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Differential expression profiles of long non-coding RNAs during the mouse pronucleus stage under normal gravity and simulated microgravity

ABSTRACT: We report the application of single-molecule-based sequencing technology for high-throughput profiling of lncRNA in mouse cells. By obtaining over 47 million bases of sequence, we identified 3,307 lncRNAs based on single-cell RNA sequencing (RNA-Seq) data, discovered 52 lncRNAs that were significantly differentially expressed, and then selected 10 lncRNAs for qRT-PCR validation. Furthermore, we found that 12 lncRNAs with the target gene Tubb4b or Actn4 might be related to the expression of microtubule and microfilament proteins and the binding relationship was confirmed in a dual-luciferase reporter assay. Finally, Gene Ontology (GO) analysis revealed that the target genes of the differentially expressed lncRNAs participated in cellular processes related to protein transport, binding, catalytic activity, membrane-bounded organelles, protein complexes and the cortical cytoskeleton. We believe the paper will be of particular interest to the readers of your journal as lncRNAs regulated the progress of the mouse early embryo development.

ORGANISM(S): Mus musculus

PROVIDER: GSE118001 | GEO | 2018/12/26

REPOSITORIES: GEO

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Project description:Purpose: Microgravity is one of crucial factors which affects astronauts’ health in space. The goals of this study are to compare SMG-pretreated macrophages infected with EPEC by RNA-sequencing to investigate the immunity-related differential expression genes and signaling pathway and to make for prevention and therapy of infectious diseases in space. Methods: 3-day SMG-pretreatment macrophages were infected with EPEC (a kind of enteropathogen) and macrophages infected with EPEC under normal gravity as control and then we used RNA sequencing on Illumina platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level by Volcano Plot, KEEG database and InnateDB database. qRT–PCR validation was performed using SYBR Green assays. Results: After RNA sequencing, we got 1272 differential expression genes (DEGs) of which 542 were up-regulated, 720 were down-regulated DEGs. KEGG pathway enrichment scatter plot showed that cytokine-cytokine receptor interaction and MAPK signaling pathway were optimal-related to infection immunity under simulated microgravity. Because of our study involved in infection immunity, we chose a database on immunity called InnateDB to screen the DEGs related to immunity. We found 14 DEGs in cytokine-cytokine receptor interaction, of which 7 were up-regulated, and 7 were down-regulated and 36 DEGs in MAPK signaling pathway, of which 11 were up-regulated, and 25 were down-regulated. In cytokine-cytokine receptor interaction signaling pathway, except for Il 33 (P>0. 05), the results of mRNA expression of DEGs in macrophages infected with EPEC were consistent with the results of RNA sequencing. In MAPK signaling pathway, the mRNA expression of Il 1b, Cd14, Hspa1a, Pdgfrb, Il 1a, Fgf7, Igf1r and Pak1 was not consistent with the RNA sequencing. Compared with normal gravity, simulated microgravity didn’t affect the mRNA expression of Il 1b, Cd14, Hspa1a and Pdgfrb (P>0. 05). The Il 1a and Fgf7 down regulated and Igf1r and Pak1 up regulated under simulated microgravity at the level of mRNA with a comparison to normal gravity, and the results of the rest of DEGs were consistent with the results of RNA sequencing. Conclusions: This study is the first high-throughput analysis on simulated microgravity of infection immunity. The comparative analysis demonstrates that cytokine-cytokine receptor interaction and MAPK signaling pathway participants in the innate immune response.

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Differential expression profiles of long non-coding RNAs during the mouse pronucleus stage under normal gravity and simulated microgravity

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