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Updated: Jul 13, 2026
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
A microarray analysis of retinal transcripts that are controlled by image contrast in mice
Christine Brand1, Frank Schaeffel, Marita Pauline Feldkaemper
1Section for Neurobiology of the Eye, University Eye Hospital Tuebingen, Tuebingen, Germany.
Purpose:
The development of myopia is controlled by still largely unknown retinal signals. The aim of this study was to investigate the changes in retinal mRNA expression after different periods of visual deprivation in mice, while controlling for retinal illuminance.
Methods:
Each group consisted of three male C57BL/6 mice. Treatment periods were 30 min, 4 h, and 6+6 h. High spatial frequencies were filtered from the retinal image by frosted diffusers over one eye while the fellow eyes were covered by clear neutral density (ND) filters that exhibited similar light attenuating properties (0.1 log units) as the diffusers. For the final 30 min of the respective treatment period mice were individually placed in a clear Perspex cylinder that was positioned in the center of a rotating (60 degrees) large drum. The inside of the drum was covered with a 0.1 cyc/degree vertical square wave grating. This visual environment was chosen to standardize illuminances and contrasts seen by the mice. Labeled cRNA was prepared and hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays. Alterations in mRNA expression levels of candidate genes with potential biological relevance were confirmed by semi-quantitative real-time reverse transcription polymerase chain reaction (RT-PCR).
Results:
In all groups, Egr-1 mRNA expression was reduced in diffuser-treated eyes. Furthermore, the degradation of the spatial frequency spectrum also changed the cFos mRNA level, with reduced expression after 4 h of diffuser treatment. Other interesting candidates were Akt2, which was up-regulated after 30 min of deprivation and Mapk8ip3, a neuron specific JNK binding and scaffolding protein that was temporally regulated in the diffuser-treated eyes only.
Conclusions:
The microarray analysis demonstrated a pattern of differential transcriptional changes, even though differences in the retinal images were restricted to spatial features. The candidate genes may provide further insight into the biochemical short-term changes following retinal image degradation in mice. Because deprivation of spatial vision leads to increased eye growth and myopia in both animals and humans, it is believed some of the identified genes play a role in myopia development.
Insights
Investigating retinal mRNA expression in mice after visual deprivation revealed changes in genes like Egr-1 and cFos. These findings may offer insights into the biochemical mechanisms underlying myopia development.
Area of Science:
- Ophthalmology
- Molecular Biology
- Genetics
Background:
- Myopia development is influenced by retinal signals that are not fully understood.
- Investigating gene expression changes in the retina is crucial for understanding myopia.
- Visual deprivation is a known factor in myopia progression.
Purpose of the Study:
- To investigate changes in retinal mRNA expression following different durations of visual deprivation in mice.
- To control for retinal illuminance during visual deprivation experiments.
- To identify candidate genes involved in the early stages of retinal image degradation.
Main Methods:
- Mice (C57BL/6) were subjected to visual deprivation using frosted diffusers or neutral density filters for 30 min, 4 h, or 6+6 h.
- Retinal illuminance and contrast were standardized using a rotating drum with a visual grating.
- Microarray analysis (Affymetrix GeneChip Mouse Genome 430 2.0) identified differentially expressed genes, with validation by real-time RT-PCR.
Main Results:
- Reduced Egr-1 mRNA expression was observed in diffuser-treated eyes across all groups.
- cFos mRNA levels decreased after 4 h of diffuser treatment.
- Akt2 and Mapk8ip3 (a neuron-specific JNK binding protein) showed temporal regulation in response to diffuser treatment.
Conclusions:
- Microarray analysis revealed differential transcriptional changes in the retina due to spatial image degradation.
- Identified candidate genes may elucidate short-term biochemical changes following retinal image degradation.
- These genes are potentially implicated in the development of myopia, given the link between spatial vision deprivation and eye growth.
