The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis

Abstract

In the developing retina, multipotent neural progenitors undergo unidirectional differentiation in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinogenesis in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell-type-specific differentiation programs. We identified developmental-stage-specific super-enhancers and showed that most epigenetic changes are conserved in humans and mice. To determine how the epigenome changes during tumorigenesis and reprogramming, we performed integrated epigenetic analysis of murine and human retinoblastomas and induced pluripotent stem cells (iPSCs) derived from murine rod photoreceptors. The retinoblastoma epigenome mapped to the developmental stage when retinal progenitors switch from neurogenic to terminal patterns of cell division. The epigenome of retinoblastomas was more similar to that of the normal retina than that of retina-derived iPSCs, and we identified retina-specific epigenetic memory.

Keywords: DNA methylation; epigenetic memory; epigenetics; iPSCs; retinal development; retinoblastoma; rod photoreceptors.

Figure 1. Cell Growth and Differentiation during Retinal Development

(A) Schematic of the developing murine CNS showing the autonomous development of the eye and retina. (B) Drawing of murine retinal development highlighting proliferative growth from E14.5 to P7. (C) Simplified diagram of the developmental birth order of retinal cell types; the area under each curve is proportional to the fraction of cells in the adult retina. The proportion of proliferating progenitor cells is represented along the bottom of the plot. Each stage of murine (Mu) and human (Hu) retinal development analyzed in this study is indicated by dashed lines. (D–G )Venn diagrams of the genes that are up or downregulated (blue) and those that are hyper or hypomethylated (orange) during mouse and human retinal development. Examples are shown, and regions with changing DNA methylation are highlighted in orange. Normalized relative expression during development is shown in the histograms.

Figure 2. Epigenetic Changes Correlate with Gene Expression Changes during Retinal Development

(A–D) Normalized relative expression of representative genes from 8 stages of mouse retinal development, as determined by RNA-seq analysis. A subset of the genes identified by hierarchical clustering (cluster 1 in Data S1, Table S3) are shown for simplicity. The G2/M genes are required for retinal progenitor cell proliferation, (A) and the progenitor genes are expressed in retinal progenitors but are not necessarily involved in cell cycle control (B). The rod genes are upregulated as rods differentiate (C), and the housekeeping genes are constitutively expressed throughout retinal development (D). (E–G) Representative traces of tracks of averaged ChIP-seq data for the retinal progenitor gene Uhrf1, which is silenced during retinal development (E). DNA-methylation data are available for all stages but only the representative E14.5 and P21 DNA-methylation data are presented here. β-value of 1.0 indicates the site is fully methylated, 0 indicates it is unmethylated. The normalized relative gene expression from RNA-seq analysis is shown in the histograms to the right of each ChIP-seq plot. Some retinal progenitor cell genes (e.g., Ascl1) are repressed by H3K27me3 and are silenced during retinal differentiation (F). A representative series of ChIP-seq traces is shown for the rod gene Stx3, which is upregulated as rods differentiate (G). Individual marks and their scales in the plots are indicated in different colors at the bottom of the figure.

Figure 3. Hidden Markov Modeling of the Retinal Epigenome

(A) Heat map of the 11 chromHMM states used in this analysis. The darker blue represents more abundance of that ChIP-seq mark in the particular HMM state. (B) Each state is color coded and then used to represent the chromHMM states for the retinal progenitor gene Uhrf1. The 2 states that are the most abundant are full-height bars, and the remaining 9 states are half the height. The intensity of each bar is proportional to the percentage of each state across all stages for that gene. For the bars that are half the height, the intensity is scaled starting at 50% of maximum intensity. Normalized relative-fold expression of Uhrf1 is shown in the histogram on the right, and the relative β-value for DNA methylation is shown for E14.5. β-value of 1.0 means the site is fully methylated, and 0 is unmethylated. The ChIP-seq traces are shown as a reference for the chromHMM states. (C, D) HHM states, DNA methylation, and gene expression of a representative rod-differentiation gene during mouse (C) or human (D) retinal development. The human retinal stages are aligned with the corresponding murine stages based on comprehensive developmental, morphological, and neuroanatomical modeling across mammalian species (http://www.translatingtime.net). (E) Representative chromHMM modeling and DNA-methylation data of the 4 distinct clusters of rod genes identified by the chromHMM data analysis. The clusters were associated with expression during development, as indicated. (F) No distinct subclusters of progenitor or G2/M genes were identified by the chromHMM data analysis. Representative chromHMM and DNA-methylation data are shown for a progenitor gene and a G2/M gene. (G, H) Venn diagrams of the overlap in genes that have corresponding changes in DNA methylation, chromHMM, and H3K27me3 for the up and downregulated genes in murine retinogenesis.

Figure 4. Developmentally Regulated Super-Enhancers during Retinal Development

(A) ChromHMM and DNA methylation of a super-enhancer (SE) 40 kb from the developmentally regulated progenitor gene Ascl1. (B) ChromHMM and DNA methylation of a representative developmentally regulated photoreceptor gene (Crx). The super-enhancers are indicated by black boxes. Magnified views of the ATAC-seq and ChIP-seq tracks for Brd4, CTCF, and H3K27Ac are shown in the corresponding boxes. (C–D) Scatterplot of all super-enhancers in the mouse genome showing chromHMM-state transitions during development, consistent with progenitor cells (i.e., active early and inactive later in development) and with differentiating rods (i.e., those that are inactive early and active later in development). The closest gene within 500 kb was identified for each super-enhancer, and the relative change in expression during development was plotted, relative to the distance from the super-enhancer. Rod, progenitor, G2/M, and housekeeping genes adjacent to super-enhancers are indicated with corresponding colors. Representative progenitor cell and G2/M (C) or rod genes (D) are indicated. The dashed box highlights the super-enhancer/gene pairs that are downregulated during development and fall within 100 kb. (E) Histogram of the normalized luciferase activity of individual regions of super-enhancers promixal to the indicated genes. Each bar represents the mean (±SD) of 5 biological replicates. CMV=strong CMV enhancer, positive control; control= region devoid of H3K27Ac in the retina, negative control. (F) Magnified views of the ATAC-seq and ChIP-seq tracks for Brd4, CTCF, and H3K27Ac for the 868-bp region of the Rbp3 super-enhancer tested in the luciferase assay in (E). (G) Crx consensus–binding site within and overlapping with the ATAC-seq peak of the Crx super-enhancer shown in (B). (H) Representative core regulatory circuit transcription factors across murine retinal development (blue boxes). Darker boxes indicate transcription factors identified in both biological replicates, lighter boxes are those found in 1 replicate.

Figure 5. 3D Localization of Genes in Rod Nuclei

(A) Representative electron micrograph of a rod nucleus in the adult mouse retina showing the 3 concentric regions of chromatin organization. (B) DAPI-stained rod nucleus showing the 3 concentric regions of chromatin organization. (C) FISH of the microsatellite repeat (MSR) region at the boundary of the heterochromatin domains. (D) Immunofluorescence of H3K4me3 at the promoters of actively transcribed genes in the euchromatin domain. (E) 3D reconstruction of rod nucleus showing the corresponding volumes of the 2 heterochromatin domains and the euchromatin domain. (F) FISH of the Crx gene (arrows) in the euchromatin domain overlapping with H3K4me3. (G, H) Automated segmentation, 3D reconstruction, and localization of Crx FISH signal (red) to the euchromatin domain (arrows). (I) Histogram showing the proportion of nuclei with each gene in the euchromatin or f-heterochromatin domains. (J) Micrograph showing FISH (arrows) for the Ascl1 gene in the f-heterochromatin domain that is exclusive from H3K4me3. Scale bars: 1 μm. Abbreviations: c-het, constitutive heterochromatin; euc, euchromatin; f-het, facultative heterochromatin

Figure 6. Epigenetic Memory in r-iPSCs

(A) Principal component analysis plot of RNA-seq data for adult mouse retina (p21 retina), 4 f-iPSC lines, 3 r-iPSC lines, and the EB5:Rx–GFP stem cell line. (B) Heatmap of select genes with differential DNA methylation that also had changes in DNA methylation and expression during retinal development. The blue shading is higher β-values for the DNA methylation, and the white shading is lower values. (C, D) Example of DNA methylation from WGBS for the coding region of the Prkca and the Rcvrn genes. Corresponding β-values are indicated for each sample. (E, F) Histograms of genes and promoters with differential chromHMM states that are increased (E) or decreased (F) in f-iPSCs relative to r-iPSCs. (G) Representative chromHMM map for Mybl2 showing an extension of state 1 in the f-iPSCs relative to r-iPSCs. (H) Histogram of combined genes and promoters with differences in ChIP-seq data between f-iPSCs and r-iPSCs. (I) Example of ChIP-seq of H3K9me3 from the Kcna4 gene with differential abundance in f-iPSCs vs r-iPSCs.

Figure 7. Photoreceptor Pathway in Human Retinoblastoma

(A–C) Changes in expression of G2/M, progenitor, and rod genes during mouse retinal development. Boxplot of expression of the same genes in retinoblastoma is shown to the right, and the intersection of those genes (blue-shaded region) with retinal development (pink-shaded region) is indicated (purple-shaded region). (D–F) Representative chromHMM, DNA methylation, and gene expression of a G2/M gene, a progenitor gene, and a rod gene are shown. (G) Simplified transcriptional network that regulates photoreceptor development in the human retina. The chromHMM states are indicated for each gene, and the expression is represented in individual pie charts next to each gene for normal human retina at FW 23/24 and retinoblastoma. Retinoblastoma gene expression is normalized to that in healthy human retina. Abbreviations: nd, none detected; * FPKM less than 10 indicates very low levels of expression in the normal retina and tumor.