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Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Pterygium by MeRIP Sequencing
Yaping Jiang1, Xin Zhang1, Xiaoyan Zhang2
1Department of Ophthalmology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.
Aim:
Pterygium is a common ocular surface disease, which is affected by a variety of factors. Invasion of the cornea can cause severe vision loss. N6-methyladenosine (m6A) is a common post-transcriptional modification of eukaryotic mRNA, which can regulate mRNA splicing, stability, nuclear transport, and translation. To our best knowledge, there is no current research on the mechanism of m6A in pterygium.
Methods:
We obtained 24 pterygium tissues and 24 conjunctival tissues from each of 24 pterygium patients recruited from Shanghai Yangpu Hospital, and the level of m6A modification was detected using an m6A RNA Methylation Quantification Kit. Expression and location of METTL3, a key m6A methyltransferase, were identified by immunostaining. Then we used m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq), RNA sequencing (RNA-seq), and bioinformatics analyses to compare the differential expression of m6A methylation in pterygium and normal conjunctival tissue.
Results:
We identified 2,949 dysregulated m6A peaks in pterygium tissue, of which 2,145 were significantly upregulated and 804 were significantly downregulated. The altered m6A peak of genes were found to play a key role in the Hippo signaling pathway and endocytosis. Joint analyses of MeRIP-seq and RNA-seq data identified 72 hypermethylated m6A peaks and 15 hypomethylated m6A peaks in mRNA. After analyzing the differentially methylated m6A peaks and synchronously differentially expressed genes, we searched the Gene Expression Omnibus database and identified five genes related to the development of pterygium (DSP, MXRA5, ARHGAP35, TMEM43, and OLFML2A).
Conclusion:
Our research shows that m6A modification plays an important role in the development of pterygium and can be used as a potential new target for the treatment of pterygium in the future.
Insights
N6-methyladenosine (m6A) modification is altered in pterygium, a common eye condition. This study identifies key genes and pathways involved, suggesting m6A as a potential therapeutic target for pterygium.
Area of Science:
- Ophthalmology
- Molecular Biology
- Epigenetics
Background:
- Pterygium is a prevalent ocular surface disease that can lead to vision impairment.
- N6-methyladenosine (m6A) is a crucial mRNA modification regulating gene expression, but its role in pterygium is unexplored.
Purpose of the Study:
- To investigate the role of m6A modification in the pathogenesis of pterygium.
- To identify specific genes and pathways affected by m6A dysregulation in pterygium.
Main Methods:
- Compared m6A modification levels in pterygium and normal conjunctival tissues using an m6A RNA Methylation Quantification Kit.
- Analyzed the expression and localization of METTL3, an m6A methyltransferase.
- Utilized m6A-RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) with bioinformatics analysis.
Main Results:
- Identified 2,949 dysregulated m6A peaks in pterygium tissue, with 2,145 upregulated and 804 downregulated.
- Found altered m6A peaks in genes associated with the Hippo signaling pathway and endocytosis.
- Identified five key genes (DSP, MXRA5, ARHGAP35, TMEM43, OLFML2A) linked to pterygium development through integrated analysis.
Conclusions:
- m6A modification is significantly dysregulated in pterygium development.
- The findings highlight m6A as a potential therapeutic target for pterygium treatment.
