RNA-seq analysis of mRNA profiles in the livers of Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice

Purpose: The goal of this study is to compare transcriptome profilings of liver from Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice. Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Wtap flox/flox and Wtap-HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina Novaseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.p6) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1). Conclusion: Our study represents the first detailed analysis of hepatic mRNA profiles in Wtapflox/flox and Wtap-HKO mice at 8 weeks old, generated by RNA-seq technology. Our results showed that 3486 genes were downregulated, and 3706 genes were upregulated. Gene ontology (GO) analysis showed that downregulated genes were associated with small molecule catabolic process, fatty acid metabolic process, amino acid metabolic process, steroid metabolic process, cholesterol metabolic process, xenobiotic metabolic process, fatty acid beta-oxidation, alcohol metabolic process, and glucose metabolic process, whereas the upregulated genes were associated with wound healing, leukocyte migration, chemotaxis, and positive regulation of cytokine production. The hepatic mRNA profiles of Wtap-HKO and Wtapflox/flox mice (n=3 for each group) were generated by deep sequencing using Illumina Novaseq platform.研究目的：本研究旨在比较Wtapflox/flox小鼠与肝细胞特异性Wtap敲除（hepatocyte-specific Wtap knockout, HKO）小鼠的肝脏转录组谱（transcriptome profilings）。 实验方法：采用Tripure分离试剂（Tripure Isolation Reagent，罗氏，德国曼海姆）提取8周龄Wtap flox/flox与Wtap-HKO小鼠肝脏的总RNA。通过Illumina NovaSeq测序平台开展深度测序以获取mRNA表达谱。将双端洁净读数比对至小鼠参考基因组（Ensemble_GRCm38.p6），比对工具为TopHat（版本2.0.12）；随后使用HTSeq-count（版本0.6.1）定量mRNA表达水平。 研究结论：本研究为首次针对8周龄Wtapflox/flox与Wtap-HKO小鼠的肝脏mRNA谱开展的详细分析，采用RNA-seq测序技术。结果显示，共计3486个基因表达下调，3706个基因表达上调。基因本体（Gene Ontology, GO）分析表明，下调基因富集于小分子分解代谢过程、脂肪酸代谢过程、氨基酸代谢过程、类固醇代谢过程、胆固醇代谢过程、异生物质代谢过程、脂肪酸β-氧化、酒精代谢过程以及葡萄糖代谢过程；而上调基因则与伤口愈合、白细胞迁移、趋化性以及细胞因子产生的正调控相关。本研究中，Wtap-HKO组与Wtapflox/flox组小鼠的肝脏mRNA谱（每组样本量n=3）均通过Illumina NovaSeq测序平台深度测序获取。