Abstract
Background: Prior studies have shown that the proliferation of V79 lung fibroblast cells could be inhibited by low background radiation (LBR) in deep underground laboratory (DUGL). In the current study, we revealed further molecular changes by performing whole transcriptome analysis on the expression profiles of long non-coding RNA (lncRNA), messenger RNA (mRNA), circular RNA (circRNA) and microRNA (miRNA) in V79 cells cultured for two days in a DUGL.Methods: Whole transcriptome analysis including lncRNA, mRNAs, circ RNA and miRNA was performed in V79 cells cultured for two days in DUGL and above ground laboratory (AGL), respectively. The differentially expressed (DE) lncRNA, mRNA, circRNA, and miRNA in V79 cells were identified by the comparison between DUGL and AGL groups. Quantitative real-time polymerase chain reaction(qRT-PCR)was conducted to verify the selected RNA sequencings. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed for the DE mRNAs which enabled to predict target genes of lncRNA and host genes of circRNA.Results: With |log2(Fold-change)| ≥ 1.0 and p < 0.05, a total of 1257 mRNAs (353 mRNAs up-regulated, 904 mRNAs down-regulated), 866 lncRNAs (145 lncRNAs up-regulated, 721 lncRNAs down-regulated), and 474 circRNAs (247 circRNAs up-regulated, 227 circRNAs down-regulated) were significantly altered between the two groups. There was no significant difference in miRNA between the two groups. The altered RNA profiles were mainly discovered in lncRNAs, mRNAs and circRNAs. DE RNAs were involved in many pathways including ECM-RI, PI3K-Akt signaling, RNA transport and the cell cycle under the LBR stress of the deep underground environment.Conclusion: Taken together, these results suggest that the LBR in the DUGL could induce transcriptional repression, thus reducing metabolic process and reprogramming the overall gene expression profile in V79 cells.
Highlights
An increasing number of countries have begun to develop deep Earth in order to cope with the space and resources of surface Earth being gradually consumed in the future (Xie et al, 2018)
GO analyses showed that the host genes of down-regulated differentially expressed (DE) circular RNA (circRNA) were enriched in metabolic processes, which was similar to the results found in both DE messenger RNA (mRNA) and target genes of DE long non-coding RNA (lncRNA)
Our study investigated the transcription patterns of lncRNAs, mRNAs, circRNAs, and miRNAs of V79 cells cultured in a deep underground laboratories (DUGLs) and an above ground laboratory (AGL) by whole-transcriptome sequencing and integrated analysis
Summary
An increasing number of countries have begun to develop deep Earth in order to cope with the space and resources of surface Earth being gradually consumed in the future (Xie et al, 2018). As China, exploring deep underground space and resources has become a national priority since 2016 (Xie et al, 2017), which shown that an increasing number of people could live and/or work in the underground space in the near future (Ranjith et al, 2017; Liu et al, 2018). Researchers who have historically focused on the growth of cultures in DUGLs have observed some interesting changes(e.g., cell growth delay, enzyme activity change and sensitivity to genetic damage factors) in living organisms exposed to low levels of radiation (Belli, 2017; Castillo and Smith, 2017; Liu et al, 2018). We revealed further molecular changes by performing whole transcriptome analysis on the expression profiles of long non-coding RNA (lncRNA), messenger RNA (mRNA), circular RNA (circRNA) and microRNA (miRNA) in V79 cells cultured for two days in a DUGL
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