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A novel strategy for regulating mRNA’s degradation via interfering the AUF1’s binding to mRNA [RNA-seq]

ABSTRACT: Purpose:To explore how JNJ-7706621 affected the cellular processes and the possible relationship between AUF1 functions, we analyzed global transcriptome alterations of SK-MEL-2 cells at certain time points (48 h) after JNJ-7706621 treatment using RNA-seq analysis. Methods: Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis Results: The quantity of gene expression was calculated by FPKM (Fragments Per Kilobase of transcript per Million fragments mapped). Genes with log2 (Fold change) >1 and P value < 0.05 were considered as differentially expressed genes (DEGs). There were 146 upregulated genes and 158 downregulated genes for a total of 304 DEGs that were results are shown in Fig. 8A. Furthermore, the enriched KEGG pathways were analyzed and the top 30 pathways involved in these 304 DEGs between the two groups are shown in Figure SI. Among the top 30 pathways, 9 pathways related to mitochondrial function had significant effects. 37 DEGs in KEGG pathway associated with mitochondrial function was conducted and analyzed. Conclusions: 70% gene was up-regulated by JNJ-7706621 and up-regulated genes mainly affect cancer and inflammatory factors according the RNA-seq analysis

ORGANISM(S): Homo sapiens

PROVIDER: GSE201278 | GEO | 2022/06/15

REPOSITORIES: GEO

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Project description:Purpose: The goal of this study is to identify the difference of immunity between wild-type and yellow mutant rainbow trout in natural flowing water pond culture environment. Methods: The transcriptomic profiles of the skin were generated by using the Hiseq™4000 sequencing platform. Results: A total of 557,976,332 clean reads were yielded from six libraries and then assembled into 38,226 genes. Using P-value of 0.05 as the threshold, 3373 differentially expressed genes (DEGs) were obtained between WR_S and YR_S rainbow trout skin including the members of HSP90, V-ATPases, GST, SUGT1, NLRP3, NOD1, TLR3, IFR3, DHX58, IFIH1, JAK1, JAK2, STAT1 and NAMPT (|log2 fold-change| ranged from 1 to 4). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed. A majority of DEGs were enriched in innate immune-related GO terms and pathways, such as activation of innate immune response, inflammatory response, innate immune response, NAD+ADP-ribosyltransferase activity and NAD biosynthetic process in sub-categories of GO terms, and RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, Phagosome, Jak-STAT signaling pathway in KEGG enrichment pathways. Meanwhile, several immune-related metabolic pathways were also identified including metabolism of Xenobiotics by cytochrome P450, Glutathione metabolism, Nicotinate and nicotinamide metabolism. Additionally, 15 DEGs were selected and validated their expression level by qRT-PCR to confirm accuracy of the RNA-seq. Conclusions: Our study is the first time to clarify the skin innate immunity difference between wild-type and yellow mutant rainbow trout in the natural flowing water pond culture environment. Our results show that the expression of most immune-related genes in the corresponding pathways were up-regulated in WR_S rainbow trout. We presumed that the disease resistance of WR_S rainbow trout might be stronger than YR_S rainbow trout.

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A novel strategy for regulating mRNA’s degradation via interfering the AUF1’s binding to mRNA [RNA-seq]

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