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Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

ABSTRACT: Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

PROVIDER: PRJNA666388 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12739817_1.fastq.gz	Fastqsanger.gz
	SRR12739817_2.fastq.gz	Fastqsanger.gz
	SRR12739818_1.fastq.gz	Fastqsanger.gz
	SRR12739818_2.fastq.gz	Fastqsanger.gz
	SRR12739819_1.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection

Project description:Refractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina. Here, we used genome-wide RNA-sequencing (RNA-seq) to conduct analysis of the retinal genetic networks underlying contrast perception and refractive eye development. We report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus. Together, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.

2021-06-03 | GSE158732 | GEO

Genome-wide analysis of gene regulatory networks in chickens reveals dynamic temporal changes in retinal signaling cascade underlying compensation to lens-imposed optical defocus [1d]

Project description:During postnatal development, the optical geometry of the eye is refined through a process called emmetropization. During eye emmetropization, positive optical defocus inhibits eye growth whereas negative optical defocus accelerates it. Increased exposure to negative optical defocus leads to the development of myopia. Although several studies investigated gene regulatory networks underlying retinal response to optical defocus, temporal changes that occur during ocular response to optical defocus are poorly understood. Here, we performed a genome-wide analysis of the retinal gene regulatory networks underlying optical-defocus-induced myopia using massive parallel RNA sequencing (RNA-seq) in chickens exposed to negative optical defocus for 1, 3 and 6 days. Our analysis revealed large-scale dynamic temporal changes in the retinal signaling pathways involved in the eye’s response to negative optical defocus. We found that different sets of pathways and biological functions were involved in the early, sustained and delayed response to optical defocus causing myopia. These data refine signaling pathways that can be targeted for myopia control and provide a framework for the development of new treatment options for myopia.

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Genome-wide analysis of gene regulatory networks in chickens reveals dynamic temporal changes in retinal signaling cascade underlying compensation to lens-imposed optical defocus [6d]

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Genome-wide analysis of gene regulatory networks in chickens reveals dynamic temporal changes in retinal signaling cascade underlying compensation to lens-imposed optical defocus [3d]

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Genome-wide analysis of gene regulatory networks in chickens reveals dynamic temporal changes in retinal signaling cascade underlying compensation to lens-imposed optical defocus [control]

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Genome-wide analysis of gene regulatory networks in chickens reveals dynamic temporal changes in retinal signaling cascade underlying compensation to lens-imposed optical defocus [lens induced]

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Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection.

Project description:BackgroundRefractive eye development is regulated by optical defocus in a process of emmetropization. Excessive exposure to negative optical defocus often leads to the development of myopia. However, it is still largely unknown how optical defocus is detected by the retina.MethodsHere, we used genome-wide RNA-sequencing to conduct analysis of the retinal gene expression network underlying contrast perception and refractive eye development.ResultsWe report that the genetic network subserving contrast perception plays an important role in optical defocus detection and emmetropization. Our results demonstrate an interaction between contrast perception, the retinal circadian clock pathway and the signaling pathway underlying optical defocus detection. We also observe that the relative majority of genes causing human myopia are involved in the processing of optical defocus.ConclusionsTogether, our results support the hypothesis that optical defocus is perceived by the retina using contrast as a proxy and provide new insights into molecular signaling underlying refractive eye development.

| S-EPMC8190860 | biostudies-literature

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.

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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 retina]

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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 [miRNA sclera]

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