Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of <i>Plukenetia volubilis</i>

Fu, Yijun; Huo, Kaisen; Pei, Xingjie; Liang, Chongjun; Meng, Xinya; Song, Xiqiang; Wang, Jia; Niu, Jun

doi:10.7717/peerj.13998

Cited by 4 publications

(3 citation statements)

References 46 publications

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“…The transcripts were annotated and indexed for expression analysis. Then, we used an annotated file as a reference gene set and estimated the related gene expression using RSEM software (v1.2.15) [ 18 ]. The differential expression was analysed using the Bioconductor package DESeq2 [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of the circRNA–miRNA–mRNA Regulatory Network in Pterygium-Associated Conjunctival Epithelium

Luo

et al. 2022

BioMed Research International

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To investigate the regulatory mechanism of pterygium formation, we detected differentially expressed messenger RNAs (DE-mRNAs) and differentially expressed circular RNAs (DE-circRNAs) in pterygium-associated conjunctival epithelium (PCE) and normal conjunctival epithelium (NCE). Genome-wide mRNA and circRNA expression profiles of PCE and NCE were determined using high-throughput sequencing. Bioinformatics analyses, including Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, gene set enrichment analysis (GSEA), and protein–protein interaction (PPI) analysis, were conducted. The microRNAs (miRNAs) interacting with the hub DE-mRNAs and DE-circRNAs were predicted and verified using real-time quantitative PCR (RT-qPCR). The data showed that there were 536 DE-mRNAs (280 upregulated and 256 downregulated mRNAs) and 78 DE-circRNAs (20 upregulated and 58 downregulated circRNAs) in PCE. KEGG enrichment analysis indicated that the DE-mRNAs were mainly involved in the following biological processes: IL-17 signalling pathway, viral protein interaction with cytokine and cytokine receptor, cytokine–cytokine receptor interaction, ECM-receptor interaction, and focal adhesion. The GSEA results revealed that the epithelial mesenchymal transition (EMT) process was significantly enriched in upregulated mRNAs. The pterygium-associated circRNA–miRNA–mRNA network was established based on the top 10 DE-circRNAs, 4 validated miRNAs (upregulated miR-376a-5p and miR-208a-5p,downregulated miR-203a-3p and miR-200b-3p), and 31 DE-mRNAs. We found that miR-200b-3p, as a regulator of FN1, SDC2, and MEX3D, could be regulated by 5 upregulated circRNAs. In addition, we screened out EMT-related DE-mRNAs, including 6 upregulated DE-mRNAs and 6 downregulated DE-mRNAs. The EMT-related circRNA–miRNA–mRNA network was established with the top 10 circRNAs, 8 validated miRNAs (upregulated miR-17-5p, miR-181a-5p, and miR-106a-5p, downregulated miR-124-3p, miR-9-5p, miR-130b-5p, miR-1-3p, and miR-26b-5P), and 12 EMT-related DE-mRNAs. We found that hsa_circ_0002406 might upregulate FN1 and ADAM12 by sponging miR-26b-5p and miR-1-3p, respectively, thus promoting EMT in pterygium. Briefly, the study provides a novel viewpoint on the molecular pathological mechanisms in pterygium formation. CircRNA–miRNA–mRNA regulatory networks participate in the pathogenesis of pterygium and might become promising targets for pterygium prevention and treatment.

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Section: Methodsmentioning

confidence: 99%

Identification of the circRNA–miRNA–mRNA Regulatory Network in Pterygium-Associated Conjunctival Epithelium

Luo

et al. 2022

BioMed Research International

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“…18 lncRNAs may participate in the potential regulation of oil accumulation in Plukenetia volubilis through glycolysis/gluconeogenesis, fatty acid biosynthesis, fatty acid elongation, fatty acid degradation, and glycerolipid metabolism pathways. 19 In addition, lncRNAs may participate in the metabolism of linolenic acid, lipid metabolism process, and other processes that affect the flag leaf aging of rice. 20 Moreover, overexpression of late embryogenesis abundant group 3 (LEA3) improved the oil content in B. napus and A. thaliana, and in LEA3-overexpressed lines, lncRNAs regulated the AT4G13180 for fatty acid synthesis.…”

Section: ■ Introductionmentioning

confidence: 99%

“…lncRNAs and protein-coding genes involved in oil biosynthesis were found in the developmental regulatory module of allopolyploid Brassica napus using transcriptome sequencing analysis . lncRNAs may participate in the potential regulation of oil accumulation in Plukenetia volubilis through glycolysis/gluconeogenesis, fatty acid biosynthesis, fatty acid elongation, fatty acid degradation, and glycerolipid metabolism pathways . In addition, lncRNAs may participate in the metabolism of linolenic acid, lipid metabolism process, and other processes that affect the flag leaf aging of rice .…”

Section: Introductionmentioning

confidence: 99%

Analysis of LncRNA43234-Associated ceRNA Network Reveals Oil Metabolism in Soybean

Zhang

Wang

et al. 2023

J. Agric. Food Chem.

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Soybean [Glycine max (Linn.) Merr.] is an important oil crop. Long noncoding RNAs (lncRNAs) play a variety of functions in plants. However, their function in the soybean oil synthesis pathway is yet to be uncovered. Here, the lncRNA43234 gene related to soybean oil synthesis was screened, and the full-length cDNA sequence of the lncRNA was obtained using rapid amplification of cDNA ends. Overexpression of lncRNA43234 increased the content of crude protein in seeds, decreased the content of oleic acid, and affected the content of alanine and arginine in free amino acids. RNA interference of the lncRNA43234 gene decreased the crude protein content in seeds. Quantitative real-time polymerase chain reaction analysis revealed that lncRNA43234 influenced the expression of XM_014775786.1 associated with phosphatidylinositol metabolism by acting as a decoy for miRNA10420, thereby affecting the content of soybean oil. Our results provide insights into how lncRNA-mediated competing endogenous RNA regulatory networks are involved in soybean oil synthesis.

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N6-methyladenosine RNA methyltransferase CpMTA1 mediates CpAphA mRNA stability through a YTHDF1-dependent m6A modification in the chestnut blight fungus

Zhao,

Wei,

Chen

et al. 2024

PLoS Pathog

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In eukaryotic cells, N6-methyladenosine (m6A) is the most prevalent RNA epigenetic modification that plays crucial roles in multiple biological processes. Nevertheless, the functions and regulatory mechanisms of m6A in phytopathogenic fungi are poorly understood. Here, we showed that CpMTA1, an m6A methyltransferase in Cryphonectria parasitica, plays a crucial role in fungal phenotypic traits, virulence, and stress tolerance. Furthermore, the acid phosphatase gene CpAphA was implicated to be a target of CpMTA1 by integrated analysis of m6A-seq and RNA-seq, as in vivo RIP assay data confirmed that CpMTA1 directly interacts with CpAphA mRNA. Deletion of CpMTA1 drastically lowered the m6A level of CpAphA and reduced its mRNA expression. Moreover, we found that an m6A reader protein CpYTHDF1 recognizes CpAphA mRNA and increases its stability. Typically, the levels of CpAphA mRNA and protein exhibited a positive correlation with CpMTA1 and CpYTHDF1. Importantly, site-specific mutagenesis demonstrated that the m6A sites, A1306 and A1341, of CpAphA mRNA are important for fungal phenotypic traits and virulence in C. parasitica. Together, our findings demonstrate the essential role of the m6A methyltransferase CpMTA1 in C. parasitica, thereby advancing our understanding of fungal gene regulation through m6A modification.

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Full-length transcriptome revealed the accumulation of polyunsaturated fatty acids in developing seeds of Plukenetia volubilis

Cited by 4 publications

References 46 publications

Identification of the circRNA–miRNA–mRNA Regulatory Network in Pterygium-Associated Conjunctival Epithelium

Identification of the circRNA–miRNA–mRNA Regulatory Network in Pterygium-Associated Conjunctival Epithelium

Analysis of LncRNA43234-Associated ceRNA Network Reveals Oil Metabolism in Soybean

N6-methyladenosine RNA methyltransferase CpMTA1 mediates CpAphA mRNA stability through a YTHDF1-dependent m6A modification in the chestnut blight fungus

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