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Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia

ABSTRACT: Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia

PROVIDER: PRJNA822796 | ENA |

REPOSITORIES: ENA

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Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA sclera]

Project description:During postnatal development, the optical geometry of the eye is refined through a process called emmetropization. During eye emmetropization, optical defocus triggers a signaling cascade that originates in the retina, propagates across other ocular tissues and results in scleral wall remodeling. This signaling is associated with large-scale changes in gene expression, which was extensively studied at the mRNA level. Although several studies investigated the role of non-coding RNAs in eye emmetropization, the role of microRNAs (miRNAs) and other non-coding RNAs remains poorly understood. We performed a genome-wide analysis of the miRNA-mRNA gene regulatory networks underlying optical-defocus-induced myopia using massive parallel RNA sequencing (RNA-seq). Our analysis revealed a widespread involvement of miRNAs in optical defocus perception and visually guided eye emmetropization underlying myopia development. We found that a relatively small number of miRNAs (39 miRNAs total) regulate expression of over 450 mRNAs, or 59% of all mRNAs differentially expressed in the eyes of mice with optical-defocus-induced myopia. MiRNAs were also found to be involved in the regulation of the absolute majority of the biological processes and signaling pathways underlying visually guided eye emmetropization and myopia.

2025-04-03 | GSE200053 | GEO

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA retina]

2025-04-03 | GSE200051 | GEO

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA sclera]

2025-04-03 | GSE200049 | GEO

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA retina]

2025-04-03 | GSE200048 | GEO

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA retina]

Project description:Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA retina]

| PRJNA822802 | ENA

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA sclera]

Project description:Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA sclera]

| PRJNA822801 | ENA

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA sclera]

Project description:Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA sclera]

| PRJNA822803 | ENA

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA retina]

Project description:Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [miRNA retina]

| PRJNA822804 | ENA

Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-04-03 | GSE200054 | GEO

Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth

Project description:Postnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development. To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.

2023-09-05 | GSE235684 | GEO

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