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Project description:Spodoptera litura (Lepidoptera: Noctuidae), which has a strong and rapid reproductive capacity, is a polyphagous pest with great destruction to many crops, causing economic loss to agricultural production worldwide. Its two testes fuse into a single one during the larva-to-pupa metamorphosis, which was favorable to the sperm development. However the mechanism of testicular fusion is still not fully understood. In this study, we analyzed long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the testes by high-throughout RNA-seq to explore the mechanism of testicular fusion in S. litura. In total, 2,150 lncRNAs, 2,742 target mRNAs and 347 miRNAs were identified in the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion). It was found that a large number of DElncRNAs, DEmRNAs and a little number of DEmiRNAs were up-regulated from L6D4 to L6D6 when the testes began to fuse, a little number of DElncRNAs, DEmRNAs and a large number of DEmiRNAs were down-regulated from L6D6 to P0D after the testicular fusion. The GO terms and KEGG pathway enrichment analysis of DElncRNAs target DEmRNAs showed that ECM remodeling enzymes including stromelysin, A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTs) and inducible metalloproteinase inhibitor protein (IMIPs), ECM-intergrin interaction pathway and cell adhesion molecules (integrin, cadherin) may be involved in the testicular fusion. The DElncRNA-DEmiRNA-DEmRNA regulatory network related to ECM remodeling enzymes and its signal pathway may play important roles in cell adhesion when the testicular fusion occured. Our study will provide comprehensive information to study the mechanism of testicular fusion, and especially, will promote the functional study of non-coding RNAs (lncRNAs and miRNAs) during the testicular fusion in S. litura.
2024-08-01 | GSE201953 | GEO
Project description:Spodoptera litura (Lepidoptera: Noctuidae), which has a strong and rapid reproductive capacity, is a polyphagous pest with great destruction to many crops, causing economic loss to agricultural production worldwide. Its two testes began to fuse into a single one during the larva-to-pupa metamorphosis, which was favorable to the sperms development in our previous study. But the mechanism of testicular fusion is still unknown. In this study, we analyzed long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the testes by high-throughout RNA-seq to explore the mechanism of testicular fusion in S. litura. In total, 2,150 lncRNAs, 2,742 target mRNAs and 347 miRNAs were identified in the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 0-day-old pupae (P0D) (after fusion). It was found that a large number of DElncRNAs, DEmRNAs and a little number of DEmiRNAs were up-regulated from L6D4 to L6D6 when the testes began to fuse, a little number of DElncRNAs, DEmRNAs and a large number of DEmiRNAs were down-regulated from L6D6 to P0D after the testicular fusion. The GO terms and KEGG pathway enrichment analysis of DElncRNAs target DEmRNAs showed that ECM remodeling enzymes: stromelysin, A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTs) and inducible metalloproteinase inhibitor protein (IMIPs), ECM-intergrin interaction pathway and cell adhesion molecules (integrin, cadherin) may be involved in the testicular fusion. The DElncRNA-DEmiRNA-DEmRNA regulatory network related to ECM remodeling enzymes and its signal pathway may play important roles in cell adhesion when the testicular fusion occured. Our study will provide comprehensive information to study the mechanism of testicular fusion, and especially, will promote the functional study of non-coding RNAs (lncRNAs and miRNAs) during the testicular fusion in S. litura.
2024-08-01 | GSE202102 | GEO
Project description:Transcriptomic analysis of non-coding RNAs reveals the regulatory network of testicular fusion in Spodoptera litura
| PRJNA834729 | ENA
Project description:Transcriptomic analysis of non-coding RNAs reveals the regulatory network of testicular fusion in Spodoptera litura [lncRNA-mRNA]
| PRJNA833729 | ENA
Project description:Transcriptomic analysis of non-coding RNAs reveals the regulatory network of testicular fusion in Spodoptera litura [miRNA-seq]
| PRJNA834737 | ENA
Project description:BACKGROUND:Lepidoptera is one group of the largest plant-feeding insects and Spodoptera litura (Lepidoptera: Noctuidae) is one of the most serious agricultural pests in Asia countries. An interesting and unique phenomenon for gonad development of Lepidoptera is the testicular fusion. Two separated testes fused into a single one during the larva-to-pupa metamorphosis, which is believed to contribute to sperm production and the prevalence in field. To study the molecular mechanism of the testicular fusion, RNA sequencing (RNA-seq) experiments of the testes from 4-day-old sixth instar larvae (L6D4) (before fusion), 6-day-old sixth instar larvae (L6D6, prepupae) (on fusing) and 4-day-old pupae (P4D) (after fusion) of S. litura were performed. RESULTS:RNA-seq data of the testes showed that totally 12,339 transcripts were expressed at L6D4, L6D6 and P4D stages. A large number of differentially expressed genes (DEGs) were up-regulated from L6D4 to L6D6, and then more genes were down-regulated from L6D6 to P4D. The DEGs mainly belongs to the genes related to the 20E signal transduction pathway, transcription factors, chitin metabolism related enzymes, the families of cytoskeleton proteins, extracellular matrix (ECM) components, ECM-related protein, its receptor integrins and ECM-remodeling enzymes. The expression levels of these genes that were up-regulated significantly during the testicular fusion were verified by qRT-PCR. The matrix metalloproteinases (MMPs) were found to be the main enzymes related to the ECM degradation and contribute to the testicular fusion. The testis was not able to fuse if MMPs inhibitor GM6001 was injected into the 5th abdomen region at L6D6 early stage. CONCLUSIONS:The transcriptome and DEGs analysis of the testes at L6D4, L6D6 and P4D stages provided genes expression information related to the testicular fusion in S. litura. These results indicated that cytoskeleton proteins, ECM-integrin interaction genes and ECM-related proteins were involved in cell migration, adhesion and fusion during the testicular fusion. The ECM degradation enzymes MMPs probably play a critical role in the fusion of testis.
| S-EPMC7029529 | biostudies-literature
Project description:Long non-coding RNAs (lncRNAs) have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA) in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on "ceRNA hypothesis". The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO) and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.
| S-EPMC5664124 | biostudies-literature
Project description:BackgroundRupture of intracranial aneurysm (IA) is the main cause of devastating subarachnoid hemorrhage, which urges our understanding of the pathogenesis and regulatory mechanisms of IA. However, the regulatory roles of long non-coding RNAs (lncRNAs) in IA is less known.ResultsWe processed the raw SRR files of 12 superficial temporal artery (STA) samples and 6 IA samples to count files. Then the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs between STAs and IAs were identified. The enrichment analyses were performed using DEmRNAs. Next, a lncRNA-miRNA-mRNA regulatory network was constructed using integrated bioinformatics analysis. In summary, 341 DElncRNAs, 234 DEmiRNAs, and 2914 DEmRNAs between the STA and IA. The lncRNA-miRNA-mRNA regulatory network of IA contains 91 nodes and 146 edges. The subnetwork of hub lncRNA PVT1 was extracted. The expression level of PVT1 was positively correlated with a majority of the mRNAs in its subnetwork. Moreover, we found that several mRNAs (CCND1, HIF1A, E2F1, CDKN1A, VEGFA, COL1A1 and COL5A2) in the PVT1 subnetwork served as essential components in the PI3K-Akt signaling pathway, and that some of the non-coding RNAs (ncRNAs) (PVT1, HOTAIR, hsa-miR-17, hsa-miR-142, hsa-miR-383 and hsa-miR-193b) interacted with these mRNAs.ConclusionOur annotations noting ncRNA's role in the pathway may uncover novel regulatory mechanisms of ncRNAs and mRNAs in IA. These findings provide significant insights into the lncRNA regulatory network in IA.
| S-EPMC7945298 | biostudies-literature
Project description:Hepatic fibrosis (HF), one of the leading global health problems, is defined as aberrant and excess production of extracellular matrix components. The pathogenesis of HF is complex and poorly understood. Long non?coding RNAs (LncRNAs) can interact with microRNAs (miRNAs) as competing endogenous RNAs (ceRNAs) to regulate the expression of target genes, which play a significant role in the initiation and progression of HF. In the present study, the LncRNA?associated ceRNA network was reconstructed based on LncRNA, miRNA and mRNA expression profiles that were downloaded from National Center for Biotechnology Information Gene Expression Omnibus. Bioinformatics assessments including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed with Database for Annotation, Visualization and Integration Discovery. The ceRNA network was composed of 220 LncRNA nodes, 24 miRNA nodes, 164 mRNA nodes and 1,149 edges. Functional assays identified that a total of 338 GO terms and 25 pathways, including regulation of cytokine and collagen, and the transforming growth factor?? and Toll?like receptor signaling pathways, were significantly enriched. In addition, 4 LncRNAs (NONMMUT036242, XR_877072, XR_378619 and XR_378418) were highly related to HF and thereby chosen as key LncRNAs. The present study uncovered a ceRNA network that could further the understanding of the mechanisms underlying HF development and provide potential novel markers for clinical diagnosis and targets for treatment.
| S-EPMC6797987 | biostudies-literature
Project description:Increasing epidemic of type 2 diabetes mellitus (T2DM) and its comorbidities makes it urgent to understand the pathogenesis and regulatory mechanism. However, little is known about the regulatory role of lncRNAs in diabetes. Here, we constructed a T2DM-related competitive endogenous RNA (ceRNA) network (DMCN) to explore biological function of lncRNAs during the development of diabetes mellitus. This network contained 351 nodes including 98 mRNAs, 86 microRNAs and 167 lncRNAs. Functional analysis showed that the mRNAs in DMCN were annotated into some diabetes-related pathways. Furthermore, mTOR-centred subnetwork was extracted and ncRNA-involved mTOR pathway was established. Finally, we validated that NEAT1 was potentially communicated with mTOR signalling target protein mLST8 via the association with miR-181b. These findings provide significant insight into lncRNA regulatory network in T2DM.
| S-EPMC5706502 | biostudies-literature