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Updated: Sep 17, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Aging reprograms the rhythmic transcriptome in the retina.

Zhijie Wang¹, Lifeng Chen², Lin Li²

¹Department of Retina Center, Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Hangzhou, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, China; Eye Research Center, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Eye Hospital, Wenzhou Medical University, Hangzhou, China.

Experimental Eye Research

|July 1, 2025

Summary

This summary is machine-generated.

Aging significantly alters the retina's daily gene expression patterns, impacting immune responses and pathways linked to age-related vision loss. This research reveals how aging disrupts the eye's natural rhythms.

Keywords:

Aging retina Circadian rhythm Diurnal transcriptome Gene expression

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Published on: March 12, 2021

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Transpupillary Two-Photon In Vivo Imaging of the Mouse Retina

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Area of Science:

Ophthalmology
Genomics
Chronobiology

Background:

Aging is a major risk factor for retinal degenerative diseases.
The impact of aging on the retina's diurnal transcriptional profile is not well understood.
Understanding these changes is critical due to the increasing prevalence of age-related retinal diseases.

Purpose of the Study:

To investigate the effects of aging on the diurnal gene expression patterns in the mouse retina.
To identify age-related changes in rhythmic and differentially expressed genes and pathways.

Main Methods:

High-throughput RNA sequencing of retinal samples from young and aged mice under a 12h:12h light-dark cycle.
Differential expression analysis using edgeR.
Rhythmicity and differential rhythmicity analysis using MetaCycle and CircaCompare packages.

Main Results:

361 differentially expressed genes (DEGs) were identified, enriched in immune-related pathways.
Aging reduced the proportion of rhythmic genes by 28%, with notable pathway shifts.
Genes in RNA degradation and proteasome pathways lost rhythmicity, while immune and AMD-associated pathways gained rhythmicity in aged retinas.

Conclusions:

Aging profoundly alters the retina's rhythmic transcriptome, affecting gene expression timing and composition.
This study provides insights into the molecular mechanisms underlying age-related retinal diseases by highlighting the interplay of aging, diurnal rhythms, and gene expression.