The Role of DNA Methylation in Lens Development and Cataract Formation

Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation

BACKGROUND

Cellular 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.

RESULTS

Using 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.

CONCLUSIONS

Our 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.

DNA Methylation in Atrial Fibrillation and Its Potential Role in Precision Medicine

Atrial fibrillation (AF), a common arrhythmia, can cause many serious consequences, including stroke and even death. The pathological mechanism of AF is very complicated. Epigenetic mechanisms, especially DNA methylation, contribute to the pathogenesis and maintenance of AF. DNA methylation is an important part of epigenetic and plays a significant role in human physiology and pathology. AF patients possess specific methylation sites (e.g., Pitx2c, RASSF1A, SURs, SERCA2a, and LINC00472), which have potential values of being biomarkers and underlie the diagnosis and prognosis of AF. These methylation sites can also benefit accurate treatment of AF. With deeper understanding into the epigenetic mechanisms of AF, the precision medicine for AF has also developed rapidly. In the future, DNA methylation omics and other research methods will be integrated to explore the epigenetic mechanisms in AF.

DNA methylation of miR-200 clusters promotes epithelial to mesenchymal transition in human conjunctival epithelial cells

Epithelial to mesenchymal transition (EMT) contributes to fibrosis associated pathologies including scarring of different ocular tissues. Recently targeting EMT is seen as an appropriate therapeutic approach for different fibrosis related eye diseases such as macular degeneration or glaucoma surgery related fibrosis. Nevertheless, for ocular surface diseases, target genes specific for particular cell type or condition are still undefined. This study aimed to expose the complex regulatory mechanisms that trigger EMT in human conjunctival epithelial (HCjE) cells. EMT was induced by prolonged treatment with two TGF-β isoforms, TGF-β1 and TGF-β2, and their combination. TGF-β1 showed the strongest potential for initiating EMT in HCjE cells, reflected on morphological changes, cell migration and the levels of mRNA expression of different epithelial (CDH1, OCLN, DSP) and mesenchymal (CDH2, FN1, VIM, SNAI1, ZEB2, TWIST1) marker genes. Co-treatment with the DNA demethylating agent 5-Azacytidine (5-AzaC) was capable of stopping the transition of HCjE cells towards a mesenchymal phenotype, based on morphological features, reduced cell mobility and mRNA and protein expression levels of epithelial and mesenchymal marker genes. An EMT qRT-PCR-based array revealed that EMT induced considerable alterations in gene expression, with downregulation of the majority of epithelial marker genes and upregulation of genes specific for the mesenchymal state. The major effect of 5-AzaC treatment was observed as a suppression of mesenchymal marker genes, suggesting the involvement of upstream negative regulator(s) whose promoter demethylation and subsequent expression will in turn promote EMT switch off. The expression level of miRNAs potentially important for EMT induction was determined using qRT-PCR-based array which pointed at members of miR-200 family as main regulators of EMT process in HCjE cells. 5-AzaC treatment induced increased expression of miR-200a, -200b, -200c and miR-141 towards the control level, indicating important role of DNA methylation in their regulation. The DNA methylation status of both miR-200 family clusters, analyzed with high-resolution melting (HRM) and bisulfite sequencing (Bis-Seq), revealed that TGF-β1-induced EMT was accompanied by increase in promoter CpG methylation of both miR-200 loci, which was reverted after 5-AzaC treatment. In conclusion, our results indicate that DNA demethylation of promoters of miR-200 loci is critically important for stopping and reverting the EMT in human conjunctival epithelial cells, suggesting the potential for the development of novel epigenetic-based therapeutic strategies for treating conjunctival conditions associated with EMT.

Epigenetic changes during ageing and their underlying mechanisms

As life expectancy increases worldwide, ageing and age-related diseases arise as a major issue for societies around the globe. Understanding the biological mechanisms underlying the ageing process is thus instrumental for the development of efficient interventions aimed to prevent and treat age-related conditions. Current knowledge in the biogerontology field points to epigenetics as a critical component of the ageing process, not only by serving as a bona-fide marker of biological age but also by controlling and conferring inheritability to cellular and organismal ageing. This is reflected by a myriad of evidences demonstrating the relationship between DNA methylation, histone modifications, chromatin remodeling and small non-coding RNAs and several age-related phenotypes. Given the reversibility of epigenetic alterations, epigenetic reprogramming may also be envisioned as a potential approach to treat age-related disorders. Here we review how different types of epigenetic mechanisms are involved in the ageing process. In addition, we highlight how interventions modulate epigenetics and thus promote health- and lifespan.

Epigenetic regulation of anterior segment diseases and potential therapeutics

In recent years, technological advances in sequencing have accelerated our understanding of epigenetics in ocular development and ophthalmic diseases. We now know that epigenetic modifications are necessary for normal ocular development and biological processes such as corneal wound healing and ocular surface repair, while aberrant epigenetic regulation underlies the pathogenesis of a wide range of ocular diseases, including cataracts and various diseases of the ocular surface. As the epigenetics of the eye is a constantly changing field of medicine, this comprehensive review focuses on innovations and scientific discoveries related to epigenetic control of anterior segment diseases that were published in the English literature in the past five years. These recent studies attempt to elucidate therapeutic targets for the anterior segment pathological processes. Already, recent studies have shown therapeutic potential in targeting epigenetic mechanisms of ocular diseases, and new epigenetic therapies are on the verge of being introduced to clinical practice. New drug targets can potentially emerge as we make further discoveries within this field.

Epigenetics-Shedding Light on the Path Ahead for Material Sciences

The harmonious regulation of bodily function is a necessity for healthy individuals. Looking from the viewpoint of material sciences, one can only marvel at the cellular factories, their renewal, and the overall control of messaging and control of responses. As aging progresses and/or pathologies arise, clinicians may be forced to look for replacement of organs/tissues with medical devices. Since all devices are tailored, a detailed understanding of developmental processes, including aberrant processes leading to pathologies, is crucial to provide clinicians with a suitable device. Although research in the field of epigenetics has produced effective therapeutics and diagnostic markers, our currently fragmented understanding of epigenetic processes as they relate to material development is inherently limited, with logical implications for the success of medical procedures. Here, we illustrate how material sciences for clinical applications, critically depend on all aspects of biomedical sciences, including the field of epigenetics.