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Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR
Published on: March 1, 2019
Expression profiles of long noncoding RNAs associated with the NSUN2 gene in HepG2 cells
Zhen Sun1, Shonglei Xue1, Hui Xu1
1Institute of Epigenetics and Epigenomics and College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, P.R. China.
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.
Insights
The study reveals how the NSUN2 protein influences gene expression in liver cancer cells. It identifies specific long noncoding RNAs (lncRNAs) regulated by NSUN2, offering insights into cancer development.
Area of Science:
- Molecular Biology
- Genomics
- Cancer Research
Background:
- NOP2/Sun domain family member 2 (NSUN2) is frequently elevated in various cancers.
- NSUN2's precise role in cell proliferation, migration, and tumorigenesis is not fully understood.
- Investigating NSUN2's regulatory functions is crucial for understanding cancer mechanisms.
Purpose of the Study:
- To explore the impact of NSUN2 deficiency on long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression.
- To identify lncRNAs and mRNAs co-expressed and correlated with NSUN2.
- To elucidate the biological pathways and functions associated with NSUN2-regulated lncRNAs.
Main Methods:
- RNA sequencing was performed on NSUN2-deficient HepG2 cells compared to wild-type cells.
- Differential expression analysis was conducted for lncRNAs and mRNAs.
- Bioinformatics tools were used to analyze co-expression networks and pathway enrichment.
Main Results:
- A total of 757 lncRNAs were differentially expressed in NSUN2-deficient cells (392 upregulated, 365 downregulated).
- 212 lncRNAs were co-expressed with 368 target mRNAs, showing both positive (290 pairs) and negative (253 pairs) correlations.
- NSUN2-regulated lncRNAs were linked to signal transduction, extracellular exosomes, and calcium ion binding, and enriched in cancer-related pathways like 'pathways in cancer' and the 'PI3K-Akt signaling pathway'.
Conclusions:
- NSUN2 significantly influences the lncRNA and mRNA expression landscape.
- The study provides a comprehensive view of the lncRNA-mRNA co-expression network regulated by NSUN2.
- These findings offer valuable insights into the molecular functions of NSUN2 in tumorigenesis and cancer progression.
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