Dataset Information

Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells.

ABSTRACT: NOP2/Sun domain family member 2 (NSUN2) is upregulated in numerous types of tumors and may be implicated in multiple biological processes, including cell proliferation, migration and human tumorigenesis. However, little is known about how NSUN2 serves a role in these processes. In the present study, expression profiles of long noncoding RNAs (lncRNAs) and mRNAs were developed in NSUN2?deficient HepG2 cells by RNA?sequencing analysis. A total of 757 lncRNAs were differentially expressed, 392 of which were upregulated, and 365 were downregulated compared with wild?type HepG2 cells. Moreover, 212 lncRNAs were co?expressed with 368 target mRNAs. It was also observed that 253 pairs of lncRNAs and mRNAs exhibited negative correlations and that 290 pairs had positive correlations. Bioinformatics analysis indicated that these lncRNAs regulated by NSUN2 were associated with 'signal transduction', 'extracellular exosome' and 'calcium ion binding', and were enriched in 'pathways in cancer', 'PI3K?Akt signaling pathway' and 'ECM?receptor interaction pathway'. These results illustrate the landscape and co?expression network of lncRNAs regulated by NSUN2 and provide invaluable information for studying the molecular function of NSUN2.

SUBMITTER: Sun Z

PROVIDER: S-EPMC6423554 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells.

Sun Zhen Z Xue Shonglei S Xu Hui H Hu Xuming X Chen Shihao S Yang Zhe Z Yang Yu Y Ouyang Juan J Cui Hengmi H

Molecular medicine reports 20190225 4

NOP2/Sun domain family member 2 (NSUN2) is upregulated in numerous types of tumors and may be implicated in multiple biological processes, including cell proliferation, migration and human tumorigenesis. However, little is known about how NSUN2 serves a role in these processes. In the present study, expression profiles of long noncoding RNAs (lncRNAs) and mRNAs were developed in NSUN2‑deficient HepG2 cells by RNA‑sequencing analysis. A total of 757 lncRNAs were differentially expressed, 392 of w ...[more]

PMID: 30816500

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Project description:Spinal cord injury (SCI) is a serious disorder of the central nervous system with a high disability rate. Long noncoding RNAs (lncRNAs) are reported to mediate many biological processes. The aim of this study was to explore lncRNA and mRNA expression profiles and functional networks after SCI. Differentially expressed genes between SCI model rats and sham controls were identified by microarray assays and analyzed by functional enrichment. Key lncRNAs were identified using a support vector machine- (SVM-) recursive feature elimination (RFE) algorithm. A trans and cis regulation model was used to analyze the regulatory relationships between lncRNAs and their targets. An lncRNA-related ceRNA network was established. We identified 5465 differentially expressed lncRNAs (DE lncRNAs) and 8366 differentially expressed mRNAs (DE mRNAs) in the SCI group compared with the sham group (fold change > 2.0, p < 0.05). Four genes were confirmed by qRT-PCR which were consistent with the microarray data. GSEA analysis showed that most marked changes occurred in pathways related to immune inflammation and nerve cell function, including cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and GABAergic synapse. Enrichment analysis identified 30 signaling pathways, including those associated with immune inflammation response. A total of 40 key lncRNAs were identified using the SVM-RFE algorithm. A key lncRNA-mRNAs coexpression network was generated for 230 951 lncRNA-mRNA pairs with half showing positive correlations. Several key DE lncRNAs were predicted to have "cis"- or "trans"-regulated target genes. The transcription factors, Sp1, JUN, and SOX10, may regulate the interaction between XR_001837123.1 and ETS 1. In addition, five pairs of ceRNA regulatory sequences were constructed. Many mRNAs and lncRNAs were found to be dysregulated after SCI. Bioinformatic analysis showed that DE lncRNAs may play crucial roles in SCI. It is anticipated that these findings will provide new insights into the underlying mechanisms and potential therapeutic targets for SCI.

Dataset Information

Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells.

Publications

Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells.

Similar Datasets

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