scholarly journals Identification of Microbiota-Induced Gene Expression Changes in the Drosophila melanogaster Head

2019 ◽  
Author(s):  
Scott A. Keith ◽  
Rory Eutsey ◽  
Heewook Lee ◽  
Brad Solomon ◽  
Stacie Oliver ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Gut Microbiota ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Functional Roles ◽  
Bacterial Microbiota ◽  
Animal Hosts ◽  
And Behavior ◽  
Host Brain

ABSTRACTSymbiotic microorganisms exert multifaceted impacts on the physiology of their animal hosts. Recent discoveries have shown the gut microbiota influence host brain function and behavior, but the host and microbial molecular factors required to actuate these effects are largely unknown. To uncover molecular mechanisms that underlie the gut-microbiota-brain axis, we used Drosophila melanogaster and its bacterial microbiota as a model to identify microbiota-dependent gene expression changes in the host brain and head. Specifically, we employed RNA-seq and nanoString nCounter technology to identify Drosophila genes that exhibit altered transcript levels in fly heads upon elimination of the microbiota. The identified genes, some of which exhibited sex-specific differences, have demonstrated or inferred functional roles in the immune response, metabolism, neuronal activity, and stress resistance. Overall, this study reveals microbiota-responsive genes in the fly head, an anatomical structure not previously investigated in this context. Our results serve as a foundation for future investigations of how microbe-driven gene expression changes impact Drosophila biology.

scholarly journals Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1610
Author(s):  
Mohammad Vatanparast ◽  
Youngjin Park
Keyword(s):  
Gene Expression ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Predatory Behavior ◽  
P Value ◽  
Molecular Response ◽  
Rna Seq ◽  
Protein Database ◽  
Brood Chamber

Solenopsis japonica, as a fire ant species, shows some predatory behavior towards earthworms and woodlice, and preys on the larvae of other ant species by tunneling into a neighboring colony’s brood chamber. This study focused on the molecular response process and gene expression profiles of S. japonica to low (9 °C)-temperature stress in comparison with normal temperature (25 °C) conditions. A total of 89,657 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 32,782 were annotated in the NR (nonredundant protein) database with gene ontology (GO) terms, gene descriptions, and metabolic pathways. The results were 81 GO subgroups and 18 EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) keywords. Differentially expressed genes (DEGs) with log2fold change (FC) > 1 and log2FC < −1 with p-value ≤ 0.05 were screened for cold stress temperature. We found 215 unigenes up-regulated and 115 unigenes down-regulated. Comparing transcriptome profiles for differential gene expression resulted in various DE proteins and genes, including fatty acid synthases and lipid metabolism, which have previously been reported to be involved in cold resistance. We verified the RNA-seq data by qPCR on 20 up- and down-regulated DEGs. These findings facilitate the basis for the future understanding of the adaptation mechanisms of S. japonica and the molecular mechanisms underlying the response to low temperatures.

scholarly journals Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shan Lin ◽  
Zhicheng Zou ◽  
Cuibing Zhou ◽  
Hancheng Zhang ◽  
Zhiming Cai
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Purine Metabolism ◽  
Expression Data ◽  
Rna Seq ◽  
Metabolism Pathway ◽  
Caterpillar Fungus ◽  
Regulated Gene Expression ◽  
Late Stages

Caterpillar fungus is a well-known fungal Chinese medicine. To reveal molecular changes during early and late stages of adenosine biosynthesis, transcriptome analysis was performed with the anamorph strain of caterpillar fungus. A total of 2,764 differentially expressed genes (DEGs) were identified (p≤0.05, |log2 Ratio| ≥ 1), of which 1,737 were up-regulated and 1,027 were down-regulated. Gene expression profiling on 4–10 d revealed a distinct shift in expression of the purine metabolism pathway. Differential expression of 17 selected DEGs which involved in purine metabolism (map00230) were validated by qPCR, and the expression trends were consistent with the RNA-Seq results. Subsequently, the predicted adenosine biosynthesis pathway combined with qPCR and gene expression data of RNA-Seq indicated that the increased adenosine accumulation is a result of down-regulation of ndk, ADK, and APRT genes combined with up-regulation of AK gene. This study will be valuable for understanding the molecular mechanisms of the adenosine biosynthesis in caterpillar fungus.

scholarly journals Transcriptome analysis of sevoflurane exposure effects at the different brain regions

2020 ◽  
Author(s):  
Hiroto Yamamoto ◽  
Yutaro Uchida ◽  
Tomoki Chiba ◽  
Ryota Kurimoto ◽  
Takahide Matsushima ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Neural Development ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Ontology Term ◽  
Whole Brain ◽  
Differently Expressed Genes

AbstractBackgroundsSevoflurane is a most frequently used volatile anaesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in whole brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis.MethodsEight-week old mice were exposed to sevoflurane. RNA from four medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted. Their gene ontology terms and the transcriptome array data of the cerebral cortex of sleeping mice were analysed using Metascape, and the gene expression patterns were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes.ResultsThe gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in the whole brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anaesthetized mice. Sevoflurane induced Klf4 upregulation in the whole brain. The transcriptional analysis result suggests that KLF4 is a potential transcriptional regulator of angiogenesis and neural development.ConclusionsKlf4 was upregulated by sevoflurane inhalation in whole brain. KLF4 might promote angiogenesis and cause the appearance of undifferentiated neural cells by transcriptional regulation. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.

scholarly journals Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

2021 ◽  
Author(s):  
Marine Guilcher ◽  
Arnaud Liehrmann ◽  
Chloé Seyman ◽  
Thomas Blein ◽  
Guillem Rigaill ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Full Length ◽  
Nanopore Sequencing ◽  
Rna Seq ◽  
Plastid Gene ◽  
Plastid Gene Expression ◽  
Short Read ◽  
Transcript Processing

Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short read RNA-seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is however crucial when it comes to understand the interplay between the various steps of plastid gene expression. Here, the study of the Arabidopsis leaf plastid transcriptome using Nanopore sequencing showed that many splicing and editing events were not independent but co-occurring. For a given transcript, maturation events also appeared to be chronologically ordered with splicing happening after most sites are edited.

scholarly journals Chromatin-enriched RNAs mark active and repressive cis-regulation: an analysis of nuclear RNA-seq

2019 ◽  
Author(s):  
Xiangying Sun ◽  
Zhezhen Wang ◽  
Carlos Perez-Cervantes ◽  
Alex Ruthenburg ◽  
Ivan Moskowitz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Specific Gene ◽  
Rna Seq ◽  
Cell Type ◽  
Neighboring Gene ◽  
Cis Regulation ◽  
Nuclear Rna ◽  
Cell Type Specific

AbstractLong noncoding RNAs (lncRNAs) localize in the cell nucleus and influence gene expression through a variety of molecular mechanisms. RNA sequencing of two biochemical fractions of nuclei reveals a unique class of lncRNAs, termed chromatin-enriched nuclear RNAs (cheRNAs) that are tightly bound to chromatin and putatively function to cis-activate gene expression. Until now, a rigorous analytic pipeline for nuclear RNA-seq has been lacking. In this study, we survey four computational strategies for nuclear RNA-seq data analysis and show that a new pipeline, Tuxedo, outperforms other approaches. Tuxedo not only assembles a more complete transcriptome, but also identifies cheRNA with higher accuracy. We have used Tuxedo to analyze gold-standard K562 cell datasets and further characterize the genomic features of intergenic cheRNA (icheRNA) and their similarity to those of enhancer RNA (eRNA). Moreover, we quantify the transcriptional correlation of icheRNA and adjacent genes, and suggest that icheRNA may be the cis-acting transcriptional regulator that is more positively associated with neighboring gene expression than eRNA predicted by state-of-art method or CAGE signal. We also explore two novel genomic associations, suggesting cheRNA may have diverse functions. A possible new role of H3K9me3 modification coincident with icheRNA may be associated with active enhancer derived from ancient mobile elements, while a potential cis-repressive function of antisense cheRNA (as-cheRNA) is likely to be involved in transiently modulating cell type-specific cis-regulation.Author SummaryChromatin-enriched nuclear RNA (cheRNA) is a class of gene regulatory non-coding RNAs. CheRNA provides a powerful way to profile the nuclear transcriptional landscape, especially to profile the noncoding transcriptome. The computational framework presented here provides a reliable approach to identifying cheRNA, and for studying cell-type specific gene regulation. We found that intergenic cheRNA, including intergenic cheRNA with high levels of H3K9me3 (a mark associated with closed/repressed chromatin), may act as a transcriptional activator. In contrast, antisense cheRNA, which originates from the complementary strand of the protein-coding gene, may interact with diverse chromatin modulators to repress local transcription. With our new pipeline, one future challenge will be refining the functional mechanisms of these noncoding RNA classes through exploring their regulatory roles, which are involved in diverse molecular and cellular processes in human and other organisms.

scholarly journals Gene Expression Changes Occurring at Bolting Time are Associated with Leaf Senescence in Arabidopsis

2020 ◽  
Author(s):  
Will E Hinckley ◽  
Judy A. Brusslan
Keyword(s):  
Gene Expression ◽  
Phase Transition ◽  
Time Series ◽  
Leaf Senescence ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Age Dependent ◽  
Temporal Coupling ◽  
Rosette Leaf ◽  
Bolting Time

AbstractIn plants, the vegetative to reproductive phase transition (termed bolting in Arabidopsis) generally precedes age-dependent leaf senescence (LS). Many studies describe a temporal link between bolting time and LS, as plants that bolt early, senesce early, and plants that bolt late, senesce late. However, the molecular mechanisms underlying this relationship are unknown and are potentially agriculturally important, as they may allow for the development of crops that can overcome early LS caused by stress-related early phase transition. We hypothesized that gene expression changes associated with bolting time were regulating LS. We used a mutant that displays both early bolting and early LS as a model to test this hypothesis. An RNA-seq time series experiment was completed to compare the early bolting mutant to vegetative WT plants of the same age. This allowed us to identify bolting time-associated genes (BAGs) expressed in an older rosette leaf at the time of inflorescence emergence. The BAG list contains many well characterized LS regulators (ORE1, WRKY45, NAP, WRKY28), and GO analysis revealed enrichment for LS and LS-related processes. These bolting associated LS regulators likely contribute to the temporal coupling of bolting time to LS.

scholarly journals The Effects of Sub-lethal dose of Insecticides on Honeybee Behavior and Transcriptome

2021 ◽  
Author(s):  
Zuyun Zhang ◽  
Zhen Li ◽  
Qiang Huang ◽  
Zhijiang Zeng
Keyword(s):  
Molecular Mechanisms ◽  
Population Decline ◽  
Lethal Dose ◽  
Odorant Receptors ◽  
Foraging Efficiency ◽  
Rna Seq ◽  
Treatment Groups ◽  
And Behavior ◽  
Royal Jelly Protein

Abstract Exposure to insecticides is the main cause of honeybee (Apis mellifera) population decline. At sub-lethal doses, these chemicals have been shown to negatively affect honeybee physiological development and behavior. Previously, we found the insecticide imidacloprid and deltamethrin significant reduced honeybee dancing and foraging efficiency. As a follow up, we performed a deep RNA-seq analysis to reveal the gene regulatory mechanisms underlying the altered foraging behavior. Genes involved in detoxification were up-regulated in both imidacloprid and deltamethrin treatment groups. Gene members in immune pathways, odorant receptors and major royal jelly protein families showed significant up or down regulation in treatment groups compared with controls. This fluctuating gene expression profile reflects that multifaceted aspects of honeybee physiology were affected by the two insecticides, leading to inaccurate communication and impaired learning and memory. Our findings reveal candidate molecular mechanisms under impaired dance performance in honeybees exposed to insecticides.

scholarly journals Genetic Variants Associated mRNA Stability in Lung

2021 ◽  
Author(s):  
Jian-Rong Li ◽  
Mabel Tang ◽  
Yafang Li ◽  
Christopher I Amos ◽  
Chao Cheng
Keyword(s):  
Gene Expression ◽  
Mrna Stability ◽  
Genetic Variants ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Tissue Expression ◽  
Rna Seq ◽  
Genetic Traits ◽  
Expression Levels ◽  
Gene Expression Levels

Abstract Background: Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs).Results: Here, we presented a computational framework that take the advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3,942 genes and 186,132 eQTLs for 4,751 genes from 15,122,700 genetic variants for 13,476 genes, respectively. Interesting, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels.

scholarly journals Mapping eQTLs With RNA-Seq Reveals Novel SLE Susceptibility Genes, Non-Coding RNAs, and Alternative-Splicing Events That Are Concealed Using Microarrays

2016 ◽  
Author(s):  
Christopher A. Odhams ◽  
Andrea Cortini ◽  
Lingyan Chen ◽  
Amy L. Roberts ◽  
Ana Vinuela ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lupus Erythematosus ◽  
Molecular Mechanisms ◽  
Complex Disease ◽  
Splice Junction ◽  
Susceptibility Genes ◽  
Eqtl Analysis ◽  
Rna Seq ◽  
Control Of Gene Expression ◽  
Non Coding Rnas

AbstractStudies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered a greater frequency of candidate-causal eQTLs using RNA-Seq, and identified novel SLE susceptibility genes that were concealed using microarrays (e.g. NADSYN1, SKP1, and TCF7). Many of these eQTLs were found to influence the expression of several genes, suggesting risk haplotypes may harbour multiple functional effects. We pinpointed eQTLs modulating expression of four non-coding RNAs; three of which were replicated in whole-blood. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, the autophagy-related gene WDFY4, and the redox coenzyme NADSYN1, through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. In doing so, we have identified novel SLE candidate genes and specific molecular mechanisms that will serve as the basis for targeted follow-up studies.

scholarly journals M1-like tumor-associated macrophages cascade a mesenchymal/stem-like phenotype of oral squamous cell carcinoma via the IL6/Stat3/THBS1 feedback loop

2022 ◽  
Vol 41 (1) ◽  
Author(s):  
Yuanhe You ◽  
Zhuowei Tian ◽  
Zhong Du ◽  
Kailiu Wu ◽  
Guisong Xu ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Feedback Loop ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Rna Seq ◽  
Stat3 Pathway ◽  
Functional Roles

Abstract Background Tumor-associated macrophages (TAMs) have a leading position in the tumor microenvironment. Previously, we have demonstrated that M1-like TAMs activated by exosome-transferred THBS1 promote malignant migration in oral squamous cell carcinoma (OSCC). However, the functional roles and associated molecular mechanisms of the activated M1-like TAMs need to be further clarified in OSCC. Methods Conditioned Media (CM) were harvested from the exosome activated M1-like TAMs. We measured the malignant behaviors of OSCC under the treatment of CM from M1-like TAMs by performing colony forming assays, invasion assays, wound-healing assays, spheroid forming assays and in vivo xenograft experiments. The underlying mechanisms were investigated by RNA-seq, cytokines analysis, intracellular signaling pathway analysis, ChIP assays, bioinformatics analysis and validation. Results M1-like TAMs significantly promoted the epithelial-mesenchymal transition (EMT) process, and induced the cancer-stem like cells (CSCs) by upregulating the expression of MME and MMP14 in OSCC cells. Cytokine analysis revealed a shark increase of IL6 secretion from M1-like TAMs. Blocking IL6 in the CM from M1-like TAMs could significantly weaken its effects on the colony forming, invasion, migration, microsphere forming and xenograft forming abilities of OSCC cells. Cellular signaling assays indicated the activation of Jak/Stat3 pathway in the OSCC cells treated by the CM from M1-like TAMs. Blocking the activation of the Jak/Stat3 pathway could significantly weaken the effects of M1-like TAMs on the colony forming, invasion, migration, microsphere forming and xenograft forming abilities of OSCC cells. Further RNA-seq analysis and bioinformatics analysis revealed an increased expression of THBS1 in the OSCC cells treated by M1-like TAMs. Bioinformatics prediction and ChIP assays revealed the activation of Stat3 by CM from M1-like TAMs could directly promote the transcription of THBS1 in OSCC cells. Conclusions We proposed that M1-like TAMs could cascade a mesenchymal/stem-like phenotype of OSCC via the IL6/Stat3/THBS1 feedback loop. A better understanding on the functional roles and associated molecular mechanisms of M1-like TAMs might facilitate the development of novel therapies for supplementing the current treatment strategies for OSCC patients.

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