Unraveling the Genetic Landscape of Eye Migration and Visual Adaptation during Flatfish Metamorphosis
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PROVIDER: PRJNA1029643 | ENA |
REPOSITORIES: ENA
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Project description:Flatfish have evolved their visual system to meet the demands of their environment through a fascinating process of metamorphosis. This morphological transformation involves a significant change in lifestyle from pelagic to benthic, accompanied by changes in body structure to achieve an asymmetrical flat shape. However, the fundamental change lies in the migration of one eye from its original position to the opposite location on the body. Although the role of thyroid hormone in triggering flatfish metamorphosis is well established, the specific gene regulatory network responsible for this extraordinary eye migration is still unknown. Here we show a global view through the creation of a general map of gene expression during the metamorphic process, encompassing both migrant and non-migrant eyes. Our research uncovers significant differences between migrant and non-migrant eyes of turbot in the pre-metamorphic and climax phases, emphasizing genetic disparities crucial for benthic adaptation.
2024-02-06 | GSE245741 | GEO
Project description:Flatfish undergo a remarkable metamorphosis from symmetrical pelagic larvae to fully asymmetrical benthic juveniles. The most distinctive features of this transformation is the migration of one eye. The molecular role of thyroid hormone in the metamorphosis process in flatfishes is well established. However, the regulatory network that facilitates eye movement remains enigmatic. This paper presents a morphological investigation of the metamorphic process in turbot eyes, using advanced imaging techniques and a global view of gene expression. The study covers migrant and non-migrant eyes and aims to identify the genes that are active during ocular migration. Our transcriptomic analysis shows a significant up-regulation of immune-related genes. The analysis of eye-specific genes reveals distinct patterns during the metamorphic process. Myosin is highlighted in the non-migrant eye, while ependymin is highlighted in the migrant eye, possibly involved in optic nerve regeneration. Furthermore, a potential association between the alx3 gene and cranial restructuring has been identified. Additionally, it confirmed simultaneous adaptation to low light in both eyes, as described by changes in opsins expression during the metamorphic process. The study also revealed that ocular migration activates systems asynchronously in both eyes, providing insight into multifaceted reorganization processes during metamorphosis of flatfish.
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Project description:Visual deprivation, either in the form of dark rearing (DR) or monocular deprivation (MD) are established paradigms for studying cortical plasticity. We have used miRNA microarray to uncover miRNAs whose expression is altered in primary visual cortex following DR and/or MD. C57BL6 mice were reared in normal light and dark conditions (control) till P28, in complete darkness since birth (DR) till P28, or were grown in normal light/dark conditions from birth till P24 and then subjected to lid suturing of one eye till P28. Mice were euthanized at P28 and their primary visual cortex areas were excised and subjected to RNA isolation. In the case of MD mice only the contralateral to lid suture primary visual cortex was extracted. 100ng of total RNA (tested and quantified using the Agilent Bioanalyzer 2100) were labeled using the Agilent miRNA labeling system and hybridized to Agilent murine miRNA arrays. Microarrays were hybridized overnight at 64 ºC, scanned using an Agilent scanner and extracted with Agilent feature extractor 10.1.
2011-09-03 | E-GEOD-31536 | biostudies-arrayexpress
Project description:Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.
2023-02-16 | GSE215396 | GEO
Project description:Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.
2023-02-15 | GSE215395 | GEO
Project description:The formation of the visual system is a complex multistep process that includes the establishment of proper connectivity of retinal ganglion cell (RGC) axon terminals with their relay neurons located in the brain. In mammals, the assembly of the different components of the visual circuit occurs at perinatal stages before eye opening. Upon reaching the target nuclei RGC axons extensively arborize and subsequently refine to establish the final connections. Spontaneous activity generated in the immature retina plays an essential role in the refinement of visual terminals at the main image-forming nuclei (IFN) that follow an eye-specific and retinotopic organization. However, the molecular mechanisms underlying spontaneous activity-dependent axon remodeling, and the influence of this activity in the connectivity of non-image forming nuclei (NIFN) that lack precise retinotopic maps and/or eye-specific segregation, are not well known. Here, by generating conditional mice with disturbed spontaneous retinal aneactivity and analyzing their retinal transcriptomic profiles, we identified novel players involved in axon refinement at the visual nuclei (e. g. Syt13). The analysis of visual projections in the NIFN of these mice revealed that correlated-retinal activity shapes final connectivity in non retinotopic or eye-specific segregating visual nuclei.
2024-10-09 | GSE193498 | GEO
Project description:The present study aims to apply a high-resolution and label-free proteomics approach to identify and quantify proteins in the eye of zebrafish. First, the results of the present study will provide a comprehensive list of proteins in the eye of zebrafish, and second, establish a platform based on sex-biased proteins that may offer clues to answer crucial questions such as sex-based differences in visual perception and impairments. Our results may improve the outcome of behavioural, developmental, toxicological, and medical experiments considering the zebrafish eye.
2024-03-04 | PXD033338 | Pride
Project description:Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis
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Project description:Eye photoreceptor membrane discs in outer rod segments are highly enriched in the visual pigment rhodopsin and the omega-3 fatty acid docosahexaenote (DHA). The eye acquires DHA from blood, but transporters for DHA uptake across the blood-retinal barrier (BRB) or retinal pigment epithelium have not been identified. Mfsd2a is a newly described sodium-dependent lysophosphatidylcholine symporter expressed at the BRB. Microarrays were used to determine difference in gene expression between wild-type and Mfsd2a KO eye cups.
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Project description:The graft-versus-host disease (GVHD) associated dry eye disease usually leads to refractory pain and visual impairment with limited treatments currently. Here we found exosome derived from mesenchymal stromal cell (MSC-exo) administered as eye drops significantly alleviates GVHD-associated dry eye disease in human and mouse models. To find out the essential elements during exosome treatment, we performed miRNA sequencing of exosomes derived from MSCs and L929 cells, and identified miR-204 in MSC-exo benefited the recovery of dry eye, which targeted IL-6/IL-6R/Stat3 signaling. Blockade of miR-204 abolished the therapeutic effect of MSC-exo while miR-204 overexpression from L929-exo markedly attenuates dry eye. Thus MSC-exo eye drops are efficacious in treating GVHD-associated dry eye and highlight miR-204 as a potential therapeutic agent.
2022-01-19 | GSE166585 | GEO