scholarly journals Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)

2019 ◽  
Vol 20 (16) ◽  
pp. 3930 ◽  
Author(s):  
Komivi Dossa ◽  
Marie A. Mmadi ◽  
Rong Zhou ◽  
Tianyuan Zhang ◽  
Ruqi Su ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Meta Analysis ◽  
Plant Responses ◽  
Proof Of Concept ◽  
Rna Seq ◽  
Wild Type ◽  
Salt Treatment ◽  
Hub Genes ◽  
Hub Gene ◽  
The Core

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.

scholarly journals Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

2017 ◽  
Author(s):  
Antoine Hocher ◽  
Myriam Ruault ◽  
Petra Kaferle ◽  
Marc Descrimes ◽  
Mickael Garnier ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Position Effect ◽  
Histone Mark ◽  
Eukaryotic Genome ◽  
Wild Type ◽  
Histone Marks ◽  
The Core ◽  
Defective Mutant ◽  
H3k79 Methylation ◽  
Subtelomeric Regions

AbstractThe eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly and man. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at various levels in yeast, and found that Sir3 spreading into Extended Silent Domains (ESD) eventually reached saturation at subtelomeres. We observed that Sir3 spreading into ESDs covered zone associated with specific histone marks in wild-type cells and stopped at zones of histone mark transitions including H3K79 tri-methylation levels. The conserved enzyme Dot1 deposits H3K79 methylation, and we found that it is essential for viability upon overexpression of Sir3, but not of a spreading-defective mutant Sir3A2Q. These data suggest that H3K79 methylation actively blocks Sir3 spreading. Lastly, our meta-analysis uncovers previously uncharacterized discrete subtelomeric domains associated with specific chromatin features offering a new viewpoint on how to separate subtelomeres from the core chromosome.

scholarly journals Subgenome Bias and Temporal Postponement of Gene Expression Contributes to the Distinctions of Fiber Quality in Gossypium Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Huan Mei ◽  
Bowen Qi ◽  
Zegang Han ◽  
Ting Zhao ◽  
Menglan Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fiber Quality ◽  
Expression Patterns ◽  
Rna Seq ◽  
Hub Genes ◽  
Hub Gene ◽  
Expression Of Genes ◽  
Multiple Dimensions ◽  
Cotton Species ◽  
Expression Bias

As two cultivated widely allotetraploid cotton species, although Gossypium hirsutum and Gossypium barbadense evolved from the same ancestor, they differ in fiber quality; the molecular mechanism of that difference should be deeply studied. Here, we performed RNA-seq of fiber samples from four G. hirsutum and three G. barbadense cultivars to compare their gene expression patterns on multiple dimensions. We found that 15.90–37.96% of differentially expressed genes showed biased expression toward the A or D subgenome. In particular, interspecific biased expression was exhibited by a total of 330 and 486 gene pairs at 10 days post-anthesis (DPA) and 20 DPA, respectively. Moreover, 6791 genes demonstrated temporal differences in expression, including 346 genes predominantly expressed at 10 DPA in G. hirsutum (TM-1) but postponed to 20 DPA in G. barbadense (Hai7124), and 367 genes predominantly expressed at 20 DPA in TM-1 but postponed to 25 DPA in Hai7124. These postponed genes mainly participated in carbohydrate metabolism, lipid metabolism, plant hormone signal transduction, and starch and sucrose metabolism. In addition, most of the co-expression network and hub genes involved in fiber development showed asymmetric expression between TM-1 and Hai7124, like three hub genes detected at 10 DPA in TM-1 but not until 25 DPA in Hai7124. Our study provides new insights into interspecific expression bias and postponed expression of genes associated with fiber quality, which are mainly tied to asymmetric hub gene network. This work will facilitate further research aimed at understanding the mechanisms underlying cotton fiber improvement.

scholarly journals Arabidopsis ATHB17 coordinates nuclear and plastidic photosynthesis gene expression in response to abiotic stress

2016 ◽  
Author(s):  
Ping Zhao ◽  
Rong Cui ◽  
Ping Xu ◽  
Jieli Mao ◽  
Yu Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Salt Tolerance ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Rna Seq ◽  
Wild Type ◽  
Knockout Mutant ◽  
Photosynthetic Genes ◽  
Reduced Salt ◽  
Photosynthesis Gene

Photosynthesis is sensitive to environmental stresses. How nuclear and plastid genome coordinate to cope with abiotic stress is not well understood. Here we report that ATHB17, an Arabidopsis HD-Zip transcription factor, coordinates the expression of nuclear encoded photosynthetic genes (NEPGs) and plastid encoded genes (PEGs) in response to abiotic stress. ATHB17-overexpressing plants display enhanced stress tolerance, whereas its knockout mutant is more sensitive compared to the wild type. Through RNA-seq analysis, we found that ATHB17 down-regulated many NEPGs while up-regulated a number of PEGs. ATHB17 could directly modulate the expression of several NEPGs by binding to their promoters. Furthermore, we identified ATSIG5, encoding a plastid sigma factor, as one of the target genes of ATHB17. Loss of ATSIG5 reduced salt tolerance while overexpression of ATSIG5 enhanced salt tolerance, similar to that of ATHB17. Taken together, our results reveal that ATHB17 is an important coordinator between NEPGs and PEGs partially through ATSIG5 to protect photosynthesis machinery in response to abiotic stresses.

Integrative meta-analysis for the identification of hub genes in chemoresistant colorectal cancer

2020 ◽  
Vol 14 (7) ◽  
pp. 525-537
Author(s):  
Nadiah Abu ◽  
Norahayu Othman ◽  
Kha W Hon ◽  
Wan FWM Nazarie ◽  
Rahman Jamal
Keyword(s):  
Colorectal Cancer ◽  
Folinic Acid ◽  
Meta Analysis ◽  
Hub Genes ◽  
Exclusion Criteria ◽  
Hub Gene ◽  
Potential Target ◽  
Microarray Studies ◽  
Microarray Datasets ◽  
Hct116 Cells

Background: Finding a new target or a new drug to overcome chemoresistance is difficult due to the heterogenous nature of cancer. Meta-analysis was performed to combine the analysis of different microarray studies to get a robust discovery. Materials & methods: Herein, we analyzed three microarray datasets on combination of folinic acid, fluorouracil, and oxaliplatin drugs (FOLFOX) resistance that fit our inclusion/exclusion criteria and performed a meta-analysis using the OmiCC system. Results: We identified several deregulated genes and we discovered HNF4A as a hub gene. We performed functional validation and observed that by targeting HNF4A, HCT116 cells were more sensitive toward both oxaliplatin and 5-fluorouracil significantly. Conclusion: Our findings show that HNF4A could be a potential target in overcoming FOLFOX chemoresistance in colorectal cancer.

scholarly journals Arabidopsis V-ATPase d2 Subunit Plays a Role in Plant Responses to Oxidative Stress

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 701 ◽  
Author(s):  
Shuang Feng ◽  
Yun Peng ◽  
Enhui Liu ◽  
Hongping Ma ◽  
Kun Qiao ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Developmental Stages ◽  
Plant Responses ◽  
Rna Seq ◽  
Wild Type ◽  
Histochemical Analysis ◽  
Qpcr Analysis ◽  
Atpase Gene ◽  
In The Wild ◽  
D Subunit

Vacuolar-type H+-ATPase (V-ATPase), a multisubunit proton pump located on the endomembrane, plays an important role in plant growth. The Arabidopsis thaliana V-ATPase d subunit (VHA-d) consists of two isoforms; AtVHA-d1 and AtVHA-d2. In this study, the function of AtVHA-d2 was investigated. Histochemical analysis revealed that the expression of AtVHA-d1 and AtVHA-d2 was generally highly overlapping in multiple tissues at different developmental stages of Arabidopsis. Subcellular localization revealed that AtVHA-d2 was mainly localized to the vacuole. AtVHA-d2 expression was significantly induced by oxidative stress. Analysis of phenotypic and H2O2 content showed that the atvha-d2 mutant was sensitive to oxidative stress. The noninvasive microtest monitoring demonstrated that the net H+ influx in the atvha-d2 roots was weaker than that in the wild-type under normal conditions. However, oxidative stress resulted in the H+ efflux in atvha-d2 roots, which was significantly different from that in the wild-type. RNA-seq combined with qPCR analysis showed that the expression of several members of the plasma membrane H+-ATPase gene (AtAHA) family in atvha-d2 was significantly different from that in the wild-type. Overall, our results indicate that AtVHA-d2 plays a role in Arabidopsis in response to oxidative stress by affecting H+ flux and AtAHA gene expression.

scholarly journals Identification of ITPR1 as a hub gene of Group 3 Medulloblastoma and coregulated genes with potential prognostic values

2021 ◽  
Author(s):  
Pablo Ferreira das Chagas ◽  
Graziella Ribeiro de Sousa ◽  
Luciana Chain Veronez ◽  
Andrea Martins-da-Silva ◽  
Carolina Alves Pereira Corrêa ◽  
...  
Keyword(s):  
Molecular Subtype ◽  
Roc Curves ◽  
Rna Seq ◽  
Sequencing Data ◽  
Hub Genes ◽  
Hub Gene ◽  
Protein Protein Interaction ◽  
Metastatic Process ◽  
Group 3 ◽  
Metastatic Risk

Abstract The Group 3 Medulloblastoma ( Grp3-MB ) is an aggressive molecular subtype with a high incidence of metastasis and deaths. In this study, were used an RNA sequencing data ( RNA-Seq ) from a Brazinian cohort of MBs to identify hub genes associated with the metastatic risk. Data validation were performed by using multiple large datasets from MBs (GSE85217, GSE37418, EGAS00001001953). DESeq2 package in R software was used to identify the differentially expressed genes ( DEGs ) in our RNA-Seq data. The DEGs data were accessed to construct the modules/graphs of coexpression and to identify hub genes through Cytoscape platform. The co-regulated genes were enriched by the Kyoto Encyclopedia of Genes and Genomes ( KEGG ) pathway and the Protein-protein interaction ( PPI ) network was visualized by Cytoscape. The Kaplan–Meier plotter and ROC curves were used to validate the diagnostic and prognostic values of specific biomarkers identified through this model. We identified that Inositol 1,4,5-triphosphate receptor type 1 ( ITPR1 ) as a downregulated hub gene, with a high diagnostic accuracy to Grp3-MBs and associated with tumor metastasis. In addition, we identified genes significantly correlated with ITPR1 that were associated with metastasis in Grp3-MB ( ATP1A2 , MTTL7A and RGL1) , and worst overall survival in MBs ( ANTXR1 and RGL1 ). Our findings suggest that the ITPR1 hub gene is potentially involved in the metastatic process for Grp3-MB. Our data also provide evidence of targets that may serve as prognostic predictors and/or regulators for the metastatic process that maybe explored for further research of individualized therapy to Grp3-MBs.

scholarly journals Arabidopsis V-ATPase d2 subunit plays a role in plant responses to oxidative stress

2020 ◽  
Author(s):  
Shuang Feng ◽  
Yun Peng ◽  
Enhui Liu ◽  
Hongping Ma ◽  
Kun Qiao ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Developmental Stages ◽  
Plant Responses ◽  
Rna Seq ◽  
Wild Type ◽  
Phenotypic Analysis ◽  
Non Invasive ◽  
Atpase Gene ◽  
D Subunit ◽  
And Oxidative Stress

Abstract Background: Vacuolar-type H + -ATPase (V-ATPase) is a multisubunit proton pump located on the endomembranes, which plays an important role in plant growth. The Arabidopsis V-ATPase d subunit consists of two isoforms, AtVHA-d1 and AtVHA-d2. Results: In this study, the function of the AtVHA-d2 gene was investigated. Histochemical analysis revealed that the AtVHA-d1 and AtVHA-d2 genes were generally and highly overlapping expressed in multiple tissues at different developmental stages of Arabidopsis. Subcellular localization showed that AtVHA-d2 was mainly localized to the vacuole. The AtVHA-d2 expression was significantly induced by oxidative stress. Furthermore, the phenotypic analysis showed that the atvha-d2 mutant was sensitive to oxidative stress. The non-invasive micro-test measurement demonstrated that the net H + influx in the atvha-d2 roots was weaker than that of the wild type under normal conditions. However, oxidative stress resulted in the H + efflux in atvha-d2 roots, which was significantly different from the wild type. RNA-seq combined with qPCR analysis showed that the expression of several members of the plasma membrane H + -ATPase gene ( AtAHA ) family in atvha-d2 were significant different from wild type under normal and oxidative stress. Conclusion: Overall, our results indicate that AtVHA-d2 plays a role in Arabidopsis in response to oxidative stress by affecting H + flux and AtAHA gene expression.

scholarly journals Putative transmembrane transporter modulates higher-level aggression in Drosophila

2017 ◽  
Vol 114 (9) ◽  
pp. 2373-2378 ◽  
Author(s):  
Budhaditya Chowdhury ◽  
Yick-Bun Chan ◽  
Edward A. Kravitz
Keyword(s):  
Causal Effect ◽  
Nerve Terminals ◽  
Rna Seq ◽  
Wild Type ◽  
Temperature Dependent ◽  
Number Of Genes ◽  
Interesting Family ◽  
Solute Carrier ◽  
Transmembrane Transporter ◽  
Selection Of

By selection of winners of dyadic fights for 35 generations, we have generated a hyperaggressive Bully line of flies that almost always win fights against the parental wild-type Canton-S stock. Maintenance of the Bully phenotype is temperature dependent during development, with the phenotype lost when flies are reared at 19 °C. No similar effect is seen with the parent line. This difference allowed us to carry out RNA-seq experiments and identify a limited number of genes that are differentially expressed by twofold or greater in the Bullies; one of these was a putative transmembrane transporter, CG13646, which showed consistent and reproducible twofold down-regulation in Bullies. We examined the causal effect of this gene on the phenotype with a mutant line for CG13646, and with an RNAi approach. In all cases, reduction in expression of CG13646 by approximately half led to a hyperaggressive phenotype partially resembling that seen in the Bully flies. This gene is a member of a very interesting family of solute carrier proteins (SLCs), some of which have been suggested as being involved in glutamine/glutamate and GABA cycles of metabolism in excitatory and inhibitory nerve terminals in mammalian systems.

scholarly journals Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 665
Author(s):  
Hui Yu ◽  
Yan Guo ◽  
Jingchun Chen ◽  
Xiangning Chen ◽  
Peilin Jia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Focal Adhesion ◽  
Biological Pathways ◽  
Postmortem Brain ◽  
Rna Seq ◽  
Hub Genes ◽  
Differential Coexpression ◽  
Pathway Crosstalk ◽  
Microarray Datasets ◽  
Transcriptomic Studies

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

scholarly journals Disentangling transcriptional responses in plant defense against arthropod herbivores

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alejandro Garcia ◽  
M. Estrella Santamaria ◽  
Isabel Diaz ◽  
Manuel Martinez
Keyword(s):  
Regulatory Networks ◽  
Pieris Rapae ◽  
Meta Analysis ◽  
Plant Response ◽  
Plant Responses ◽  
Transcriptional Responses ◽  
Crop Species ◽  
Physiological Processes ◽  
Meta Analyses ◽  
Plant Herbivore

AbstractThe success in the response of a plant to a pest depends on the regulatory networks that connect plant perception and plant response. Meta-analyses of transcriptomic responses are valuable tools to discover novel mechanisms in the plant/herbivore interplay. Considering the quantity and quality of available transcriptomic analyses, Arabidopsis thaliana was selected to test the ability of comprehensive meta-analyses to disentangle plant responses. The analysis of the transcriptomic data showed a general induction of biological processes commonly associated with the response to herbivory, like jasmonate signaling or glucosinolate biosynthesis. However, an uneven induction of many genes belonging to these biological categories was found, which was likely associated with the particularities of each specific Arabidopsis-herbivore interaction. A thorough analysis of the responses to the lepidopteran Pieris rapae and the spider mite Tetranychus urticae highlighted specificities in the perception and signaling pathways associated with the expression of receptors and transcription factors. This information was translated to a variable alteration of secondary metabolic pathways. In conclusion, transcriptomic meta-analysis has been revealed as a potent way to sort out relevant physiological processes in the plant response to herbivores. Translation of these transcriptomic-based analyses to crop species will permit a more appropriate design of biotechnological programs.

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