Chromatin access regulates the formation of Müller glia‐derived progenitor cells in the retina

Abstract

Chromatin access and epigenetic control over gene expression play important roles in regulating developmental processes. However, little is known about how chromatin access and epigenetic gene silencing influence mature glial cells and retinal regeneration. Herein, we investigate the expression and functions of S‐adenosylhomocysteine hydrolase (SAHH; AHCY) and histone methyltransferases (HMTs) during the formation of Müller glia (MG)‐derived progenitor cells (MGPCs) in the chick and mouse retinas. In chick, AHCY, AHCYL1 and AHCYL2, and many different HMTs are dynamically expressed by MG and MGPCs in damaged retinas. Inhibition of SAHH reduced levels of H3K27me3 and potently blocks the formation of proliferating MGPCs. By using a combination of single cell RNA‐seq and single cell ATAC‐seq, we find significant changes in gene expression and chromatin access in MG with SAHH inhibition and NMDA‐treatment; many of these genes are associated with glial and neuronal differentiation. A strong correlation across gene expression, chromatin access, and transcription factor motif access in MG was observed for transcription factors known to convey glial identity and promote retinal development. By comparison, in the mouse retina, inhibition of SAHH has no influence on the differentiation of neuron‐like cells from Ascl1‐overexpressing MG. We conclude that in the chick the activity of SAHH and HMTs are required for the reprogramming of MG into MGPCs by regulating chromatin access to transcription factors associated with glial differentiation and retinal development.

ID factors regulate the ability of Müller glia to become proliferating neurogenic progenitor‐like cells

“…For scATAC-seq analysis, including motif enrichment and motif scoring, all reference or annotation genomes were in NCBI/Ensembl format. The original detailed analysis of these scATAC-seq libraries are described elsewhere (Campbell et al, 2023). Similar to previous reports (Fischer et al, 2009, b;Ghai et al, 2009)…”

“…We further analyzed expression of ID factors in a scRNA-seq database that we generated for early time-points, 3 and 12 h, after NMDAtreatment (Campbell et al, 2023;Campbell, Blum, et al, 2021) (Figure 2h). These scRNA-seq libraries were generated with different reagents and sensitivities.…”

ID transcription factors regulate the ability of Müller glia to become proliferating neurogenic progenitor-like cells

“…We further analyzed expression of ID TFs in a scRNA-seq database that we generated for early time-points, 3 and 12 hours, after NMDA-treatment (Campbell et al, 2021b, 2023) (Fig. 2j).…”

“…We treated with saline or NMDA and harvested retinal cells 24hrs after injection to generate scATAC-seq libraries, as described previously (Campbell et al, 2023). UMAP embedding of cells revealed distinct clusters of different types of neurons and glia (Fig.…”

“…For scATAC-seq analysis, including motif enrichment and motif scoring, all reference or annotation genomes were in NCBI/Ensembl format. The original detailed analysis of these scATAC-seq libraries are described elsewhere (Campbell et al, 2023).…”