scholarly journals Comparative transcriptomic and metabolomic analyses of carotenoid biosynthesis reveal the basis of white petal color in Brassica napus

Planta ◽  
2021 ◽  
Vol 253 (1) ◽  
Author(s):  
Ledong Jia ◽  
Junsheng Wang ◽  
Rui Wang ◽  
Mouzheng Duan ◽  
Cailin Qiao ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Molecular Mechanisms ◽  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Differentially Expressed ◽  
Transcriptome Data ◽  
Oilseed Crops ◽  
Qrt Pcr ◽  
Carotenoid Metabolism ◽  
Rapeseed Cultivar

Abstract Main conclusion The molecular mechanism underlying white petal color in Brassica napus was revealed by transcriptomic and metabolomic analyses. Abstract Rapeseed (Brassica napus L.) is one of the most important oilseed crops worldwide, but the mechanisms underlying flower color in this crop are known less. Here, we performed metabolomic and transcriptomic analyses of the yellow-flowered rapeseed cultivar ‘Zhongshuang 11’ (ZS11) and the white-flowered inbred line ‘White Petal’ (WP). The total carotenoid contents were 1.778-fold and 1.969-fold higher in ZS11 vs. WP petals at stages S2 and S4, respectively. Our findings suggest that white petal color in WP flowers is primarily due to decreased lutein and zeaxanthin contents. Transcriptome analysis revealed 10,116 differentially expressed genes with a fourfold or greater change in expression (P-value less than 0.001) in WP vs. ZS11 petals, including 1,209 genes that were differentially expressed at four different stages and 20 genes in the carotenoid metabolism pathway. BnNCED4b, encoding a protein involved in carotenoid degradation, was expressed at abnormally high levels in WP petals, suggesting it might play a key role in white petal formation. The results of qRT-PCR were consistent with the transcriptome data. The results of this study provide important insights into the molecular mechanisms of the carotenoid metabolic pathway in rapeseed petals, and the candidate genes identified in this study provide a resource for the creation of new B. napus germplasms with different petal colors.

scholarly journals Combined Analysis of ceRNA Regulatory Network and DNA Methylation in CAD

2021 ◽  
Author(s):  
Yue Zhao ◽  
Chen Wang ◽  
Wangxia Li ◽  
Bingyu Jin ◽  
Yang Xiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Clinical Samples ◽  
Gene Expressions ◽  
Qrt Pcr ◽  
Cerna Network ◽  
Differentially Methylated Genes

Abstract BackgroundThe mobidity and mortality of coronary artery disease (CAD) is increasing year by year. Hence it is urgent to probe into the molecular mechanism of CAD and seek new therapeutic strategies. The purpose of our study was to screen genes associated with the development of CAD by using bioinformatics tools and clinical samples. MethodsMicroarray datasets from the Gene Expression Omnibus (GEO) database of peripheral blood cells (PBLs) were chosen for this study, and candidate differentially expressed microRNAs (DEMs) were screened using the limma and weighted co-expression network analysis (WGCNA) packages in R (v4.0). Subsequently, we construct a competitive endogenous RNAs (ceRNA) network and perform enrichment analysis of genes in the network. Meanwhile, differentially methylated genes (DMGs) in PBLs were identified using the "ChAMP" package in a DNA methylation chip. We then constructed the methylation-associated ceRNA network in CAD. Eventually, the methylation levels of genes and the relationship with the expression of genes in ceRNA were validated in PBLs samples using the Illumina Methylation 850K chip and transcriptome sequencing, while gene expressions were verified by qRT-PCR. And the regulation of DNA methylation on gene expression was verified in the THP-1 cells treated with 5-Aza-2'-deoxycytidine (5-AZA). ResultsA total of 71 differentially expressed miRNAs were screened by both WGCNA and limma. Then the ceRNA network in CAD was constructed with 269 nodes and 705 edges, which were significantly enriched in the chemokine-mediated signaling pathway and so on. Furthermore, from 4354 identified DMGs in a methylation data, 34 methylation-associated differentially expressed genes (DEGs) and 1 differentially expressed lncRNA (DEL) were obtained. After verification of methylation experiments in study population A, three genes were found to have altered methylation consistent with the bioinformatics results. And these genes were correlated in terms of methylation and expression levels. Corresponding with the bioinformatics results, qRT-PCR results in validation set B also showed that the expression of AGPAT4 and FAM169A were significantly lower in CAD. In addition, 5-AZA treatment could increase the expression of AGPAT4 and FAM169A in THP-1 cells. ConclusionsOur study deepens the understanding of the molecular mechanisms underlying the pathogenesis of CAD and provides new ideas for its treatment.

scholarly journals Joint RNA-Seq and miRNA Profiling Analyses to Reveal Molecular Mechanisms in Regulating Thickness of Pod Canopy in Brassica napus

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 591 ◽  
Author(s):  
Chen ◽  
Huo ◽  
Yang ◽  
Jian ◽  
Qu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Differentially Expressed ◽  
Oilseed Crop ◽  
Flower Bud ◽  
Mirna Profiling ◽  
Differentially Expressed Mirnas ◽  
Yield Formation ◽  
Architecture Component

Oilseed rape (Brassica napus) is the second largest oilseed crop worldwide. As an architecture component of B. napus, thickness of pod canopy (TPC) plays an important role in yield formation, especially under high-density cultivation conditions. However, the mechanisms underlying the regulation of TPC remain unclear. RNA and microRNA (miRNA) profiling of two groups of B. napus lines with significantly different TPC at the bolting with a tiny bud stage revealed differential expressions of numerous genes involved in nitrogen-related pathways. Expression of several nitrogen-related response genes, including ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15, was dramatically changed in the thick TPC lines compared to those in the thin TPC lines. Differentially expressed miRNAs also included many involved in nitrogen-related pathways. Expression of most target genes was negatively associated with corresponding miRNAs, such as miR159, miR6029, and miR827. In addition, 12 (including miR319, miR845, and miR158) differentially expressed miRNAs between two plant tissues sampled (stem apex and flower bud) were identified, implying that they might have roles in determining overall plant architecture. These results suggest that nitrogen signaling may play a pivotal role in regulating TPC in B. napus.

scholarly journals Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241174
Author(s):  
Yajie Hu ◽  
Zhen Yang ◽  
Shenglan Wang ◽  
Danxiong Sun ◽  
Mingmei Zhong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Control Group ◽  
Protein Coding ◽  
Qrt Pcr ◽  
Protein Coding Genes

Coxsackievirus A16 (CV-A16) is one of the viruses that is most frequently associated with hand-foot-and-mouth disease (HFMD). Previous studies have shown that CV-A16 infections are mostly self-limiting, but in recent years, it has been gradually found that CV-A16 infections can also induce neurological complications and eventually cause death in children with HFMD. Moreover, no curative drugs or preventative vaccines have been developed for CV-A16 infection. Therefore, it is particularly important to investigate the mechanism of CV-A16 infection-induced neuropathy. In the current study, transcriptome sequencing technology was used to identify changes in the transcriptome of SH-SY5Y cells infected with CV-A16, which might hide the mechanism of CV-A16-induced neuropathology. The transcriptome profiling showed that 82,406,974, 108,652,260 and 97,753,565 clean reads were obtained in the Control, CV-A16-12 h and CV-A16-24 h groups, respectively. And it was further detected that a total of 136 and 161 differentially expressed genes in CV-A16-12 h and CV-A16-24 h groups, respectively, when compared with Control group. Then, to explore the mechanism of CV-A16 infection, we focused on the common differentially expressed genes at different time points of CV-A16 infection and found that there were 34 differentially expressed genes based on which clustering analysis and functional category enrichment analysis were performed. The results indicated that changes in oxidation levels were particularly evident in the GO term analysis, while only the “Gonadotropin-releasing hormone receptor pathway” was enriched in the KEGG pathway analysis, which might be closely related to the neurotoxicity caused by CV-A16 infection. Meanwhile, the ID2 closely related to nervous system has been demonstrated to be increased during CV-A16 infection. Additionally, the data on differentially expressed non-protein-coding genes of different types within the transcriptome sequencing results were analyzed, and it was speculated that these dysregulated non-protein-coding genes played a pivotal role in CV-A16 infection. Ultimately, qRT-PCR was utilized to validate the transcriptome sequencing findings, and the results of qRT-PCR were in agreement with the transcriptome sequencing data. In conclusion, transcriptome profiling was carried out to analyze response of SH-SY5Y cells to CV-A16 infection. And our findings provide important information to elucidate the possible molecular mechanisms which were linked to the neuropathogenesis of CV-A16 infection.

scholarly journals Differential Transcription Profiling in Bone Marrow Mononuclear Cells Between Myasthenia Gravis Patients With or Without Thymoma

2021 ◽  
Author(s):  
Jingqun Tang ◽  
Ziming Ye ◽  
Yi Liu ◽  
Mengxiao Zhou ◽  
chao qin
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Myasthenia Gravis ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Mononuclear Cells ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Bone Marrow Mononuclear Cells ◽  
Qrt Pcr

Abstract PurposeDefective stem cells have been recognized as being associated with autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, autoimmune cytopenias and myasthenia gravis (MG). However, the differential gene expression profile of bone marrow mononuclear cells (BMMCs) and the molecular mechanisms underlying MG pathogenesis have not been fully elucidated. Therefore, we investigated the abnormal expression and potential roles and mechanisms of mRNAs in BMMCs among patients with MG with or without thymoma.MethodsTranscription profiling of BMMCs in patients with MG without thymoma (M2) and patients with thymoma-associated MG (M1) was undertaken by using high-throughput RNA sequencing (RNA-Seq), and disease-related differentially expressed genes were validated by quantitative real-time polymerase chain reaction (qRT-PCR).ResultsRNA-Seq demonstrated 60 significantly upregulated and 65 significantly downregulated genes in M2 compared with M1. Five disease-related differentially expressed genes were identified and validated by qRT-PCR analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to predict the functions of aberrantly expressed genes. Recombination activating 1 (RAG1), RAG2, BCL2-like 11, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform and repressor element-1-silencing transcription factor might play roles in MG pathogenesis involving the primary immunodeficiency signaling pathway, signaling pathways regulating pluripotency of stem cells and forkhead box O signaling pathway.ConclusionThe aberrantly expressed genes of BMMCs in M1 or M2 patients demonstrate the underlying mechanisms governing the pathogenesis of MG.

scholarly journals Transcriptome analysis provides new insight into the molecular mechanisms in regulating carotenoid accumulation in pericarp of fruits from two pummelo cultivars Citrus grandis (L.) Osbeck

2019 ◽  
Author(s):  
Xinkun Lu ◽  
Yanqing Lu ◽  
Yanjin Lin
Keyword(s):  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Profile Analysis ◽  
Differentially Expressed ◽  
Post Translational Modification ◽  
Mutant Type ◽  
Carotenoid Accumulation ◽  
Carotenoid Metabolism ◽  
Colour Development

Abstract Background Carotenoid improves fruit external quality and benefits to human health. Although the mechanism underlining carotenoid metabolism is clear, the regulation of carotenoid accumulation remains poorly understand. Recently, ‘Huangbao’ pummelo was selected from the bud mutation of ‘Guanxi’ pummelo (yellow pericarp). The pericarp of mutant-type fruits is characterized by red colour development during fruit ripening stage. The aim of the study is to explore the molecular mechanisms in regulating pericarp colouration based on transcriptomic profile analysis of the two cultivars. Results Lycopene content in the pericarp of ripe fruits from ‘Huangbao’ (160.29 µg g-1 FW) was significantly higher than that of from ‘Guanxi’ (0.91µg g-1 FW). Lycopene is a main contributor for pericarp colouration. 929 differentially expressed genes (DEGs) were indentified through transcriptional profiling in the pericarp of ripe fruits from the two cultivars. Expression levels of the Genes encoding for fructose-bisphosphate aldolase, enolase and pyruvate kinase isozyme were significantly higher in ‘Huangbao’ than that of in ‘Guanxi’, which possibly promote 3-phosphate-glyceraldehyde and pyruvic acid biosyntheses. This two productions act as precursors for the biosyntheses of Isopentenylpyrophosphate (IPP) and Dimethylallyl pyrophosphate (DMAPP) in Methylerythritol phosphate (MEP) pathway. Genes ecoding for phytoene synthase and prolycopene isomerase were unexpected down-regulated in ‘Huangbao’. Gibberellin-2-β-dioxygenase (GA2OX) gene was specially expressed in ‘Huangbao’, while the transcript amounts of genes related to auxin response and auxin transport as well as several negative regulators in ethylene signaling in ‘Huangbao’ were all down regulated. Additionally, Transcription factors (DELLA, NAC, MADS-box, WRKY) and post translational modification proteins (histone acetyltransferase and E2 ubiquitin-conjugating enzyme) involved in regulating ethylene and carotenoid metabolisms were also differentially expressed in the two pummelo cultivars. Conclusions The main differences in the carotenoid metabolism in the pericarp of ripen fruits from ‘Huangbao’ and ‘Guanxi’ were observed in the carotenoid precursor biosynthetic pathway. Differentially expressed genes in gibberellin, auxin and ethylene metabolisms and plant hormone signaling pathways, as well as several transcription factors and post translational modification protein genes involved in regulating ethylene and carotenoid metabolisms provide targets for further exploration in revealing mechanisms underlying fruit colour development.

scholarly journals Construction of a circRNA - Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection

2021 ◽  
Author(s):  
De-Bin Liu ◽  
You-Fu He ◽  
Gui-Jian Chen ◽  
Hua Huang ◽  
Xu-Ling Xie ◽  
...  
Keyword(s):  
Aortic Dissection ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Qrt Pcr ◽  
Cerna Network ◽  
Arterial Blood

Abstract Background Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circular RNAs (circRNAs) play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed to elucidate the underlying molecular mechanisms of circRNAs regulation in aortic dissection based on the circRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network. Methods Expression profiles of circRNAs (GSE97745), miRNAs (GSE92427), and mRNAs (GSE52093) were downloaded from Gene Expression Omnibus (GEO) databases, and the differentially expressed RNAs (DERNAs) were subsequently identified in AD by bioinformatics analysis. Further bioinformatics analyses, including circRNA-miRNA-mRNA ceRNA network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, were used to predict the potential functions of circRNA-associated ceRNA regulatory network. RNA was isolated from human arterial blood samples after which quantitative real-time PCR (qRT-PCR) was performed to confirm the DERNAs. Results We identified 14 (5 up-regulated and 9 down-regulated) differentially expressed circRNAs (DEcircRNAs), 17 (8 up-regulated and 9 down-regulated) differentially expressed miRNAs (DEmiRNAs) and 527 (297 up-regulated and 230 down-regulated) differentially expressed mRNAs (DEmRNAs) when AD samples were compared with normal ascending aorta samples (adjusted P-value < 0.05 and | log2FC |> 1.0). KEGG pathway analysis indicated that DEmRNAs were related to focal adhesion and extracellular matrix (ECM) receptor interaction signaling pathways. Simultaneously, the present study successfully constructed a ceRNA regulatory network based on 1 circRNAs (hsa_circRNA_082317), 1 miRNAs (hsa-miR-149-3p) and 10 mRNAs (MLEC, ENTPD7, SLC16A3, SLC7A8, TBC1D16, PAQR4, MAPK13, PIK3R2, ITGA5, SERPINA1) in AD. Furthermore, qRT-PCR demonstrated that hsa_circRNA_082317 andα5 integrin (ITGA5) were significantly up-regulated in AD (n = 3), and hsa-miR-149-3p was dramatically down-regulated in AD (n = 3). The expression of hsa-miR-149-3p target mRNA, ITGA5, was positively modulated by hsa_circRNA_082317. Conclusion This is the first study to demonstrate the circRNA-associated ceRNA regulatory network is altered in AD, implying that circRNAs may play important roles in regulating the onset and progression of AD and thus may serve as potential biomarkers for the diagnosis and treatment of AD.

scholarly journals Identification and Verification of Candidate Genes Regulating Human Umbilical Vein Endothelial Cells Behavior Under Hyperglycemia

2020 ◽  
Author(s):  
XIAOYE MA ◽  
YUCHEN ZHOU ◽  
JUNCHAO XIE ◽  
GUILIN MENG ◽  
YICHEN ZHAO ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Umbilical Vein ◽  
Life Quality ◽  
Differentially Expressed ◽  
Therapeutic Interventions ◽  
Control Group ◽  
Human Umbilical Cord ◽  
Qrt Pcr

Abstract Background: Diabetes is a metabolic disease that has been widely demonstrated to be correlated with many microvascular and macrovascular diseases that seriously damage the patient’s life quality. This study intended to investigate the underlying molecular mechanisms of endothelial dysfunction under hyperglycemia. Methods: The gene expression profile of GSE49524 was downloaded and differentially expressed genes (DEGs) in hyperglycemia human umbilical cord endothelial cells (HUVECs) samples compared with normoglycemia HUVECs samples were identified by R software. Afterward, we analyzed the data by applying a combination of the bioinformatics method and used the microRNAs (miRNAs) databases to predict microRNAs that target key genes. The expression of the top 10 differentially expressed genes was validated through quantitative real-time PCR (qRT-PCR). Results: A total of 65 genes were distinguished as DEGs. The dominant GO (gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways which were significantly overrepresented in the hyperglycemia HUVECs were identified. The results of the protein-protein interaction networks demonstrated that fibronectin 1 (FN1) is of the highest degree. In addition, several predicted miRNAs that target FN1 were obtained too. The further verification of the top 10 DEGs through qRT-PCR illustrated that nine of the up-regulated DEGs were up-regulated significantly in the hyperglycemia group when compared to the control group. Conclusions:This exploratory study may help to prompt an understanding of the underlying molecular mechanisms of the effect of hyperglycemia on the behavior of HUVECs and contribute to the production of effective therapeutic interventions.

scholarly journals Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling

2019 ◽  
Author(s):  
Gezahegn Girma ◽  
Satoshi Natsume ◽  
Anna Vittoria Carluccio ◽  
Hiroki Takagi ◽  
Hideo Matsumura ◽  
...  
Keyword(s):  
Sex Determination ◽  
Candidate Genes ◽  
Flower Development ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Quantitative Real Time Pcr ◽  
Common Features ◽  
Qrt Pcr ◽  
Guinea Yam

AbstractDioecy (distinct male and female individuals) combined with scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata). SuperSAGE analysis generated a total of 20,236 unique tags, of which 13,901 were represented by a minimum of 10 tags. Of these, 88 tags were significantly differentially expressed in male, female and monoecious plants. Of the 88 differentially expressed SuperSAGE tags, 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of four candidate genes. Our findings suggest that mechanisms of flowering and sex determination are likely conserved in Dioscorea. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two years, revealing that over 85% of the accessions are either male or non-flowering, and that less than 15% are female, while monoecious plants are rare. Intensity of flowering appeared to be a function of sex, with male plants flowering more abundantly than female ones. Candidate genes identified in this study can be targeted with the aim to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve the efficiency of yam breeding.

scholarly journals Selection and Validation of Reference Genes for Quantitative Real-Time PCR Analysis of Development and Tissue-Dependent Flower Color Formation in Cymbidium lowianum

2022 ◽  
Vol 23 (2) ◽  
pp. 738
Author(s):  
Xiu-Mei Dong ◽  
Wei Zhang ◽  
Shi-Bao Zhang
Keyword(s):  
Real Time ◽  
Reference Gene ◽  
Reference Genes ◽  
Molecular Mechanisms ◽  
Gene Selection ◽  
Expression Profiles ◽  
Flower Color ◽  
Pcr Analysis ◽  
Color Formation ◽  
Qrt Pcr

The development and tissue-dependent color formation of the horticultural plant results in various color pattern flowers. Anthocyanins and carotenoids contribute to the red and yellow colors, respectively. In this study, quantitative real-time polymerase chain reaction (qRT-PCR) is used to analyze the expression profiles of anthocyanin and carotenoids biosynthesis genes in Cymbidium lowianum (Rchb.f.) Rchb.f. Appropriate reference gene selection and validation are required before normalization of gene expression in qRT-PCR analysis. Thus, we firstly selected 12 candidate reference genes from transcriptome data, and used geNorm and Normfinder to evaluate their expression stability in lip (divided into abaxial and adaxial), petal, and sepal of the bud and flower of C. lowianum. Our results show that the two most stable reference genes in different tissues of C. lowianum bud and flower are EF1δ and 60S, the most unstable reference gene is 26S. The expression profiles of the CHS and BCH genes were similar to FPKM value profiles after normalization to the two most stable reference genes, EF1δ and 60S, with the upregulated CHS and BCH expression in flower stage, indicating that the ABP and CBP were activated across the stages of flower development. However, when the most unstable reference gene, 26S, was used to normalize the qRT-PCR data, the expression profiles of CHS and BCH differed from FPKM value profiles, indicating the necessity of selecting stable reference genes. Moreover, CHS and BCH expression was highest in the abaxial lip and adaxial lip, respectively, indicating that the ABP and CBP were activated in abaxial and adaxial lip, respectively, resulting in a presence of red or yellow segments in abaxial and adaxial lip. This study is the first to provide reference genes in C. lowianum, and also provide useful information for studies that aim to understand the molecular mechanisms of flower color formation in C. lowianum.

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