{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Roxana Radu A."],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16049"],"description":["Stargardt disease (STGD1), the most common inherited juvenile macular degeneration, is caused by biallelic mutations in the ABCA4 gene. Currently, there is no approved treatment. In this study, we investigated early-stage epigenomic changes in the retinal pigment epithelium (RPE) of Abca4-/- mice, a well-established model of STGD1. Reduced representation bisulfite sequencing (RRBS) revealed hypermethylation of gene regions associated with disease-related pathways, implicating methyl-CpG-binding protein 2 (MeCP2) and RE1-silencing transcription factor (REST) as potential regulators. Notably, DNA methylation of a subset of genes preceded their transcriptional change and disease phenotypes in Abca4-/- RPE. Together with the detected age-dependent increase in MeCP2 levels in Abca4-/- RPE, these findings suggest that early DNA methylation changes may contribute to RPE dysfunction and eventual cell loss in STGD1."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Mice were euthanized by cervical dislocation, and eyes were harvested for obtaining RPE/eyecup separated from neural retina. In 1x phosphate buffer saline (PBS, pH 7.4), the anterior segment of the eye was removed, followed by the separation of the neural retina from the eyecup. RPE/Eyecups were stored in a −80 °C freezer until further processing.","Library Construction - RRBS libraries were prepared by a Zymo-Seq RRBS Library kit (Zymo research, Irvine, CA, USA, Cat# D5460). The libraries were subjected to size selection using magnetic AMPure XP beads (Beckman Coulter Life Sciences, Indianapolis, IN, USA) to enrich DNA fragments of the desired size. The quality control of the final libraries (size-selected and barcoded) was performed using an Agilent TapStation 4200 (D1000, D5000; Agilent Technologies, Santa Clara, CA, USA).","Sequencing - Pooled libraries were run on a NovaSeq 6000 as 100 bp single-end reads (Illumina, San Diego, CA, USA).","Nucleic Acid Extraction - DNA was extracted from mice, one RPE/eyecup per sample, using the Dneasy Blood & Tissue Kit (Qiagen, Hilden, Germany, Cat# 69506). DNA was eluted in 50 μL AE Buffer. The concentration was measured with a Qubit instrument (Life Technologies, Carlsbad, CA, USA), and 100 ng of genomic DNA was treated with RNAse enzyme at 37 °C for 30 min to remove contaminating RNA."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were aligned to the mm10 mouse reference genome (GCF_000001635.26) using Bsbolt, followed by methylation calling using default parameters. Unsupervised and differential methylation analyses were conducted with RnBeads2. Briefly, sites were filtered based on coverage of 10 or more across 80% of the samples. Here, 653489 sites met the criteria. Methylation values were calculated as a value between 0 and 1, where 0 is not methylated and 1 is fully methylated. One sample was flagged as an outlier and removed from downstream analysis. Differential methylation analysis was performed using hierarchical linear models from the limma package and fitted using an empirical Bayes model as implemented in the RnBeads2 package. Sites were considered differentially methylated if they reached an FDR-corrected significance level below 0.05 and a difference in the methylation value between the two groups of at least 10%. Differentially methylated sites were then annotated using the annotatr package in R and ChipSeeker. Percentage distribution of CpGs and DMCs on genomic regions was derived from the summarize_annotations() function from the annotatr package, and the results were represented as percentages of the total number of CpG sites. Gene ontology and enrichment analysis were performed using clusterProfiler and Metascape (v3.5.20250701) with the mouse reference genome as a background."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["n/a","Illumina NovaSeq 6000"],"study_type":["Bisulfite-seq"],"species":["Mus musculus"],"pubmed_authors":["Roxana Radu A."],"additional_accession":[]},"is_claimable":false,"name":"Dysregulated DNA Methylation in Abca4-/- Retinal Pigment Epithelium: Insights into Early Stage of Stargardt Disease","description":"Stargardt disease (STGD1), the most common inherited juvenile macular degeneration, is caused by biallelic mutations in the ABCA4 gene. Currently, there is no approved treatment. In this study, we investigated early-stage epigenomic changes in the retinal pigment epithelium (RPE) of Abca4-/- mice, a well-established model of STGD1. Reduced representation bisulfite sequencing (RRBS) revealed hypermethylation of gene regions associated with disease-related pathways, implicating methyl-CpG-binding protein 2 (MeCP2) and RE1-silencing transcription factor (REST) as potential regulators. Notably, DNA methylation of a subset of genes preceded their transcriptional change and disease phenotypes in Abca4-/- RPE. Together with the detected age-dependent increase in MeCP2 levels in Abca4-/- RPE, these findings suggest that early DNA methylation changes may contribute to RPE dysfunction and eventual cell loss in STGD1.","dates":{"release":"2025-11-04T00:00:00Z","modification":"2026-05-27T15:25:49.888Z","creation":"2025-11-03T13:39:16.29Z"},"accession":"E-MTAB-16049","cross_references":{"ENA":["ERP183580"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003753","EFO_0005518","EFO_0003816","EFO_0004184"]}}