M6A mRNA Methylation Was Associated With Gene Expression and Lipid Metabolism in Liver of Broilers Under Lipopolysaccharide Stimulation.

Feng Guo,Yan Yu,Mengna Jing,Jinyou Ma,Pei Gao,Zhiyong Xu,Xiaobing Wei,Yanhong Zhang,Qiuxia Wang,Li Wang

doi:10.3389/fgene.2022.818357

Abstract

Hepatic inflammation is always accompanied with abnormal lipid metabolism. Whether N6-methyladenosine (m6A) mRNA methylation affects irregular inflammatory lipid level is unclear. Here, the m6A modification patterns in chicken liver at the acute stage of LPS-stimulated inflammation and at the normal state were explored via m6A and RNA sequencing and bioinformatics analysis. A total of 7,815 m6A peaks distributed in 5,066 genes were identified in the normal chicken liver and were mostly located in the CDS, 3′UTR region, and around the stop codon. At 2 h after the LPS intraperitoneal injection, the m6A modification pattern changed and showed 1,200 different m6A peaks. The hyper- and hypo-m6A peaks were differentially located, with the former mostly located in the CDS region and the latter in the 3′UTR and in the region near the stop codon. The hyper- or hypo-methylated genes were enriched in different GO ontology and pathways. Co-analysis revealed a significantly positive relationship between the fold change of m6A methylation level and the relative fold change of mRNA expression. Moreover, computational prediction of protein–protein interaction (PPI) showed that genes with altered m6A methylation and mRNA expression levels were clustered in processes involved in lipid metabolism, immune response, DNA replication, and protein ubiquitination. CD18 and SREBP-1 were the two hub genes clustered in the immune process and lipid metabolism, respectively. Hub gene AGPAT2 was suggested to link the immune response and lipid metabolism clusters in the PPI network. This study presented the first m6A map of broiler chicken liver at the acute stage of LPS induced inflammation. The findings may shed lights on the possible mechanisms of m6A-mediated lipid metabolism disorder in inflammation.

Highlights

N6-methyladenosine (m6A) is the most common RNA modification in mammalian mRNA
Among the m6A readers, the YTH-domain family 1 (YTHDF1), YTH domain family 2 (YTHDF2), and YTHDF3 proteins can directly bind to the m6A position to control the translation and decay of their target mRNA in cytosol
This diversity of responsible m6A enzymes after LPS stimulation suggested varying mechanisms of m6A in the LPSinduced inflammation in different cell lines or species. All these findings revealed that m6A and the associated modulators play important role in the LPS-induced inflammation response in different cell types and species. m6A modification plays important roles in the lipid metabolism regulation

Summary

Introduction

With MeRIP-Seq technology, more than 7,000 mammalian genes were detected with m6A modification (Meyer et al, 2012). These m6A sites preferentially distribute near the stop codons and in the 3′UTRs and are highly conserved among humans, mice, and pigs (Dominissini et al, 2012; Wang et al, 2018). Among the m6A readers, the YTH-domain family 1 (YTHDF1), YTHDF2, and YTHDF3 proteins can directly bind to the m6A position to control the translation and decay of their target mRNA in cytosol. YTHDF1-3 are the three YT521B (YTH) family of proteins, YTHDF1 increases the translational rates of its mRNA targets (Wang et al, 2014), YTHDF2 induces mRNA decay (Du et al, 2016), and YTHDF3 promotes the function of YTHDF1 and YTHDF2

Methods

Results

Conclusion