Construction of RNA m6A profiles in liver tissue of mice in sepsis-induced liver injury based on m6A MeRIP-seq and RNA-seq

Sepsis-induced liver injury (SILI) indicates liver functional or structural impairment occurring during sepsis and is one of the common complications of sepsis. N6-methyladenosine (m6A) modification plays a significant role in the pathological processes of SILI, but its specific mechanisms remain unclear and require further elucidation. In this study, an experimental sepsis model exhibiting characteristic symptoms and hepatic damage was established through cecal ligation and puncture (CLP) surgery. Comprehensive analyses of hepatic tissues from CLP-treated and Sham operation mice through RNA Sequencing (RNA-Seq) and Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) methodologies revealed distinct m6A peaks and differentially expressed genes (DEGs). A total of 2002 m6A peaks were detected (|log2FC|≥ 1, p < 0.05). Our analyses demonstrated that 71% of m6A peaks clustered within the coding sequences (CDS) and 3' untranslated region starts (3' UTR) of transcripts. When compared with the Sham group, the CLP group showed an increase of 1741 DEGs and a decrease of 1815 DEGs. And 458 genes exhibited both m6A modifications and changes in mRNA levels. Functional enrichment assessments through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that m6A-modified hepatic genes in septic mice were significantly enriched in the cytoplasm, nucleus and protein binding, which mainly involved in regulating cell survival, immune responses, inflammatory responses and other related pathways. The results of Cell Counting Kit-8 (CCK8) assay and 5-ethynyl-2'-deoxyuridine (EdU) assay showed that the proliferation ability of liver cell lines was enhanced after knocking down m6A regulatory factor METTL3, which indicates the m6A modifications play an important role in the proliferation ability of normal liver cells. This study validated the presence of m6A-epitranscriptomic modifications and their regulatory roles in sepsis-affected hepatic systems, establishing comprehensive m6A landscapes in septic liver tissues.