scholarly journals Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qizhen Xiao ◽  
Zekun Huang ◽  
Yawei Shen ◽  
Yang Gan ◽  
Yi Wang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Alternative Splicing ◽  
Thermal Resistance ◽  
Molecular Mechanisms ◽  
Southern China ◽  
Expression Patterns ◽  
Pathway Enrichment Analysis ◽  
High Survival ◽  
Genetic Characteristics ◽  
Alternative Splicing Events

Abstract Background Heterosis has been exploited for decades in different animals and crops due to it resulting in dramatic increases in yield and adaptability. Hybridization is a classical breeding method that can effectively improve the genetic characteristics of organisms through heterosis. Abalone has become an increasingly economically important aquaculture resource with high commercial value. However, due to changing climate, abalone is now facing serious threats of high temperature in summer. Interspecific hybrid abalone (Haliotis gigantea ♀ × H. discus hannai ♂, SD) has been cultured at large scale in southern China and has been shown high survival rates under heat stress in summer. Therefore, SD has become a good model material for heterosis research, but the molecular basis of heterosis remains elusive. Results Heterosis in thermal tolerance of SD was verified through Arrhenius break temperatures (ABT) of cardiac performance in this study. Then RNA-Sequencing was conducted to obtain gene expression patterns and alternative splicing events at control temperature (20 °C) and heat stress temperature (30 °C). A total of 356 (317 genes), 476 (435genes), and 876 (726 genes) significantly diverged alternative splicing events were identified in H. discus hannai (DD), H. gigantea (SS), and SD in response to heat stress, respectively. In the heat stress groups, 93.37% (20,512 of 21,969) of the expressed genes showed non-additive expression patterns, and over-dominance expression patterns of genes account for the highest proportion (40.15%). KEGG pathway enrichment analysis showed that the overlapping genes among common DEGs and NAGs were significantly enriched in protein processing in the endoplasmic reticulum, mitophagy, and NF-κB signaling pathway. In addition, we found that among these overlap genes, 39 genes had undergone alternative splicing events in SD. These pathways and genes may play an important role in the thermal resistance of hybrid abalone. Conclusion More alternative splicing events and non-additive expressed genes were detected in hybrid under heat stress and this may contribute to its thermal heterosis. These results might provide clues as to how hybrid abalone has a better physiological regulation ability than its parents under heat stress, to increase our understanding of heterosis in abalone.

scholarly journals Molecular Cloning and Characterization of Three Glucosinolate Transporter (GTR) Genes from Chinese Kale

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 202
Author(s):  
Ding Jiang ◽  
Jianjun Lei ◽  
Bihao Cao ◽  
Siyuan Wu ◽  
Guoju Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Southern China ◽  
Expression Patterns ◽  
Protein Structures ◽  
Hormone Treatment ◽  
Glucosinolate Content ◽  
Rnai Technology ◽  
Chinese Kale ◽  
Nutritional Qualities ◽  
Different Tissues

Chinese kale is a native vegetable in Southern China and the flowering stalk is the most commonly used edible part due to its high glucosinolate content and other nutritional qualities. The GTR protein played important roles in the glucosinolate transport process. In this study, three BocGTR1 genes were cloned from Chinese kale for the first time. Their gene structure, physicochemical properties, signal peptides, transmembrane structures, functional domains, second and third-order protein structures, and phylogenetic relationships were predicted. The expression levels of BocGTR1a and BocGTR1c were much higher than those of BocGTR1b in various tissues, especially in leaves and buds. In addition, the expression patterns of three genes were examined under various abiotic stresses or hormone treatment, including those induced by wounding, heat stress, methyl jasmonate, salicylic acid, salt, and MgCl2 treatment. BocGTR1a and BocGTR1c were strongly induced by wounding and heat stress. The expression of BocGTR1a and BocGTR1c was significantly silenced in plants transformed by RNAi technology. Total glucosinolate content was significantly decreased in mature leaves and increased in roots of RNAi-transformed plants compared to wild-type plants. In addition, we found that BocGTR1a and BocGTR1c may participate in glucosinolate accumulation in different tissues with a selection for specific glucosinolates. These results indicated that BocGTR1a and BocGTR1c may be the key genes involved in the glucosinolate accumulation in different tissues of Chinese kale.

scholarly journals Gene expression profiles during short-term heat stress; branchingvs.massive Scleractinian corals of the Red Sea

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1814 ◽  
Author(s):  
Keren Maor-Landaw ◽  
Oren Levy
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Redox Regulation ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Marker Genes ◽  
Stylophora Pistillata ◽  
Stress Genes

It is well-established that there is a hierarchy of susceptibilities amongst coral genera during heat-stress. However, molecular mechanisms governing these differences are still poorly understood. Here we explored if specific corals possessing different morphologies and different susceptibilities to heat stress may manifest varied gene expression patterns. We examined expression patterns of seven genes in the branching coralsStylophora pistillataandAcropora eurystomaand additionally in the massive robust coral,Poritessp. The tested genes are representatives of key cellular processes occurring during heat-stress in Cnidaria: oxidative stress, ER stress, energy metabolism, DNA repair and apoptosis. Varied response to the heat-stress, in terms of visual coral paling, algal maximum quantum yield and host gene expression was evident in the different growth forms. The two branching corals exhibited similar overall responses that differed from that of the massive coral.A. eurystomathat is considered as a susceptible species did not bleach in our experiment, but tissue sloughing was evident at 34 °C. Interestingly, in this species redox regulation genes were up-regulated at the very onset of the thermal challenge. InS. pistillata, bleaching was evident at 34 °C and most of the stress markers were already up-regulated at 32 °C, either remaining highly expressed or decreasing when temperatures reached 34 °C. The massivePoritesspecies displayed severe bleaching at 32 °C but stress marker genes were only significantly elevated at 34 °C. We postulate that by expelling the algal symbionts fromPoritestissues, oxidation damages are reduced and stress genes are activated only at a progressed stage. The differential gene expression responses exhibited here can be correlated with the literature well-documented hierarchy of susceptibilities amongst coral morphologies and genera in Eilat’s coral reef.

scholarly journals Posttranscriptional Regulation of Splicing Factor SRSF1 and Its Role in Cancer Cell Biology

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Vânia Gonçalves ◽  
Peter Jordan
Keyword(s):  
Alternative Splicing ◽  
Cancer Cell ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Current Knowledge ◽  
Expression Patterns ◽  
Regulatory Protein ◽  
Gene Transcript

Over the past decade, alternative splicing has been progressively recognized as a major mechanism regulating gene expression patterns in different tissues and disease states through the generation of multiple mRNAs from the same gene transcript. This process requires the joining of selected exons or usage of different pairs of splice sites and is regulated by gene-specific combinations of RNA-binding proteins. One archetypical splicing regulator is SRSF1, for which we review the molecular mechanisms and posttranscriptional modifications involved in its life cycle. These include alternative splicing of SRSF1 itself, regulatory protein phosphorylation events, and the role of nuclear versus cytoplasmic SRSF1 localization. In addition, we resume current knowledge on deregulated SRSF1 expression in tumors and describe SRSF1-regulated alternative transcripts with functional consequences for cancer cell biology at different stages of tumor development.

scholarly journals Alternative splicing events implicated in carcinogenesis and prognosis of thyroid gland cancer

2020 ◽  
Author(s):  
zenghong wu ◽  
Yi Zhong ◽  
Fu-Cheng Cai
Keyword(s):  
Thyroid Cancer ◽  
Alternative Splicing ◽  
Practical Knowledge ◽  
Splice Variants ◽  
Expression Patterns ◽  
Prognostic Models ◽  
Clinicopathological Parameters ◽  
Oncology Research ◽  
Kaplan Meier ◽  
Alternative Splicing Events

Abstract Background: Alternative splicing events (ASEs), a critical post-transcriptional regulatory mechanism, expands gene expression patterns, resulting in increased protein diversity and more than 95% of human genes experience AS and encode splice variants in the regular physiological processes. While the role of AS in the thyroid cancer as yet missing, therefore, it was necessary to carry out this study to provide more information about the combination of splicing and clinical parameters, as well as potential mechanism of the survival-related splicing events in thyroid cancer. Materials and methods: Here, we draw all-around AS profiles of thyroid cancer by analyzing RNA-seq data. We also constructed prognostic models via combining splicing signatures and clinicopathological parameters. Splicing network was constructed as a way to offer functional insight into the full practical knowledge of AS in the initiation and development of thyroid cancer. Results: There were 10446 genes, and 45150 AS events in 506 TC patients, which indicates that ASEs are universal in TC. Moreover, 1819 AS signatures were identified to be significantly related to OS of TC patients and among the seven types of ASES, ES was the most common, followed by AP and AT. Kaplan-Meier survival curves results suggested that seven types of ASEs were related to bad prognosis in TC patients (P<0.05). In TC, AA (AUC: 0.937), AD (AUC: 0.965), AT (AUC: 0.964), ES (AUC: 0.999), ME (AUC: 0.999), RI (AUC: 0.837) all demonstrated an AUC over 0.6, of which ES and ME best predict the incidence of TC. We found that age and risk score (All) were risk factors for TC patients. As for ASEs is regulated by SFs, we study if the TC-ASEs were regulated by various SFs and the results demonstrated that the expression of 90 SFs was related to 469 ASEs OS in the TC cohort. Conclusions: In sum, the findings in the current study may provide a basis for spliceosomes in TC, and the methods used in this study could provide novel perspectives in other fields of tumor study to help shed light on future oncology research.

scholarly journals Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Laura Entrambasaguas ◽  
Miriam Ruocco ◽  
Koen J. F. Verhoeven ◽  
Gabriele Procaccini ◽  
Lazaro Marín-Guirao
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Life History ◽  
Heat Stress ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Posidonia Oceanica ◽  
Life History Strategies ◽  
Gene Body ◽  
Marine Plants

AbstractThe role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpGO/E ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants’ latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants.

scholarly journals Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 387 ◽  
Author(s):  
Zengkui Lu ◽  
Mingxing Chu ◽  
Qing Li ◽  
Meilin Jin ◽  
Xiaojuan Fei ◽  
...  
Keyword(s):  
Heat Stress ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
P Value ◽  
Comprehensive Overview

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

scholarly journals Physiological Analysis and Transcriptome Analysis of Asian Honey Bee (Apis cerana cerana) in Response to Sublethal Neonicotinoid Imidacloprid

Insects ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 753
Author(s):  
Jing Gao ◽  
San-Sheng Jin ◽  
Yan He ◽  
Jin-Hong Luo ◽  
Chun-Qin Xu ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Honey Bee ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Apis Cerana ◽  
Pathway Enrichment Analysis ◽  
Indigenous Species ◽  
A Genome ◽  
Asian Honey Bee

Asian honey bee (Apis cerana) is the most important Chinese indigenous species, while its toxicological characteristic against neonicotinoids is poorly known. Here, we combined physiological experiments with a genome-wide transcriptome analysis to understand the molecular basis of genetic variation that responds to sublethal imidacloprid at different exposure durations in A. cerana. We found that LC5 dose of imidacloprid had a negative impact on climbing ability and sucrose responsiveness in A. cerana. When bees were fed with LC5 dose of imidacloprid, the enzyme activities of P450 and CarE were decreased, while the GSTs activity was not influenced by the pesticide exposure. The dynamic transcriptomic profiles of A. cerana workers exposed to LC5 dose of imidacloprid for 1 h, 8 h, and 16 h were obtained by high-throughput RNA-sequencing. We performed the expression patterns of differentially expressed genes (DEGs) through trend analysis, and conducted the gene ontology analysis and KEGG pathway enrichment analysis with DEGs in up- and down-regulated pattern profiles. We observed that more genes involved in metabolism, catalytic activity, and structural molecule activity are down-regulated; while more up-regulated genes were enriched in terms associated with response to stimulus, transporter activity, and signal transducer activity. Additionally, genes related to the phenylalanine metabolism pathway, FoxO signaling pathway, and mTOR signaling pathway as indicated in the KEGG analysis were significantly up-related in the exposed bees. Our findings provide a comprehensive understanding of Asian honey bee in response to neonicotinoids sublethal toxicity, and could be used to further investigate the complex molecular mechanisms in Asian honey bee under pesticide stress.

scholarly journals Comprehensive Transcriptomic Analysis of Mouse Gonadal Development Involving Sexual Differentiation, Meiosis and Gametogenesis

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Wang ◽  
Geng G. Tian ◽  
Zhuxia Zheng ◽  
Bo Li ◽  
Qinghe Xing ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Candidate Genes ◽  
Sexual Differentiation ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Gonadal Development ◽  
Transcriptome Database ◽  
Alternatively Spliced ◽  
Expression Module

Abstract Background Mammalian gonadal development is crucial for fertility. Sexual differentiation, meiosis and gametogenesis are critical events in the process of gonadal development. Abnormalities in any of these events may cause infertility. However, owing to the complexity of these developmental events, the underlying molecular mechanisms are not fully understood and require further research. Results In this study, we employed RNA sequencing to examine transcriptome profiles of murine female and male gonads at crucial stages of these developmental events. By bioinformatics analysis, we identified a group of candidate genes that may participate in sexual differentiation, including Erbb3, Erbb4, and Prkg2. One hundred and two and 134 candidate genes that may be important for female and male gonadal development, respectively, were screened by analyzing the global gene expression patterns of developing female and male gonads. Weighted gene co-expression network analysis was performed on developing female gonads, and we identified a gene co-expression module related to meiosis. By alternative splicing analysis, we found that cassette-type exon and alternative start sites were the main forms of alternative splicing in developing gonads. A considerable portion of differentially expressed and alternatively spliced genes were involved in meiosis. Conclusion Taken together, our findings have enriched the gonadal transcriptome database and provided novel candidate genes and avenues to research the molecular mechanisms of sexual differentiation, meiosis, and gametogenesis.

scholarly journals Integrative Analysis for the Roles of lncRNAs in the Immune Responses of Mouse PBMC Exposed to Low-Dose Ionizing Radiation

Dose-Response ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 155932582091380 ◽  
Author(s):  
Zhenhua Qi ◽  
Sitong Guo ◽  
Changyong Li ◽  
Qi Wang ◽  
Yaqiong Li ◽  
...  
Keyword(s):  
Ionizing Radiation ◽  
Immune Responses ◽  
Signaling Pathways ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
Low Dose ◽  
Expression Patterns ◽  
Pathway Enrichment Analysis ◽  
Immune Signaling ◽  
Lncrna Expression

It is well accepted that low-dose ionizing radiation (LDIR) modulates a variety of immune responses that have exhibited the properties of immune hormesis. Alterations in messenger RNA (mRNA) and long noncoding RNA (lncRNA) expression were to crucially underlie these LDIR responses. However, lncRNAs in LDIR-induced immune responses have been rarely reported, and its functions and molecular mechanisms have not yet been characterized. Here, we used microarray profiling to determine lncRNA in BALB/c mice exposed to single (0.5 Gy×1) and chronic (0.05 Gy×10) low-dose γ-rays radiation (Co60). We observed that a total of 8274 lncRNAs and 7240 mRNAs were altered in single LDIR, while 2077 lncRNAs and 796 mRNAs in chronic LDIR. The biological functions of these upregulated mRNAs in both 2 groups using Gene Ontology functional and pathway enrichment analysis were significantly enriched in immune processes and immune signaling pathways. Subsequently, we screened out the lncRNAs involved in regulating these immune signaling pathways and examined their potential functions by lncRNAs-mRNAs coexpression networks. This is the first study to comprehensively identify lncRNAs in single and chronic LDIR responses and to demonstrate the involvement of different lncRNA expression patterns in LDIR-induced immune signaling pathways. Further systematic research on these lncRNAs will provide new insights into our understanding of LDIR-modulated immune hormesis responses.

scholarly journals Prognostic Signature of Alternative Splicing Events in Bladder Urothelial Carcinoma Based on Spliceseq Data from 317 Cases

2018 ◽  
Vol 48 (3) ◽  
pp. 1355-1368 ◽  
Author(s):  
Rong-quan He ◽  
Xian-guo Zhou ◽  
Qiao-yong Yi ◽  
Cai-wang Deng ◽  
Jia-min Gao ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Urothelial Carcinoma ◽  
Risk Score ◽  
Regulatory Network ◽  
Pearson Correlation ◽  
Risk Scores ◽  
Pathway Enrichment Analysis ◽  
Splicing Factors ◽  
Bladder Urothelial Carcinoma ◽  
Alternative Splicing Events

Background/Aims: Increasing evidences indicated the important roles of alternative splicing in the progression and prognosis of bladder urothelial carcinoma (BLCA). However, most previous research has focused on one or several alternative splicing events, without a comprehensive evaluation of the prognostic value of splicing events in BLCA. In this study, we aimed to determine risk scores for predicting prognosis of BLCA patients based on splicing events. Methods: RNA-sequencing data and clinical information of BLCA patients were downloaded from The Cancer Genome Atlas, and data of splicing events were obtained from the SpliceSeq database. Univariate and multivariate Cox regression analyses were employed to identify survival-associated alternative spicing events (SASEs) and to calculate risk scores. Protein-protein interaction analysis of genes of the SASEs was performed using STRING, a database of known and predicted protein-protein interactions, and pathway enrichment analysis of the genes was implemented using the Database for Annotation, Visualization and Integrated Discovery (version 6.8). Receiver operating characteristic (ROC) curves and Kaplan-Meier analysis were used to evaluate the clinical significance of genes from the SASEs for building a risk score in BLCA. Correlation between splicing events of splicing factors and non-splicing factors were analyzed with Pearson correlation coefficient. A potential regulatory network was then built using Cytoscape 3.5. Results: In total, 39,508 alternative splicing events in 317 patients with BLCA were analyzed, including 4,632 SASEs. The area under the curve of the ROC of risk score (all) was 0.748 for predicting survival status of BLCA patients. Low- and high-risk score groups classified using the median “risk score (all)” value displayed remarkably different survival time (Low vs. High = 3304.841±239.758 vs 1198.614±152.460 days). The potential regulatory network with SASEs of splicing factors and other genes was constructed, which might be part of the biological mechanisms associated with prognosis of BLCA patients. Conclusions: In this study, prognostic signatures constructed using splicing events could be used for predicting the prognosis of BLCA patients.

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