Figure - available from: Epigenetics & Chromatin
This content is subject to copyright. Terms and conditions apply.
Comparison of methylation between lens and non-lens cells at Pax6 and Six3 loci. APax6 locus including Pax6os1. All lens and NPC samples exhibit a broad continuous ~ 38 kb domain of reduced DNA methylation (boxed in the NPC track) in all four lens samples with the lowest signal across this region in E14.5 lens epithelium. BSix3 locus including Six3os1. The region of low methylation in NPC is boxed. The individual tracks include evolutionarily conserved regions and DNA methylation in E14.5 lens epithelium (epi), E14.5 lens fibers, P0.5 lens epithelium (epi), P0.5 lens fibers, NPC and ES cells
Source publication
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 f...
Citations
... Given that changes in DNA methylation are often associated with changes in chromatin accessibility [15], we sought to evaluate chromatin accessibility within the ID4 gene. To address this, we conducted an in silico approach using ATAC-seq data obtained from 72 breast cancer patients in the GDC-TCGA cohort. ...
Purpose
Inhibitor of differentiation 4 (ID4) is a dominant-negative regulator of basic helix–loop–helix (bHLH) transcription factors. The expression of ID4 is dysregulated in various breast cancer subtypes, indicating a potential role for ID4 in subtype-specific breast cancer development. This study aims to elucidate the epigenetic regulation of ID4 within breast cancer subtypes, with a particular focus on DNA methylation and chromatin accessibility.
Methods
Bioinformatic analyses were conducted to assess DNA methylation and chromatin accessibility in ID4 regulatory regions across breast cancer subtypes. Gene Set Enrichment Analysis (GSEA) was conducted to identify related gene sets. Transcription factor binding within ID4 enhancer and promoter regions was explored. In vitro experiments involved ER+ breast cancer cell lines treated with estradiol (E2) and Tamoxifen.
Results
Distinct epigenetic profiles of ID4 were observed, revealing increased methylation and reduced chromatin accessibility in luminal subtypes compared to the basal subtype. Gene Set Enrichment Analysis (GSEA) implicated estrogen-related pathways, suggesting a potential link between estrogen signaling and the regulation of ID4 expression. Transcription factor analysis identified ER and FOXA1 as regulators of ID4 enhancer regions. In vitro experiments confirmed the role of ER, demonstrating reduced ID4 expression and increased methylation with estradiol treatment. Conversely, Tamoxifen treatment increased ID4 expression, indicating the potential involvement of ER signaling through ERα in the epigenetic regulation of ID4 in breast cancer cells.
Conclusion
This study shows the intricate epigenetic regulation of ID4 in breast cancer, highlighting subtype-specific differences in DNA methylation and chromatin accessibility.
... A study of liver biopsy samples from individuals with NAFLD revealed a negative association between methylation levels at the promoter region of the PGC1α gene, which controls the process of fatty acid oxidation, and its expression. Furthermore, a significant direct correlation was found between methylation levels and insulin resistance [100]. ...
Non-alcoholic fatty liver disease (NAFLD) has become one of the most frequent chronic liver diseases worldwide in recent decades. Metabolic diseases like excessive blood glucose, central obesity, dyslipidemia, hypertension, and liver function abnormalities cause NAFLD. NAFLD significantly increases the likelihood of liver cancer, heart disease, and mortality, making it a leading cause of liver transplants. Non-alcoholic steatohepatitis (NASH) is a more advanced form of the disease that causes scarring and inflammation of the liver over time and can ultimately result in cirrhosis and hepatocellular carcinoma. In this review, we briefly discuss NAFLD's pathogenic mechanisms, their progression into NASH and afterward to NASH-related cirrhosis. It also covers disease epidemiology, metabolic mechanisms, glucose and lipid metabolism in the liver, macrophage dysfunction, bile acid toxicity, and liver stellate cell stimulation. Additionally, we consider the contribution of intestinal microbiota, genetics, epigenetics, and ecological factors to fibrosis progression and hepatocellular carcinoma risk in NAFLD and NASH patients.
... Many amino acid residues, mostly at the N-terminal tail protruding out of the core histone, are subjected to covalent post-translational modifications. The rate of transcription of a gene is affected by different sites/degrees of histone modifications (e.g., H3K27ac, H3K9me2, H3K9me3, and H3K27me3), which influence the association between DNA and histone proteins, thus affecting the chromatin accessibility [20][21][22]. In addition, histone modifications are recognized by proteins like ATP-dependent chromatin remodelers which affect local chromatin status and regulate the expression of the gene [19,23]. ...
Genetic information in eukaryotic organisms is stored, replicated, transcribed, and inherited through the nucleus of a cell. Epigenetic modifications in the genetic material, including DNA methylation, histone modification, changes in ncRNA biogenesis and chromatin architecture, play important roles in determining the genomic landscape and regulating gene expression. Genome architecture (structural features of chromatin, affected by epigenetic modifications) is a major driver of genomic functions/activities. Segregation of euchromatin (transcriptionally active) from heterochromatin (transcriptionally repressed chromosome) and positioning of genes in specific nuclear space in eukaryotic cells emphasise non-randomness in the organization of the genetic information. Not only does the base sequence of a gene carry the genetic information but the covalent modifications of bases, three-dimensional positioning of the genome, and chromatin loops are vital for switching on/off the gene and regulating its expression during growth/environmental stress. The epigenetic dynamics depend on the activities of writers and erasers under changing environmental conditions. The discovery of non-coding RNAs (one of the players in de novo methylation of DNA), increased DNA methylation protein (guide for the DNA demethylase), and methylation monitoring sequence (that helps keep a balance between DNA demethylation and methylation) have been some of the new developments in the era of epigenomics. To respond to environmental stimuli, plants depend on modulating gene expression through different mechanisms including biochemical, molecular, genetic, and epigenetic alterations. Studies on plants might provide better insights into epigenetic stress memory and molecular bases of adaptability to enable (epi)genome editing of crops for climate resilience and sustainable agriculture in the present era of multifaceted climate change.
... Additionally, the study of Disatham et al. also described chromatin accessibility profiles across these lens regions, allowing correlation between the state of chromatin and RNA abundance in a coarse spatial manner (Disatham et al., 2019). Other studies performed in the mouse focused on establishing correlation between chromatin state and gene expression in whole lenses (Sun et al., 2015) or in isolated epithelial and fiber cells (Chang et al., 2023;Zhao et al., 2019b). ...
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataracts. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq and CUT&RUN-seq to discover previously unreported mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Furthermore, we identify an epigenetic paradigm of cellular differentiation, defined by progressive loss of the H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
... In addition to RNA-seq, the latter study also described global chromatin accessibility profiles related to these distinct lens regions, thus allowing correlation between the state of the chromatin and RNA abundance in a coarse spatial manner across the tissue 43 . Other studies performed in the mouse similarly focused on defining the correlation between chromatin state and gene expression in either whole lenses 57 or the isolated epithelium and fiber cells 58,59 . While helpful, advanced technologies now allow new opportunities to investigate developing tissues and their underlying molecular networks at singlecell resolution. ...
Ocular lens development entails epithelial to fiber cell differentiation, defects in which cause congenital cataract. We report the first single-cell multiomic atlas of lens development, leveraging snRNA-seq, snATAC-seq, and CUT&RUN-seq to discover novel mechanisms of cell fate determination and cataract-linked regulatory networks. A comprehensive profile of cis- and trans-regulatory interactions, including for the cataract-linked transcription factor MAF, is established across a temporal trajectory of fiber cell differentiation. Further, we divulge a conserved epigenetic paradigm of cellular differentiation, defined by progressive loss of H3K27 methylation writer Polycomb repressive complex 2 (PRC2). PRC2 localizes to heterochromatin domains across master-regulator transcription factor gene bodies, suggesting it safeguards epithelial cell fate. Moreover, we demonstrate that FGF hyper-stimulation in vivo leads to MAF network activation and the emergence of novel lens cell states. Collectively, these data depict a comprehensive portrait of lens fiber cell differentiation, while defining regulatory effectors of cell identity and cataract formation.
... In addition to PTMs, loading of the H3.3 histone variant onto chromatin seems to be required for neuronal differentiation and, in particular, for activation of mature neuronspecific genes [94,95]. For example, during mouse lens fiber cell differentiation, high concentrations of H3.3 were observed at the level of transcribed regions in chromatin, like those including genes encoding crystallins, gap junction components, and intermediate filaments [96]. Actually, H3.3, together with an H2A variant known as H2A.Z, contributes to opening chromatin structure to transcription factors, by increasing accessibility of the upstream regulatory sequences present in the genes to which they are bound [57,97,98]. ...
All the cells of an organism contain the same genome. However, each cell expresses only a minor fraction of its potential and, in particular, the genes encoding the proteins necessary for basal metabolism and the proteins responsible for its specific phenotype. The ability to use only the right and necessary genes involved in specific functions depends on the structural organization of the nuclear chromatin, which in turn depends on the epigenetic history of each cell, which is stored in the form of a collection of DNA and protein modifications. Among these modifications, DNA methylation and many kinds of post-translational modifications of histones play a key role in organizing the complex indexing of usable genes. In addition, non-canonical histone proteins (also known as histone variants), the synthesis of which is not directly linked with DNA replication, are used to mark specific regions of the genome. Here, we will discuss the role of the H3.3 histone variant, with particular attention to its loading into chromatin in the mammalian nervous system, both in physiological and pathological conditions. Indeed, chromatin modifications that mark cell memory seem to be of special importance for the cells involved in the complex processes of learning and memory.
... Recent advances in multiomics approaches including RNA-seq, assay for transposase accessible chromatin with sequencing (ATAC-seq), whole-genome bisulfite sequencing (WGBS), chromatin immunoprecipitation with sequencing (ChIP-seq), and cleavage under targets and release using nuclease (CUT&RUN) have enabled the assembly of genomewide data encompassing a wide-range of features and regulatory pathways important for lens differentiation [85,[101][102][103][104]. Analysis of these data has allowed for the integration of differentiation state-specific transcriptional networks with essential gene expressionspecific chromatin features that have confirmed the importance of a multitude of previously identified lens differentiation pathways and have identified entirely novel pathways as described below. ...
... To identify evolutionarily conserved transcription factors most associated with open chromatin regions near differentially expressed genes in lens differentiation, open chromatin regions identified in ATAC-seq data obtained from E13 microdissected chicken lenses [48] and ATAC-seq data obtained from E14.5 microdissected mouse lenses [104] were reanalyzed to identify the nearest gene transcription start site for each open chromatin region. DNA sequences contained within open chromatin regions nearest to the evolutionarily conserved epithelial cell genes and those nearest to the evolutionarily conserved fiber cell genes were separately submitted to the AME tool [163] from MEME-Suite [164] to identify the significantly enriched transcription factor motifs from the JASPAR database [173] (Figures 9 and 10). ...
... Whole-genome bisulfite sequencing (WGBS) has been instrumental in understanding the complex mechanisms of lens differentiation, as demonstrated by two recent studies examining the role of DNA methylation in this process [102,104]. These studies have provided new insights into the relationship between DNA methylation, chromatin accessibility, and gene expression during lens differentiation. ...
Recent advances in next-generation sequencing and data analysis have provided new gateways for identification of novel genome-wide genetic determinants governing tissue development and disease. These advances have revolutionized our understanding of cellular differentiation, homeostasis, and specialized function in multiple tissues. Bioinformatic and functional analysis of these genetic determinants and the pathways they regulate have provided a novel basis for the design of functional experiments to answer a wide range of long-sought biological questions. A well-characterized model for the application of these emerging technologies is the development and differentiation of the ocular lens and how individual pathways regulate lens morphogenesis, gene expression, transparency, and refraction. Recent applications of next-generation sequencing analysis on well-characterized chicken and mouse lens differentiation models using a variety of omics techniques including RNA-seq, ATAC-seq, whole-genome bisulfite sequencing (WGBS), chip-seq, and CUT&RUN have revealed a wide range of essential biological pathways and chromatin features governing lens structure and function. Multiomics integration of these data has established new gene functions and cellular processes essential for lens formation, homeostasis, and transparency including the identification of novel transcription control pathways, autophagy remodeling pathways, and signal transduction pathways, among others. This review summarizes recent omics technologies applied to the lens, methods for integrating multiomics data, and how these recent technologies have advanced our understanding ocular biology and function. The approach and analysis are relevant to identifying the features and functional requirements of more complex tissues and disease states.
Background
Nuclear organization of interphase chromosomes involves individual chromosome territories, “open” and “closed” chromatin compartments, topologically associated domains (TADs) and chromatin loops. The DNA- and RNA-binding transcription factor CTCF together with the cohesin complex serve as major organizers of chromatin architecture. Cellular differentiation is driven by temporally and spatially coordinated gene expression that requires chromatin changes of individual loci of various complexities. Lens differentiation represents an advantageous system to probe transcriptional mechanisms underlying tissue-specific gene expression including high transcriptional outputs of individual crystallin genes until the mature lens fiber cells degrade their nuclei.
Results
Chromatin organization between mouse embryonic stem (ES) cells, newborn (P0.5) lens epithelium and fiber cells were analyzed using Hi-C. Localization of CTCF in both lens chromatins was determined by ChIP-seq and compared with ES cells. Quantitative analyses show major differences between number and size of TADs and chromatin loop size between these three cell types. In depth analyses show similarities between lens samples exemplified by overlaps between compartments A and B. Lens epithelium-specific CTCF peaks are found in mostly methylated genomic regions while lens fiber-specific and shared peaks occur mostly within unmethylated DNA regions. Major differences in TADs and loops are illustrated at the ~ 500 kb Pax6 locus, encoding the critical lens regulatory transcription factor and within a larger ~ 15 Mb WAGR locus, containing Pax6 and other loci linked to human congenital diseases. Lens and ES cell Hi-C data (TADs and loops) together with ATAC-seq, CTCF, H3K27ac, H3K27me3 and ENCODE cis-regulatory sites are shown in detail for the Pax6, Sox1 and Hif1a loci, multiple crystallin genes and other important loci required for lens morphogenesis. The majority of crystallin loci are marked by unexpectedly high CTCF-binding across their transcribed regions.
Conclusions
Our study has generated the first data on 3-dimensional (3D) nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells. These findings generate novel insights into lens-specific transcriptional gene control, open new research avenues to study transcriptional condensates in lens fiber cells, and enable studies of non-coding genetic variants linked to cataract and other lens and ocular abnormalities.
Objective
Cold shock proteins such as YB-1 (ybx1) function in the regulation of transcription, mRNA stability, and translation. Consequently, YB-1 contributes to differentiation, stress responses and oncogenesis. Eye development is a complex process involving the differentiation of a signifiant number of cell-types with distinct functions. Additionally, the adult eye is exposed to UV-radiation causing significant oxidative stress. We therefore hypothesized that YB-1 plays a role in eye development as well as stress defence. As a first step to understand YB-1 function in this context, we analyzed its expression in the developing and adult mouse eye by immunohistochemistry.
Results
Expression of the YB-1 protein in the developing mouse eye at stages (E12, E15 and E18) and in adult eyes (P14) was detected in all retinal cells and in cells of the cornea and the lens epithelium at all stages investigated. These findings support a significant function of YB-1 in the eye, may be related to development and differentiation.
