Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.)

Liang, Fan; Zhou, Yiyong; Wang, Xiaodan; Yang, Shuo; Fang, Ting; Zheng, Shaoquan; Zeng, Lihui

doi:10.3389/fpls.2022.923183

Cited by 4 publications

(3 citation statements)

References 95 publications

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“…There are various mechanisms for the lncRNA regulation of target genes, and the most common forms of regulation are cis and trans regulation [ 47 ]. Based on the results of RNA-seq, we predicted the target genes for the differentially expressed lncRNAs in cis and trans regulation.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of lncRNA–mRNA Expression Profiles in Depression-like Responses of Mice Related to Polystyrene Nanoparticle Exposure

Liu

Zhang

et al. 2023

Toxics

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Plastics in the environment can break down into nanoplastics (NPs), which pose a potential threat to public health. Studies have shown that the nervous system constitutes a significant target for nanoplastics. However, the potential mechanism behind nanoplastics’ neurotoxicity remains unknown. This study aimed to investigate the role of lncRNA in the depressive-like responses induced by exposure to 25 nm polystyrene nanoplastics (PS NPs). Forty mice were divided into four groups administered doses of 0, 10, 25, and 50 mg/kg via gavage for 6 months. After conducting behavioral tests, RNA sequencing was used to detect changes in mRNAs, miRNAs, and lncRNAs in the prefrontal cortex of the mice in the 0 and 50 mg/kg PS NPs groups. The results revealed that mice exposed to chronic PS NPs developed depressive-like responses in a dose-dependent manner. It was demonstrated that 987 mRNAs, 29 miRNAs, and 116 lncRNAs were significantly different between the two groups. Then, a competing endogenous RNA (ceRNA) network containing 6 lncRNAs, 18 miRNAs, and 750 mRNAs was constructed. Enrichment results suggested that PS NPs may contribute to the onset of depression-like responses through the activation of axon guidance, neurotrophin-signaling pathways, and dopaminergic synapses. This study provided evidence of the molecular relationship between PS NPs and depression-like responses.

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Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of lncRNA–mRNA Expression Profiles in Depression-like Responses of Mice Related to Polystyrene Nanoparticle Exposure

Liu

Zhang

et al. 2023

Toxics

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show abstract

“…This study identified a significantly correlated module based on a correlation coefficient (r) ≥ 0.9 and p < 0.01. The coexpression networks of lncRNAs and hub lncRNAs in highly correlated modules were generated with the Cytoscape software (version 3.7.1) [ 85 ].…”

Section: Methodsmentioning

confidence: 99%

Illumina RNA and SMRT Sequencing Reveals the Mechanism of Uptake and Transformation of Selenium Nanoparticles in Soybean Seedlings

Xiong

Xiang

Xiao

et al. 2023

Plants

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Selenium (Se) is an essential element for mammals, and its deficiency in the diet is a global problem. Agronomic biofortification through exogenous Se provides a valuable strategy to enhance human Se intake. Selenium nanoparticles (SeNPs) have been regarded to be higher bioavailability and less toxicity in comparison with selenite and selenate. Still, little has been known about the mechanism of their metabolism in plants. Soybean (Glycine max L.) can enrich Se, providing an ideal carrier for Se biofortification. In this study, soybean sprouts were treated with SeNPs, and a combination of next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing was applied to clarify the underlying molecular mechanism of SeNPs metabolism. A total of 74,662 nonredundant transcripts were obtained, and 2109 transcription factors, 9687 alternative splice events, and 3309 long non-coding RNAs (lncRNAs) were predicted, respectively. KEGG enrichment analysis of the DEGs revealed that metabolic pathways, biosynthesis of secondary metabolites, and peroxisome were most enriched both in roots and leaves after exposure to SeNPs. A total of 117 transcripts were identified to be putatively involved in SeNPs transport and biotransformation in soybean. The top six hub genes and their closely coexpressed Se metabolism-related genes, such as adenylylsulfate reductase (APR3), methionine-tRNA ligase (SYM), and chloroplastic Nifs-like cysteine desulfurases (CNIF1), were screened by WGCNA and identified to play crucial roles in SeNPs accumulation and tolerance in soybean. Finally, a putative metabolism pathway of SeNPs in soybean was proposed. These findings have provided a theoretical foundation for future elucidation of the mechanism of SeNPs metabolism in plants.

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“…org). The conservation analysis of lncRNAs was assessed using the E-value, where a threshold of E-value <1x10 -5 was used (24). After conservation analysis among species (Table IV…”

Section: Characteristics Of Differentially Expressed Lncrnasmentioning

confidence: 99%

Construction of chronic glomerulonephritis‑related lncRNA‑mRNA regulatory network and lncRNA‑miRNA‑mRNA ceRNA network by bioinformatics analysis

et al. 2023

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Long non-coding RNAs (lncRNAs) are ncRNA transcripts >200 nucleotides that are important genetic regulators. LncRNAs can directly regulate mRNA through a lncRNA-mRNA regulatory mode and can also regulate mRNA through competitive binding to micro (mi)RNA, which is generally known as the competitive endogenous RNA (ceRNA) network. The present study evaluated the functional roles and regulatory networks of lncRNAs in chronic glomerulonephritis (CGN). The proliferative ability of mouse glomerular mesangial cells (GMCs) induced by different concentrations of lipopolysaccharide (LPS) was assessed using the Cell Counting Kit-8 assay, and RNA sequencing (RNA-seq) was performed to identify differentially expressed lncRNAs in LPS-induced GMCs. Based on the sequencing results, six lncRNAs were selected for validation using reverse transcription-quantitative PCR (RT-qPCR). Furthermore, the lncRNA-mRNA regulatory network and the lncRNA-miRNA-mRNA ceRNA network were constructed to assess the role and mechanism of CGN-related lncRNAs. To elucidate the biological functions of lncRNAs, Gene Ontology (GO) biological process term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on all mRNAs involved in the lncRNA-mRNA regulatory network and in the ceRNA network. A total of 1,532 differentially expressed lncRNAs, including 594 upregulated lncRNAs and 938 downregulated lncRNAs, were identified using RNA-seq.The results of RT-qPCR validation were consistent with RNA-seq results. An lncRNA-mRNA regulatory network, including 236 lncRNAs and 556 mRNAs, and a ceRNA network, including 6 lncRNAs, 18 miRNAs and 419 mRNAs, were successfully constructed. The GO biological process term enrichment and KEGG pathway enrichment analyses demonstrated that those lncRNAs were often related to inflammatory response and substance metabolism. The present study identified key CGN-related lncRNAs in LPS-induced GMCs, and further demonstrated a global view of the lncRNA-mRNA regulatory network and ceRNA network involved in CGN. These results offered novel insights into the roles of lncRNAs in the pathogenesis of CGN and identified potential diagnostic biomarkers.

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Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.)

Cited by 4 publications

References 95 publications

Comprehensive Analysis of lncRNA–mRNA Expression Profiles in Depression-like Responses of Mice Related to Polystyrene Nanoparticle Exposure

Comprehensive Analysis of lncRNA–mRNA Expression Profiles in Depression-like Responses of Mice Related to Polystyrene Nanoparticle Exposure

Illumina RNA and SMRT Sequencing Reveals the Mechanism of Uptake and Transformation of Selenium Nanoparticles in Soybean Seedlings

Construction of chronic glomerulonephritis‑related lncRNA‑mRNA regulatory network and lncRNA‑miRNA‑mRNA ceRNA network by bioinformatics analysis

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Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.)

Cited by 4 publications

References 95 publications

Comprehensive Analysis of lncRNA–mRNA Expression Profiles in Depression-like Responses of Mice Related to Polystyrene Nanoparticle Exposure

Comprehensive Analysis of lncRNA–mRNA Expression Profiles in Depression-like Responses of Mice Related to Polystyrene Nanoparticle Exposure

Illumina RNA and SMRT Sequencing Reveals the Mechanism of Uptake and Transformation of Selenium Nanoparticles in Soybean Seedlings

Construction of chronic glomerulonephritis‑related lncRNA‑mRNA regulatory network and lncRNA‑­miRNA‑mRNA ceRNA network by bioinformatics analysis

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Product

Resources

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Construction of chronic glomerulonephritis‑related lncRNA‑mRNA regulatory network and lncRNA‑miRNA‑mRNA ceRNA network by bioinformatics analysis