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A Method for Measuring RNA N6-methyladenosine Modifications in Cells and Tissues
Published on: December 5, 2016
Alteration of N6-methyladenosine epitranscriptome profile in lipopolysaccharide-induced mouse mesangial cells
Tao Liu1,2, Xing Xing Zhuang2,3, Xiu Juan Qin1
1Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.
Abstract:
N6-Methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in eukaryotes. The underlying molecular mechanisms of m6A modification in chronic glomerulonephritis (CGN) remain unexplored. Here, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) analyses to assess the alterations of epitranscriptome-wide m6A profile in lipopolysaccharide (LPS)-induced mouse mesangial cells (MMC). The results of our data showed 2153 significantly differential m6A peaks and 358 significantly differentially expressed genes. Furthermore, integrated analysis from MeRIP-seq and RNA-seq identified a total of 64 genes with differential m6A modification and expressed levels, of which 5 genes displayed hypermethylation and upregulation, 42 genes displayed hypermethylation and downregulation, 11 genes displayed hypomethylation and upregulation, and 8 genes displayed hypomethylation and downregulation. Many of them (including Fosl1, Sorbs1, Ambp, Fgfr3, Nedd9, Fgg, Trim13, Fgf22, Mylk, and Muc6) are implicated in the regulation of the immune and inflammatory response. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis found that differential 64 genes were mainly enriched in fatty acid oxidation, apoptosis signaling pathway, complement and coagulation cascades, and PPAR signaling pathway. Together, our study provided a new perspective on the understanding of molecular features of m6A modification in CGN pathogenic pathogenesis.
Insights
N6-Methyladenosine (m6A) RNA modifications are altered in chronic glomerulonephritis (CGN). This study reveals key m6A changes in mouse mesangial cells, offering new insights into CGN pathogenesis.
Area of Science:
- Molecular Biology
- Epigenetics
- Immunology
Background:
- N6-Methyladenosine (m6A) is the most common internal modification of messenger RNA (mRNA) in eukaryotes.
- The role of m6A modification in the pathogenesis of chronic glomerulonephritis (CGN) is currently unknown.
Purpose of the Study:
- To investigate the epitranscriptome-wide m6A profile alterations in lipopolysaccharide (LPS)-induced mouse mesangial cells (MMC) relevant to CGN.
- To identify genes with differential m6A modification and expression levels in the context of CGN.
Main Methods:
- Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was employed to map m6A peaks.
- RNA sequencing (RNA-seq) was used to assess gene expression levels.
- Integrated analysis of MeRIP-seq and RNA-seq data was performed.
Main Results:
- The study identified 2153 differential m6A peaks and 358 differentially expressed genes.
- A total of 64 genes exhibited differential m6A modification and expression, categorized by hyper/hypomethylation and up/downregulation.
- Enriched pathways included fatty acid oxidation, apoptosis, complement and coagulation cascades, and PPAR signaling.
Conclusions:
- This research provides a comprehensive overview of m6A modification changes in LPS-induced mouse mesangial cells.
- The findings offer novel molecular insights into the pathogenesis of chronic glomerulonephritis.
- Specific genes involved in immune and inflammatory responses were identified with altered m6A profiles.
