همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

The Regulatory Role of DNA Methylation in Age-Related Macular Degeneration (AMD)

نویسندگان :

Shohreh Yazdani¹ Alireza Fotuhi Siahpirani²

1- Department of Bioinformatics, Kish International Campus, University of Tehran 2- Laboratory of Bioinformatics and Computational Genomics (LBCG), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran

کلمات کلیدی :

Age-Related Macular Degeneration (AMD)،Epigenetics،DNA Methylation،Gene Expression،MethReg

چکیده :

Age-related macular degeneration (AMD) is a leading cause of vision loss in the elderly, and understanding its molecular underpinnings is crucial for developing targeted therapies. Recent studies have focused on investigating how epigenetic changes such as DNA methylation affect this disease. Advani and colleagues have used methylation array to measure DNA methylation in 160 postmortem AMD and normal retina samples (Advani et al. 2024). Of these samples, 90 are included in a study by Ratnapriya and colleageus where RNA-seq was used to measure gene expression data in 523 AMD and normal postmortem samples (Ratnapriya et al. 2019). The methylation and RNA-seq datasets were retrieved from GEO database (GSE231536 and GSE115828 respectively). Differentially expressed genes (DEGs) and Differentially methylated probes (DMPs) were identified using DESeq2 and ChAMP packages. Next, we used MethReg package to identify distal DMPs that can affect the expression of DEGs. MethReg was designed to identify combinatorial effect of DNA methylation and transcription factor binding on gene expression (Silva et al. 2022). Using this package, we can identify transcription factors where changes in the DNA methylation of their binding site affects the expression of their target genes. The resulting regulatory network will improve our understanding of the underlying regulatory mechanisms in age-related macular degeneration.