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Project description:The World Health Organization has recognized testicular function with temperature dependence. Testicular heat exposure caused by occupational factors, lifestyle and clinical disease, etc., can lead to different degrees of reproductive obstacles. The aim of this study is to reveal the transcriptional regulatory network and their potential crucial roles in testicular heat exposure. After passing quality control, the high throughput sequencing data of mouse testicular tissue for scrotum heat exposure and control group were carried out various analyses including differentially expressed transcriptome exploration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and network regulation. Differential transcriptome expression analysis revealed that 172 circRNA (91 upregulation and 81 downregulation), 465 lncRNA (96 upregulation and 369 downregulation) and 2721 mRNA (2003 upregulation and 718 downregulation) were identified as significant differential expression in the mouse testicular tissue of heat exposure compared with control group using the cut-off of log2fold change >= 0.585, p value <= 0.05 and q value <= 1.00. Through GO term analysis, differentially expressed lncRNA and mRNA may play important functions in negative regulation of cellular process [GO:0048523], meiotic cell cycle [GO:0051321], cytoplasm [GO:0005737], membrane raft [GO:0045121], amide binding [GO:0033218], extracellular matrix binding [GO: 0050840]. KEGG pathway analysis of differentially expressed lncRNA and mRNA can be classified into MAPK signaling [mmu04010], purine metabolism [mmu00230], homologous recombination [mmu03440], RNA transport [mmu03013], nod-like receptor signaling pathway [mmu04621]. This research provides high throughput sequencing data of transcriptome in testicular heat exposure model and lays the foundation for further study on the circRNA and lncRNA in male reproductive diseases related to elevated testicular temperature.
2021-01-29 | GSE165696 | GEO
Project description:Integrated study of the circRNA, lncRNA, mRNA and miRNA networks in testicular heat exposure
| PRJNA695494 | ENA
Project description:The World Health Organization has recognized testicular function with temperature dependence. Testicular heat exposure caused by occupational factors, lifestyle and clinical disease, etc., can lead to different degrees of reproductive obstacles. The aim of this study is to reveal the transcriptional regulatory network and their potential crucial roles in testicular heat exposure. After passing quality control, the high throughput sequencing data of mouse testicular tissue for scrotum heat exposure and control group were carried out various analyses including differentially expressed transcriptome exploration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and network regulation. Differential transcriptome expression analysis revealed that 279 miRNAs (138 upregulation and 141 downregulation) were identified as significant differential expression in the mouse testicular tissue of heat exposure compared with control group using the cut-off of log2fold change >= 0.585, p value <= 0.05 and q value <= 1.00. This research provides high throughput sequencing data of transcriptome in testicular heat exposure model and lays the foundation for further study on the miRNA in male reproductive diseases related to elevated testicular temperature.
2021-01-29 | GSE165697 | GEO
Project description:Integrated study of the circRNA, lncRNA and mRNA networks in testicular heat exposure
| PRJNA695496 | ENA
Project description:Integrated study of the miRNA networks in testicular heat exposure
| PRJNA695497 | ENA
Project description:Osteoarthritis (OA) is a joint disease that is pervasive in life, and the incidence and mortality of OA are increasing, causing many adverse effects on people's life. Therefore, it is very vital to identify new biomarkers and therapeutic targets in the clinical diagnosis and treatment of OA. ncRNA is a nonprotein-coding RNA that does not translate into proteins but participates in protein translation. At the RNA level, it can perform biological functions. Many studies have found that miRNA, lncRNA, and circRNA are closely related to the course of OA and play important regulatory roles in transcription, post-transcription, and post-translation, which can be used as biological targets for the prevention, diagnosis, and treatment of OA. In this review, we summarized and described the various roles of different types of miRNA, lncRNA, and circRNA in OA, the roles of different lncRNA/circRNA-miRNA-mRNA axis in OA, and the possible prospects of these ncRNAs in clinical application.
| S-EPMC8714905 | biostudies-literature
Project description:Accumulating evidence has indicated that noncoding RNAs are involved in intervertebral disc degeneration (IDD); however, the competing endogenous RNA (ceRNA)‑mediated regulatory mechanisms in IDD remain rarely reported. The present study aimed to comprehensively investigate the alterations in expression levels of circular RNA (circRNA), long noncoding RNA (lncRNA), microRNA (miRNA/miR) and mRNA in the nucleus pulposus (NP) of patients with IDD. In addition, crucial lncRNA/circRNA‑miRNA‑mRNA ceRNA interaction axes were screened using the GSE67567 microarray dataset obtained from the Gene Expression Omnibus database. After data preprocessing, differentially expressed circRNAs (DECs), lncRNAs (DELs), miRNAs (DEMs) or genes (DEGs) between IDD and normal controls were identified using the Linear Models for Microarray data method. A protein‑protein interaction (PPI) network was constructed for DEGs based on protein databases, followed by module analysis. The ceRNA network was constructed based on the interaction between miRNAs and mRNAs, and lncRNAs/circRNAs and miRNAs. The underlying functions of mRNAs were predicted using the Database for Annotation, Visualization and Integrated Discovery database. The present study identified 636 DECs, 115 DELs, 84 DEMs and 1,040 DEGs between patients with IDD and control individuals. PPI network analysis demonstrated that Fos proto‑oncogene, AP‑1 transcription factor subunit (FOS), mitogen‑activated protein kinase 1 (MAPK1), hypoxia inducible factor 1 subunit α (HIF1A) and transforming growth factor β1 (TGFB1) were hub genes and enriched in modules. Metastasis‑associated lung adenocarcinoma transcript 1 (MALAT1)/hsa_circRNA_102348‑hsa‑miR‑185‑5p‑TGFB1/FOS, MALAT1‑hsa‑miR‑155‑5p‑HIF1A, hsa_circRNA_102399‑hsa‑miR‑302a‑3p‑HIF1A, MALAT1‑hsa‑miR‑519d‑3p‑MAPK1 and hsa_circRNA_100086‑hsa‑miR‑509‑3p‑MAPK1 ceRNA axes were obtained by constructing the ceRNA networks. In conclusion, these identified ceRNA interaction axes may be crucial targets for the treatment of IDD.
| S-EPMC6755180 | biostudies-literature
Project description: Not available
| S-EPMC10888550 | biostudies-literature
Project description:Recent advances in sequencing technologies and the discovery of non-coding RNAs (ncRNAs) have provided new insights in the molecular pathogenesis of cancers. Several studies have implicated the role of ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and recently discovered circular RNAs (circRNAs) in tumorigenesis and metastasis. Unlike linear RNAs, circRNAs are highly stable and closed-loop RNA molecules. It has been established that circRNAs regulate gene expression by controlling the functions of miRNAs and RNA-binding protein (RBP) or by translating into proteins. The circRNA-miRNA-mRNA regulatory axis is associated with human diseases, such as cancers, Alzheimer's disease, and diabetes. In this study, we explored the interaction among circRNAs, miRNAs, and their target genes in various cancers using state-of-the-art bioinformatics tools. We identified differentially expressed circRNAs, miRNAs, and mRNAs on multiple cancers from publicly available data. Furthermore, we identified many crucial drivers and tumor suppressor genes in the circRNA-miRNA-mRNA regulatory axis in various cancers. Together, this study data provide a deeper understanding of the circRNA-miRNA-mRNA regulatory mechanisms in cancers.
| S-EPMC8149909 | biostudies-literature
Project description:Circular RNA (circRNA) is a novel type of endogenous noncoding RNA with covalently closed loop structures, which are widely expressed in various tissues and have functional implications in cellular processes. Acting as competing endogenous RNAs (ceRNAs), circRNAs are important regulators of miRNA activities. The identification of these circRNAs underlines the increasing complexity of ncRNA-mediated regulatory networks. However, more biological evidence is required to infer direct circRNA-miRNA associations while little attention has been paid to circRNAs in plants as compared to the abundant research in mammals. PlantCircNet is presented as an integrated database that provides visualized plant circRNA-miRNA-mRNA regulatory networks containing identified circRNAs in eight model plants. The bioinformatics integration of data from multiple sources reveals circRNA-miRNA-mRNA regulatory networks and helps identify mechanisms underlying metabolic effects of circRNAs. An enrichment analysis tool was implemented to detect significantly overrepresented Gene Ontology categories of miRNA targets. The genomic annotations, sequences and isoforms of circRNAs were also investigated. PlantCircNet provides a user-friendly interface for querying detailed information of specific plant circRNAs. The database may serve as a resource to facilitate plant circRNA research. Several circRNAs were identified to play potential regulatory roles in flower development and response to environmental stress from regulatory networks related with miR156a and AT5G59720, respectively. This present research indicated that circRNAs could be involved in diverse biological processes. Database URL: http://bis.zju.edu.cn/plantcircnet/index.php.
| S-EPMC5727401 | biostudies-literature