Transcriptomic changes in the hypothalamus of ovariectomized mice: Data from RNA-seq analysis

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

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Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)

Applied Sciences ◽

10.3390/app11083562 ◽

2021 ◽

Vol 11 (8) ◽

pp. 3562

Author(s):

Yong Jin Lee ◽

Sang Yong Park ◽

Dae Yeon Kim ◽

Jae Yoon Kim

Keyword(s):

Abscisic Acid ◽

Differential Expression Analysis ◽

Preharvest Sprouting ◽

Global Changes ◽

Rna Seq ◽

Hormone Metabolism ◽

Global Issue ◽

End Use ◽

Transcriptomic Changes

Preharvest sprouting (PHS) is a key global issue in production and end-use quality of cereals, particularly in regions where the rainfall season overlaps the harvest. To investigate transcriptomic changes in genes affected by PHS-induction and ABA-treatment, RNA-seq analysis was performed in two wheat cultivars that differ in PHS tolerance. A total of 123 unigenes related to hormone metabolism and signaling for abscisic acid (ABA), gibberellic acid (GA), indole-3-acetic acid (IAA), and cytokinin were identified and 1862 of differentially expressed genes were identified and divided into 8 groups by transcriptomic analysis. DEG analysis showed the majority of genes were categorized in sugar related processes, which interact with ABA signaling in PHS tolerant cultivar under PHS-induction. Thus, genes related to ABA are key regulators of dormancy and germination. Our results give insight into global changes in expression of plant hormone related genes in response to PHS.

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Integrated Physiological and Transcriptomic Analyses Responses to Altitude Stress in Oat (Avena sativa L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.638683 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yu Jinqiu ◽

Li Bing ◽

Song Tingting ◽

He Jinglei ◽

KongLing Zelai ◽

...

Keyword(s):

High Altitude ◽

Avena Sativa ◽

Molecular Mechanisms ◽

Rna Seq ◽

High Altitudes ◽

Genome Wide ◽

New Findings ◽

Polymerase Chain ◽

Transcriptomic Changes ◽

Stressful Environments

Oat is an annual gramineous forage grass with the remarkable ability to survive under various stressful environments. However, understanding the effects of high altitude stresses on oats is poor. Therefore, the physiological and the transcriptomic changes were analyzed at two sites with different altitudes, low (ca. 2,080 m) or high (ca. 2,918 m), respectively. Higher levels of antioxidant enzyme activity, reactive oxygen and major reductions in photosynthesis-related markers were suggested for oats at high altitudes. Furthermore, oat yields were severely suppressed at the high altitude. RNA-seq results showed that 11,639 differentially expressed genes were detected at both the low and the high altitudes in which 5,203 up-regulated and 6,436 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment tests were conducted and a group of major high altitude-responsive pigment metabolism genes, photosynthesis, hormone signaling, and cutin, suberine and wax biosynthesis were excavated. Using quantitative real-time polymerase chain response, we also confirmed expression levels of 20 DEGs (qRT-PCR). In summary, our study generated genome-wide transcript profile and may be useful for understanding the molecular mechanisms of Avena sativa L. in response to high altitude stress. These new findings contribute to our deeper relevant researches on high altitude stresses and further exploring new candidategenes for adapting plateau environment oat molecular breeding.

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Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.654177 ◽

2021 ◽

Vol 9 ◽

Author(s):

Minhye Shin ◽

Heeyoung Park ◽

Sooah Kim ◽

Eun Joong Oh ◽

Deokyeol Jeong ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Xylose Fermentation ◽

Sugar Metabolism ◽

Pentose Phosphate ◽

Biofuel Production ◽

Rna Seq ◽

Loss Of Function ◽

Lignocellulosic Biofuel ◽

Pentose Sugar ◽

Transcriptomic Changes

Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.

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Assessment of Embryo-Induced Transcriptomic Changes in Hamster Uterus Using RNA-Seq

Cellular Physiology and Biochemistry ◽

10.1159/000489371 ◽

2018 ◽

Vol 46 (5) ◽

pp. 1868-1878 ◽

Cited By ~ 6

Author(s):

Ming-Yu Huang ◽

Wen-Qian Zhang ◽

Miao Zhao ◽

Can Zhu ◽

Jia-Peng He ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Embryo Implantation ◽

Bioinformatic Analysis ◽

Differentially Expressed ◽

Implantation Site ◽

Rna Seq ◽

Promoter Regions ◽

Functional Clustering ◽

Gene Network Analysis ◽

Transcriptomic Changes

Background/Aims: The mouse is widely used as an animal model for studying human embryo implantation. However, the mouse is unique in that both ovarian progesterone and estrogen are critical to implantation, whereas in the majority of species (e.g. human and hamster) implantation can occur in the presence of progesterone alone. Methods: In this study, we analyzed embryo-induced transcriptomic changes in the hamster uterus during embryo implantation by using RNA-seq. Differentially expressed genes were characterized by bioinformatic analysis. Results: We identified a total of 781 differentially expressed genes, of which 367 genes were up-regulated and 414 genes were down-regulated at the implantation site compared to the inter-implantation site. Functional clustering and gene network analysis highlighted the cell cycle process in uterus upon embryo implantation. By examining of the promoter regions of differentially expressed genes, we identified 7 causal transcription factors. Additionally, through connectivity map (CMap) analysis, multiple compounds were identified to have potential anti-implantation effects due to their ability to reverse embryo-induced transcriptomic changes. Conclusion: Our study provides a valuable resource for in-depth understanding of the mechanism underlying embryo implantation.

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Transcriptomic changes associated with DKK4 overexpression in pancreatic cancer cells detected by RNA-Seq

Tumor Biology ◽

10.1007/s13277-015-4379-x ◽

2016 ◽

Vol 37 (8) ◽

pp. 10827-10838 ◽

Cited By ~ 5

Author(s):

Yongsheng Ouyang ◽

Juncheng Pan ◽

Qiang Tai ◽

Jingfang Ju ◽

Huaizhi Wang

Keyword(s):

Pancreatic Cancer ◽

Cancer Cells ◽

Rna Seq ◽

Pancreatic Cancer Cells ◽

Transcriptomic Changes

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Optogenetic and transcriptomic interrogation of enhanced muscle function in the paralyzed mouse whisker pad

10.1101/473298 ◽

2018 ◽

Author(s):

Thomas J. Vajtay ◽

Akhil Bandi ◽

Aman Upadhyay ◽

Mavis. R. Swerdel ◽

Ronald P. Hart ◽

...

Keyword(s):

Facial Nerve ◽

Muscle Function ◽

Time Course ◽

Critical Factor ◽

Transcriptome Profiling ◽

Gene Families ◽

Nerve Transection ◽

Rna Seq ◽

Whisker Pad ◽

Transcriptomic Changes

AbstractThe functional state of denervated muscle is a critical factor in the ability to restore movement after injury- or disease-related paralysis. Here we used peripheral optogenetic stimulation and transcriptome profiling in the mouse whisker system to investigate the time course of changes in neuromuscular function following complete unilateral facial nerve transection. While most skeletal muscles rapidly lose functionality after lower motor neuron denervation, optogenetic muscle stimulation of the paralyzed whisker pad revealed sustained increases in the sensitivity, velocity, and amplitude of whisker movements, and reduced fatigability, starting 48 h after denervation. RNA-seq analysis showed distinct regulation of multiple gene families in denervated whisker pad muscles compared to the atrophy-prone soleus, including prominent changes in ion channels and contractile fibers. Together, our results define the unique functional and transcriptomic landscape of denervated facial muscles, and have general implications for restoring movement after neuromuscular injury or disease.New & NoteworthyOptogenetic activation of muscle can be used to non-invasively induce movements and probe muscle function. We used this technique in mice to investigate changes in whisker movements following facial nerve transection. We found unexpectedly enhanced functional properties of whisker pad muscle following denervation, accompanied by unique transcriptomic changes. Our findings highlight the utility of the mouse whisker pad for investigating the restoration of movement after paralysis.

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Transcriptomic analysis of cadmium stressed Tamarix hispida revealed novel transcripts and the importance of ABA network

10.21203/rs.3.rs-759346/v1 ◽

2021 ◽

Author(s):

Caiqiu Gao ◽

Pei-Long Wang ◽

Xiao-Jin Lei ◽

Yuan-Yuan Wang ◽

Bai-chao Liu ◽

...

Keyword(s):

Environmental Problem ◽

Salt Content ◽

Tamarix Hispida ◽

Rna Seq ◽

Cd Stress ◽

Ros Metabolism ◽

Hormone Responses ◽

Novel Transcripts ◽

Stress Sensing ◽

Transcriptomic Changes

Abstract Aim Cadmium (Cd) pollution is widely detected in soil and has been recognized as a major environmental problem. Tamarix hispida is a woody halophyte, which can form natural forest on desert and the soil with 0.5–1% salt content, making it an ideal plant for research investigating the effects of various stresses on plants. However, no systematic study has investigated the molecular mechanism of Cd tolerance in T. hispida.Methods In this study, the RNA-seq technique was applied to analyze the transcriptomic changes in T. hispida treated with 150 µmol L− 1 CdCl2 for 24, 48 and 72 h compared with control.Results In total, 72764 unigenes exhibited similar sequences in the NR database, while 41528 unigenes (36.3% of all the unigenes) did not exhibit similar sequences, which may be new transcripts. In addition, 6778, 8282 and 8601 DEGs were detected at 24, 48 and 72 h, respectively. Functional annotation analysis indicated that many genes may be involved in several aspects of the Cd stress response, including ion bonding, signal transduction, stress sensing, hormone responses and ROS metabolism. A ThUGT gene from the abscisic acid (ABA) signaling pathway can enhance the Cd resistance ability of T. hispida by regulating the production of reactive oxygen species under Cd stress and inhibiting T. hispida absorption of Cd.Conclusion The new transcriptome resources and data that we present in this study for T. hispida may substantially facilitate molecular studies of the mechanisms governing Cd resistance.

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Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss

BMC Genomics ◽

10.1186/s12864-021-07812-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Daniel Oropeza ◽

Valentina Cigliola ◽

Agustín Romero ◽

Simona Chera ◽

Santiago A. Rodríguez-Seguí ◽

...

Keyword(s):

Cell Loss ◽

Rna Seq ◽

Β Cell ◽

Transcriptional Responses ◽

Transcriptomic Response ◽

Tetratricopeptide Repeats ◽

Cell Ablation ◽

Insulin Secreting Cells ◽

Transcriptional Changes ◽

Transcriptomic Changes

Abstract Background Loss of pancreatic insulin-secreting β-cells due to metabolic or autoimmune damage leads to the development of diabetes. The discovery that α-cells can be efficiently reprogrammed into insulin-secreting cells in mice and humans has opened promising avenues for innovative diabetes therapies. β-cell loss triggers spontaneous reprogramming of only 1–2% of α-cells, limiting the extent of regeneration. Most α-cells are refractory to conversion and their global transcriptomic response to severe β-cell loss as well as the mechanisms opposing their reprogramming into insulin producers are largely unknown. Here, we performed RNA-seq on FAC-sorted α-cells to characterize their global transcriptional responses at different time points after massive β-cell ablation. Results Our results show that α-cells undergo stage-specific transcriptional changes 5- and 15-days post-diphtheria toxin (DT)-mediated β-cell ablation. At 5 days, α-cells transiently upregulate various genes associated with interferon signaling and proliferation, including Interferon Induced Protein with Tetratricopeptide Repeats 3 (Ifit3). Subsequently, at 15 days post β-cell ablation, α-cells undergo a transient downregulation of genes from several pathways including Insulin receptor, mTOR and MET signaling. Conclusions The results presented here pinpoint novel markers discriminating α-cells at different stages after acute β-cell loss, and highlight additional signaling pathways that are modulated in α-cells in this context.

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Transcriptomic changes resulting fromSTK32Boverexpression identifies pathways potentially relevant to essential tremor

10.1101/552901 ◽

2019 ◽

Cited By ~ 2

Author(s):

Calwing Liao ◽

Faezah Sarayloo ◽

Daniel Rochefort ◽

Fulya Akçimen ◽

Greer S. Diamond ◽

...

Keyword(s):

Axon Guidance ◽

Essential Tremor ◽

Rna Seq ◽

Transcriptome Profile ◽

Gwas Study ◽

Genetic Studies ◽

High Heritability ◽

Cerebellar Tissue ◽

The One ◽

Transcriptomic Changes

AbstractEssential tremor (ET) is a common movement disorder that has a high heritability. A number of genetic studies have associated different genes and loci with ET, but few have investigated the biology of any of these genes.STK32Bwas significantly associated with ET in a large GWAS study and was found to be overexpressed in ET cerebellar tissue. Here, we overexpressedSTK32Bin human cerebellar DAOY cells and used an RNA-Seq approach to identify differentially expressed genes by comparing the transcriptome profile of these cells to the one of control DAOY cells. Pathway and gene ontology enrichment identified axon guidance, olfactory signalling and calcium-voltage channels as significant. Additionally, we show that overexpressingSTK32Baffects transcript levels of previously implicated ET genes such asFUS. Our results investigate the effects of overexpressedSTK32Band suggest that it may be involved in relevant ET pathways and genes.

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