ArticleEpigenetics & chromatin2023
Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation.
Article in Epigenetics & chromatin, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 39 citations in OpenAlex.
- Multi-omics characterization of chronic social defeat stress recall-activated nuclei in Arc-GFP mice.Molecular psychiatry · 2026Article
- The role of DNMT3B, GSK-3β and GJA3 in lens epithelial cell apoptosis and age-related cataract.BMC ophthalmology · 2026Article
- A comparison of differential DNA methylation analysis methods for continuous outcomes: implications for epigenetic studies.Epigenomics · 2026Article
- Integrated analysis of DNA methylome and transcriptome of the backfat and longissimus dorsi muscle of Chinese-European hybrid pigs.BMC genomics · 2026Article
- Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.BMC genomics · 2026Article
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- Unraveling the interplay of DNA methylation and chromosome organization.Biochemical Society transactions · 2025Review
- Targeting TET3 suppresses group 3 medulloblastoma stemness and progression via impairing hypomethylation of Otx2 super-enhancer.Cell reports. Medicine · 2025Article
- Key post-translational modifications of crystallin: from mechanism to target exploration for cataract diagnosis and treatment.Molecular biology reports · 2025Review
- Hypoxia-Driven Histone Modifications Govern Gene Regulation for Mature Eye Lens Formation.Investigative ophthalmology & visual science · 2025Article
- Immunohistochemical analysis of YB-1 expression in the developing mouse eye.European journal of histochemistry : EJH · 2025Article
- DNA Methylation Dynamics in a Mouse Model of Retinitis Pigmentosa.The American journal of pathology · 2025Article
- Targeting epigenetic regulators as a promising avenue to overcome cancer therapy resistance.Signal transduction and targeted therapy · 2025Review
- Mettl3 Regulates Lens Development by Promoting the Differentiation Processes of Secondary Fiber Cells.Investigative ophthalmology & visual science · 2025Article
- Endocrine-disrupting chemicals (EDCs) and epigenetic regulation in embryonic development: Mechanisms, impacts, and emerging trends.Toxicology reports · 2025Review
- Molecular regulation of whole genome DNA methylation in heat stress response of dairy cows.BMC genomics · 2025Article
- Induction of DNA Demethylation: Strategies and Consequences.Epigenomes · 2025Review
- Aging activates escape of the silent X chromosome in the female mouse hippocampus.Science advances · 2025Article
- Integrated multiomics signatures to optimize the accurate diagnosis of lung cancer.Nature communications · 2025Article
- Comprehensive computational analysis via Adverse Outcome Pathways and Aggregate Exposure Pathways in exploring synergistic effects from radon and tobacco smoke on lung cancer.Frontiers in public health · 2025Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
backgroundCellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels. DNA methylation represents a universal mechanism to control chromatin organization and its accessibility. Cytosine methylation of CpG dinucleotides regulates binding of methylation-sensitive DNA-binding transcription factors within regulatory regions of transcription, including promoters and distal enhancers. Ocular lens differentiation represents an advantageous model system to examine these processes as lens comprises only two cell types, the proliferating lens epithelium and postmitotic lens fiber cells all originating from the epithelium.
resultsUsing whole genome bisulfite sequencing (WGBS) and microdissected lenses, we investigated dynamics of DNA methylation and chromatin changes during mouse lens fiber and epithelium differentiation between embryos (E14.5) and newborns (P0.5). Histone H3.3 variant chromatin landscapes were also generated for both P0.5 lens epithelium and fibers by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Tissue-specific features of DNA methylation patterns are demonstrated via comparative studies with embryonic stem (ES) cells and neural progenitor cells (NPCs) at Nanog, Pou5f1, Sox2, Pax6 and Six3 loci. Comparisons with ATAC-seq and RNA-seq data demonstrate that reduced methylation is associated with increased expression of fiber cell abundant genes, including crystallins, intermediate filament (Bfsp1 and Bfsp2) and gap junction proteins (Gja3 and Gja8), marked by high levels of histone H3.3 within their transcribed regions. Interestingly, Pax6-binding sites exhibited predominantly DNA hypomethylation in lens chromatin. In vitro binding of Pax6 proteins showed Pax6's ability to interact with sites containing one or two methylated CpG dinucleotides.
conclusionsOur study has generated the first data on methylation changes between two different stages of mammalian lens development and linked these data with chromatin accessibility maps, presence of histone H3.3 and gene expression. Reduced DNA methylation correlates with expression of important genes involved in lens morphogenesis and lens fiber cell differentiation.
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