Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in aorta samples of F. nucleatum-infected mice
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ABSTRACT:
PROVIDER: PRJNA936575 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23524800_1.fastq.gz | Fastqsanger.gz | |||
| SRR23524800_2.fastq.gz | Fastqsanger.gz | |||
| SRR23524801_1.fastq.gz | Fastqsanger.gz | |||
| SRR23524801_2.fastq.gz | Fastqsanger.gz | |||
| SRR23524802_1.fastq.gz | Fastqsanger.gz |
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Project description:Periodontitis is an independent risk factor for atherosclerosis, and F. nucleatum is one of the periodontal pathogens. Several studies have confirmed that non-coding RNAs could affect all aspects of AS disease progression, including lipid metabolism, foam cell formation, cell necrosis, etc. However, no studies have explored whether F. nucleatum could affect AS disease progression by regulating non-coding RNAs. In this study, we intend to acquire mRNAs, lncRNAs and circRNAs expression profiles of aorta samples of AS mice from the F. nucleatum group and the Control group by next-generation sequencing(NGS) and perform bioinformatics analysis. Results revealed that 465 mRNA expression were up-regulated and 382 mRNA expression were down-regulated significantly. Some lncRNAs and circRNAs could suppress the binding of miRNA with target genes in post-transcriptional regulation. By integrating with DE-miRNAs-DEGs pairs and screening the common miRNAs, and mRNAs, lncRNAs, circRNAs that have targeted and negatively correlated relationship with the common miRNAs, lncRNA-miRNA-mRNA (including 34 DE-miRNAs, 42 DE-lncRNAs, and 111 DE-mRNAs) and circRNA-miRNA-mRNA (including 19 DE-miRNAs, 49 DE-circRNAs, and 87 DE-mRNAs) regulatory co-expression networks were constructed. GO enrichment analysis was performed on the differentially expressed mRNAs, which were found to be related to molecular functions, biological processes and cellular components such as protein binding, nucleus, postsynaptic dense zone, protein phosphorylation. KEGG analysis showed that they were related to ErbB signaling pathway, neurotrophic factor signaling pathway, glucagon signaling pathway and apoptosis signaling pathway. This suggested that F. nucleatum could promote the development of atherosclerosis through non-coding RNAs network regulation.
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Project description:F. nucleatum is an opportunistic pathogen that usually colonize in oral cavity, thereby closely associated with the development of periodontitis.However, the immune regulation mechanism of F. nucleatum to macrophage’s function in disease progress has not been clearly elucidated.Long non-coding RNA (lncRNA) and circular RNA (circRNA) were discovered to play an important role in regulating occurrence and progression of many diseases and identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of mRNA, lncRNA and circRNA associated with F. nucleatum infection were investigated for the first time. The results revealed that the expressions of 375 mRNAs, 64 lncRNAs, and 180 circRNAs were altered during F. nucleatum infection. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis showed that the target genes were mainly involved in the MAPK signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway and apoptosis. Conclusions: The present study firstly provides the expression profiles of mRNAs, lncRNAs and circRNAs during F. nucleatum infection, and describes a novel perspective on the potential roles of lncRNAs and circRNAs underlying the pathogenesis mechanism of F. nucleatum infection.
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Project description:Genome-wide analysis of differentially expressed profiles of miRNAs, mRNAs, lncRNAs and circRNAs in F. nucleatum infection
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Project description:Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), which were proved to play a crucial role in regulating cell differentiation and tissue development. However, the expression profiles of different RNAs, such as mRNA, lncRNAs, and circRNAs in different adipose tissues, are still largely unclear. To shed light on this issue, we performed the systematic analysis of mRNAs, lncRNAs, and circRNAs obtained from intramuscular adipose tissues (IAT), subcutaneous adipose tissues (SAT), visceral adipose tissues (RPAT), and mesenteric adipose tissues (MAT) tissues of Chinese Erhualian pigs using high-throughput sequencing. A total of 1,695, 1,878, 494, 1,300, 902, and 355 differentially expressed (DE) mRNAs, 318, 399, 192, 251, 249, and 347 DE lncRNAs, 1,367, 1,007, 999, 1,153, 1,256, and 837 DE circRNAs were identified in IAT versus SAT, IAT versus RPAT, SAT versus RPAT, MAT versus IAT, MAT versus SAT, and MAT versus RPAT, respectively. Gene ontology (GO) enrichment analyses showed these DE genes were mainly involved in lipid metabolic and immune response. Next the co-expression network construction of mRNAs-lncRNAs revealed several key lncRNAs such as MSTRG.604204 and MSTRG.604206 might associated with lipid metabolic. Tissue specific analysis indicated that circRNA exhibited the highest tissue specificity than lncRNA and mRNA, and the IAT had the most tissue specific lncRNA, mRNA, and circRNA compared with other tissues. Taken together, this study gives us a novel clue to the role of mRNAs, lncRNAs and circRNAs in fat metabolism, thus improving our understanding of the regulation mechanism of different gene expression profiles in adipose deposition
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