Abstract

To evaluate the contribution of the DNA methylation and DNA demethylation pathways in retinal development, we studied DNA methylation in retinal progenitor cells (RPCs) and retinal neurons using a combination of whole genome bisulfite sequencing (WGBS) data obtained in our study and WGBS data collected from previous studies. The data was analyzed using Hidden Markov Model- and change point-based methods to identify methylome states in different segments of the studied genomes following genome annotation. We found that promoters of rod and cone phototransduction genes and rod photoreceptor genes, but not genes required for the development and function of other retinal phenotypes, were highly methylated in DNA isolated from human and murine fetal retinas (which mostly contain RPCs) and postnatal murine RPCs. While these highly methylated genomic regions were inherited by non-photoreceptor phenotypes during RPC differentiation, the methylation of these promoters was significantly reduced during RPC differentiation into photoreceptors and accompanied by increased expression of these genes. Our analysis of DNA methylation during embryogenesis revealed low methylation levels in genomic regions containing photoreceptor genes at the inner cell mass stage, but a sharp increase in methylation at the epiblast stage, which remained the same later on (except for DNA demethylation in photoreceptors). Thus, our data suggest that the DNA demethylation pathway is required for photoreceptor phenotypes in the developing retina. Meanwhile, the role of the DNA methylation and DNA demethylation pathways during RPC differentiation into non-photoreceptor retinal phenotypes might be less important.

Highlights

  • While significant progress has been made in the understanding of signaling cascades that regulate retinal development, the role of epigenetic mechanisms has been explored to a lesser degree (Xiang, 2013; Corso-Díaz et al, 2018)

  • Opposed to our observations for retinal progenitor cells (RPCs) and non-photoreceptor retinal phenotypes, we found that many promoters of genes controlling rod photoreceptor development and the rod and cone phototransduction process were located in highly methylated regions of RPC genomic DNA (Figure 1A, Supplementary Table S1)

  • To analyze DNA methylation dynamics during RPC differentiation into retinal neurons, we examined the methylation profiles of genomic DNA isolated from murine retinal ganglion cell (RGC), horizontal cells (HC), starburst amacrine cells (SBAC), cone photoreceptors, rod photoreceptors, and the retinas of P21 mice

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Summary

Introduction

While significant progress has been made in the understanding of signaling cascades that regulate retinal development, the role of epigenetic mechanisms has been explored to a lesser degree (Xiang, 2013; Corso-Díaz et al, 2018). DNA demethylation can be carried out passively by not methylating (via Dnmt1) the newly synthesized strand after DNA replication, or actively by the DNA demethylation pathway, which includes the Ten-Eleven Translocation (TET) protein family (Koh and Rao, 2013; Huang and Rao, 2014). Both the DNA methylation and DNA demethylation pathways are vital during cellular differentiation. Balance between DNA methylation and DNA demethylation during development is critical for cell differentiation and generation of normal tissue

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