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Nuclear Organization of Lens Epithelium and Fiber Cells in Newborn Lens

ABSTRACT: Cellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels within the nucleus. Sequence-specific DNA-binding transcription factor CTCF EDIT. Topologically associated domains (TADs). Using Hi-C, we investigated changes in chromatin organization between newborn (P0.5) mouse lens fiber and epithelium and compared them to embryonic stem (ES) cells. Compartments A and B. Using ChIP-seq, we determined localization of CTCF in both lens tissues Formation of lens-specific TADs is demonstrated via comparative studies of chromatin at Pax6, Prox1, Gata3, Hsf4, and crystallin loci (to be updated) between lens and ES cell nuclei. Our study has generated the first data on nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE243851 | GEO | 2023/10/16

REPOSITORIES: GEO

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Project description:Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular composition of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein composition between the lens epithelium and fibers, we employed tandem mass spectrometry (2DLC/ MS) analysis of micro-dissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular process and subcellular localization, were adapted for lens. Expression levels of both epithelial and fiber proteomes were compared with their temporal and spatial mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins, translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown function in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets established reference mouse lens epithelium and fiber cell proteomes, provided quantitative analyses of protein and RNA-Seq data, and probed the major proteome remodeling required to form the mature lens fiber cells.

Dataset Information

Nuclear Organization of Lens Epithelium and Fiber Cells in Newborn Lens

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