scholarly journals Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 305 ◽  
Author(s):  
Zhou ◽  
Sun ◽  
Dai ◽  
Feng ◽  
Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Low Temperatures ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Early Spring ◽  
Rna Seq ◽  
Itraq Proteomics

Temperature is one of the most important environmental factors affecting flowering in plants. Adonis amurensis, a perennial herbaceous flower that blooms in early spring in northeast China where the temperature can drop to −15 °C, is an ideal model for studying the molecular mechanisms of flowering at extremely low temperatures. This study first investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome and iTRAQ proteomics. Finally, 123 transcription factors (TFs) were detected in both the transcriptome and the proteome. Of these, 66 TFs belonging to 14 families may play a key role in multiple signaling pathways of flowering in A. amurensis. The TFs FAR1, PHD, and B3 may be involved in responses to light and temperature, while SCL, SWI/SNF, ARF, and ERF may be involved in the regulation of hormone balance. SPL may regulate the age pathway. Some members of the TCP, ZFP, MYB, WRKY, and bHLH families may be involved in the transcriptional regulation of flowering genes. The MADS-box TFs are the key regulators of flowering in A. amurensis. Our results provide a direction for understanding the molecular mechanisms of flowering in A. amurensis at low temperatures.

scholarly journals Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

2018 ◽  
Vol 19 (10) ◽  
pp. 3071 ◽  
Author(s):  
Li Wang ◽  
Chengjiang Ruan ◽  
Lingyue Liu ◽  
Wei Du ◽  
Aomin Bao
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Acyl Carrier Protein ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Accumulation ◽  
Carboxylase Activity

Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.

scholarly journals RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

2020 ◽  
Author(s):  
Maria G. Ivanchenko ◽  
Olivia R. Ozguc ◽  
Stephanie R. Bollmann ◽  
Valerie N. Fraser ◽  
Molly Megraw
Keyword(s):  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cyclophilin A ◽  
Developmental Pathways ◽  
Root Tip ◽  
Rna Seq ◽  
Tomato Root ◽  
Initial Comparison ◽  
Insight Into

AbstractCyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (‘Ailsa Craig’) and dgt tissues from three spatially separated developmental stages of the tomato root tip, with three replicates for each tissue and genotype. We also identify differentially expressed genes, provide an initial comparison of genes affected in each genotype and tissue, and provide the pipeline used to analyze the data. Further analysis of this dataset can be used to gain insight into the effects of DGT on various root developmental pathways in tomato.

scholarly journals Nr4a2 Transcription Factor in Hippocampal Synaptic Plasticity, Memory and Cognitive Dysfunction: A Perspective Review

2021 ◽  
Vol 14 ◽  
Author(s):  
Judit Català-Solsona ◽  
Alfredo J. Miñano-Molina ◽  
José Rodríguez-Álvarez
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Synaptic Plasticity ◽  
Nuclear Receptor ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Memory Formation ◽  
Synaptic Dysfunction ◽  
Hippocampal Synaptic Plasticity

Long-lasting changes of synaptic efficacy are largely mediated by activity-induced gene transcription and are essential for neuronal plasticity and memory. In this scenario, transcription factors have emerged as pivotal players underlying synaptic plasticity and the modification of neural networks required for memory formation and consolidation. Hippocampal synaptic dysfunction is widely accepted to underlie the cognitive decline observed in some neurodegenerative disorders including Alzheimer’s disease. Therefore, understanding the molecular pathways regulating gene expression profiles may help to identify new synaptic therapeutic targets. The nuclear receptor 4A subfamily (Nr4a) of transcription factors has been involved in a variety of physiological processes within the hippocampus, ranging from inflammation to neuroprotection. Recent studies have also pointed out a role for the activity-dependent nuclear receptor subfamily 4, group A, member 2 (Nr4a2/Nurr1) in hippocampal synaptic plasticity and cognitive functions, although the underlying molecular mechanisms are still poorly understood. In this review, we highlight the specific effects of Nr4a2 in hippocampal synaptic plasticity and memory formation and we discuss whether the dysregulation of this transcription factor could contribute to hippocampal synaptic dysfunction, altogether suggesting the possibility that Nr4a2 may emerge as a novel synaptic therapeutic target in brain pathologies associated to cognitive dysfunctions.

scholarly journals Transcriptome Analysis of Apple Leaves Infected by the Rust Fungus Gymnosporangium yamadae at Two Sporulation Stages

2020 ◽  
Vol 33 (3) ◽  
pp. 444-461 ◽  
Author(s):  
Si-Qi Tao ◽  
Lucas Auer ◽  
Emmanuelle Morin ◽  
Ying-Mei Liang ◽  
Sébastien Duplessis
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Rust Fungus ◽  
Gene Expression Profiles ◽  
Effector Proteins ◽  
Rna Seq ◽  
Fungal Community Composition ◽  
Rust Disease ◽  
General Reaction ◽  
Apple Leaves

Apple rust disease caused by Gymnosporangium yamadae is one of the major threats to apple orchards. In this study, dual RNA-seq analysis was conducted to simultaneously monitor gene expression profiles of G. yamadae and infected apple leaves during the formation of rust spermogonia and aecia. The molecular mechanisms underlying this compatible interaction at 10 and 30 days postinoculation (dpi) indicate a significant reaction from the host plant and comprise detoxication pathways at the earliest stage and the induction of secondary metabolism pathways at 30 dpi. Such host reactions have been previously reported in other rust pathosystems and may represent a general reaction to rust infection. G. yamadae transcript profiling indicates a conserved genetic program in spermogonia and aecia that is shared with other rust fungi, whereas secretome prediction reveals the presence of specific secreted candidate effector proteins expressed during apple infection. Unexpectedly, the survey of fungal unigenes in the transcriptome assemblies of inoculated and mock-inoculated apple leaves reveals that G. yamadae infection may modify the fungal community composition in the apple phyllosphere at 30 dpi. Collectively, our results provide novel insights into the compatible apple–G. yamadae interaction and advance the knowledge of this heteroecious demicyclic rust fungus.

scholarly journals Global Gene Expression Responses to Cadmium Toxicity in Escherichia coli

2005 ◽  
Vol 187 (9) ◽  
pp. 3259-3266 ◽  
Author(s):  
Anyou Wang ◽  
David E. Crowley
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Cadmium Toxicity ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Temporal Gene Expression ◽  
Genes Encoding

ABSTRACT Genome-wide analysis of temporal gene expression profiles in Escherichia coli following exposure to cadmium revealed a shift to anaerobic metabolism and induction of several stress response systems. Disruption in the transcription of genes encoding ribosomal proteins and zinc-binding proteins may partially explain the molecular mechanisms of cadmium toxicity.

Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis

2016 ◽  
Vol 28 (11) ◽  
pp. 1810 ◽  
Author(s):  
Christina D. Marth ◽  
Neil D. Young ◽  
Lisa Y. Glenton ◽  
Drew M. Noden ◽  
Glenn F. Browning ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Cell Communication ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Rna Seq ◽  
Complete Understanding ◽  
Pathway Enrichment ◽  
Uterine Inflammation ◽  
Global Gene Expression Analysis

The physiological changes associated with the varying hormonal environment throughout the oestrous cycle are linked to the different functions the uterus needs to fulfil. The aim of the present study was to generate global gene expression profiles for the equine uterus during oestrus and Day 5 of dioestrus. To achieve this, samples were collected from five horses during oestrus (follicle >35 mm in diameter) and dioestrus (5 days after ovulation) and analysed using high-throughput RNA sequencing techniques (RNA-Seq). Differentially expressed genes between the two cycle stages were further investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The expression of 1577 genes was found to be significantly upregulated during oestrus, whereas 1864 genes were expressed at significantly higher levels in dioestrus. Most genes upregulated during oestrus were associated with the extracellular matrix, signal interaction and transduction, cell communication or immune function, whereas genes expressed at higher levels in early dioestrus were most commonly associated with metabolic or transport functions, correlating well with the physiological functions of the uterus. These results allow for a more complete understanding of the hormonal influence on gene expression in the equine uterus by functional analysis of up- and downregulated genes in oestrus and dioestrus, respectively. In addition, a valuable baseline is provided for further research, including analyses of changes associated with uterine inflammation.

scholarly journals Transcriptional Landscape of Vero E6 Cells during Early Swine Acute Diarrhea Syndrome Coronavirus Infection

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 674
Author(s):  
Siying Zeng ◽  
Ouyang Peng ◽  
Ruipu Sun ◽  
Qiuping Xu ◽  
Fangyu Hu ◽  
...  
Keyword(s):  
Acute Diarrhea ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Functional Enrichment ◽  
Economic Losses ◽  
Pathogenic Virus ◽  
Host Virus Interactions ◽  
Diarrhea Syndrome

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly emerged and highly pathogenic virus that is associated with fatal diarrhea disease in piglets, causing significant economic losses to the pig industry. At present, the research on the pathogenicity and molecular mechanisms of host-virus interactions of SADS-CoV are limited and remain poorly understood. Here, we investigated the global gene expression profiles of SADS-CoV-infected Vero E6 cells at 12, 18, and 24 h post-infection (hpi) using the RNA-sequencing. As a result, a total of 3324 differentially expressed genes (DEG) were identified, most of which showed a down-regulated expression pattern. Functional enrichment analyses indicated that the DEGs are mainly involved in signal transduction, cellular transcription, immune and inflammatory response, and autophagy. Collectively, our results provide insights into the changes in the cellular transcriptome during early infection of SADS-CoV and may provide information for further study of molecular mechanisms.

scholarly journals Identifying potential novel insights for COVID-19 pathogenesis and therapeutics using an integrated bioinformatics analysis of host transcriptome

2021 ◽  
Author(s):  
Salem El-aarag ◽  
Amal Mahmoud ◽  
Mahmoud ElHefnawi
Keyword(s):  
Transcription Factors ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Hub Genes ◽  
Drug Candidates ◽  
Protein Protein Interaction ◽  
Target Network ◽  
Novel Drug

Abstract The molecular mechanisms underlying the pathogenesis of COVID-19 has not been fully discovered. This study aims to decipher potentially hidden parts of the pathogenesis of COVID-19, potential novel drug targets, and to identify potential drug candidates. Two gene expression profiles (GSE147507-GSE153970) were analyzed and overlapping differentially expressed genes (DEGs) were selected for which top enriched transcription factors and kinases were identified and pathway analysis was performed. Protein-protein interaction (PPI) of DEGs was constructed, hub genes were identified and module analysis was also performed. DGIdb database was used to identify drugs for the potential targets (hub genes and the most enriched transcription factors and kinases for DEGs). A drug-potential target network was constructed and drugs are ranked according to the degree. L1000FDW web-based utility was used to identify drugs that can reverse transcriptional profiles of COVID-19. We identified drugs currently in clinical trials and novel potential 8 drugs. Besides the well-known pathogenic pathways, It was found that axon guidance is a potential pathogenic pathway. Sema7A, which may exacerbate hypercytokinemia, is considered a potential novel drug target. Another potential novel pathway is related to TINF2 overexpression which may induce potential telomere dysfunction and hence DNA damage that may exacerbate lung fibrosis.

scholarly journals Global transcriptome analysis of theMyxococcus xanthusmulticellular developmental program

2019 ◽  
Author(s):  
J. Muñoz-Dorado ◽  
A. Moraleda-Muñoz ◽  
F.J. Marcos-Torres ◽  
F.J. Contreras-Moreno ◽  
A.B. Martin-Cuadrado ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Myxococcus Xanthus ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Developmental Cycle ◽  
Fruiting Bodies ◽  
Rna Seq ◽  
Developmental Program ◽  
Specific Time Point ◽  
Global Transcriptome

ABSTRACTThe bacteriaMyxococcus xanthusexhibit a complex multicellular life cycle. In the presence of nutrients, cells prey cooperatively. Upon starvation, they enter a developmental cycle wherein cells aggregate to produce macroscopic fruiting bodies filled with resistant myxospores. We used RNA-Seq technology to examine the global transcriptome of the 96 h developmental program. This data revealed that many genes were sequentially expressed in discrete modules, with expression peaking during aggregation, in the transition from aggregation to sporulation, or during sporulation. Analysis of genes expressed at each specific time point provided a global framework integrating regulatory factors coordinating motility and differentiation in the developmental program. These data provided insights as to how starving cells obtain energy and precursors necessary for assembly of fruiting bodies and into developmental production of secondary metabolites. This study offers the first global view of developmental transcriptional profiles and provides an important scaffold for future studies.IMPACT STATEMENTInvestigation of global gene expression profiles during formation of theMyxococcus xanthusspecialized biofilm reveals a genetic regulatory network that coordinates cell motility, differentiation, and secondary metabolite production.

scholarly journals Comparative transcriptional profiling of medullary and cortical thymic cell types identifies epigenetic and transcription factors that uniquely define the mTEChi and cTEC lineages.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Expression Profiles ◽  
Transcriptional Profiling ◽  
Gene Expression Profiles ◽  
Global Gene Expression ◽  
Cell Types ◽  
Self Tolerance ◽  
In Trans ◽  
Differential Gene

The thymus has the unique ability to impart lymphocytes in trans the concept of self-tolerance by negative selection and to enforce positive selection of lymphocytes that express optimal T-cell receptors (1,2). The thymus possesses a cortex and a medulla (4), and epithelial cells known as mTEC and cTEC are intimately involved in these processes (5). Here I compared the transcriptomes of mTEChi and cTEC (6) using global differential gene expression analysis. I present a series of epigenetic molecules and transcription factors that represent the most significant differences in the global gene expression profiles between these two cell types.

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