genes of the EGF and insulin signaling pathways and the transcriptional regulators Myc, Jun, and p53 were selectively altered by hypoxia in astrocytes. Indeed, Western blot analysis confirmed that two major signal transducers mediating insulin and EGF action, Akt and MEK1/2, were activated by hypoxia in astrocytes. These results provide a global view of the signaling and regulatory network mediating oxygen regulation in human astrocytes.

scholarly journals Expression Profiling Identifies TWIST2 Target Genes in Setleis Syndrome Patient Fibroblast and Lymphoblast Cells

2021 ◽  
Vol 18 (4) ◽  
pp. 1997
Author(s):  
Noe E. Crespo ◽  
Alexandra Torres-Bracero ◽  
Jessicca Y. Renta ◽  
Robert J. Desnick ◽  
Carmen L. Cadilla
Keyword(s):  
Expression Profiling ◽  
Target Genes ◽  
Expression Profiles ◽  
Gene Activation ◽  
Gene Expression Profiles ◽  
Autosomal Recessive Disorder ◽  
Cell Types ◽  
Skin Lesions ◽  
Altered Expression ◽  
Facial Development

Background: Setleis syndrome (SS) is a focal facial dermal dysplasia presenting with bilateral temporal skin lesions, eyelash abnormalities and absent meibomian glands. SS is a rare autosomal recessive disorder caused by mutations in the TWIST2 gene, which codes for a transcription factor of the bHLH family known to be involved in skin and facial development. Methods: We obtained gene expression profiles by microarray analyses from control and SS patient primary skin fibroblast and lymphoblastoid cell lines. Results: Out of 983 differentially regulated genes in fibroblasts (fold change ≥ 2.0), 479 were down-regulated and 509 were up-regulated, while in lymphoblasts, 1248 genes were down-regulated and 73 up-regulated. RT-PCR reactions confirmed altered expression of selected genes. Conclusions: TWIST2 is described as a repressor, but expression profiling suggests an important role in gene activation as well, as evidenced by the number of genes that are down-regulated, with a much higher proportion of down-regulated genes found in lymphoblastoid cells from an SS patient. As expected, both types of cell types showed dysregulation of cytokine genes. These results identify potential TWIST2 target genes in two important cell types relevant to rare disorders caused by mutations in this bHLH gene.

Sign in / Sign up

Export Citation Format

Share Document