Ezh2 Control of Bivalent Genes Fine-Tunes Developmental Competence During Retinogenesis

<h4>Purpose</h4>Chromatin-based repression is essential for retinal development, yet the genome-wide binding landscape of Polycomb repressive complex 2 (PRC2) in the developing retina has not been defined. In particular, how the PRC2 catalytic subunit EZH2 associates with chromatin and relates to transcriptional control in retinal progenitor cells (RPCs) remains incompletely characterized.<h4>Methods</h4>Genome-wide EZH2 binding and H3K27me3 deposition were profiled in the developing mouse retina and integrated with transcriptomic analyses following conditional Ezh2 deletion in RPCs. Chromatin state annotations and enhancer-promoter interaction data were used to examine regulatory features associated with EZH2-bound loci.<h4>Results</h4>EZH2 binding was enriched at promoter regions and strongly associated with H3K27me3-marked chromatin. Integration with transcriptomic data revealed that genes upregulated following Ezh2 loss were frequently EZH2-bound and enriched for loci exhibiting overlapping H3K27me3 and H3K4me3 signals at the population level. Among upregulated genes, those bound by EZH2 showed greater fold-change magnitude than unbound genes, whereas H3K27me3 occupancy alone did not differentiate fold-change within the upregulated set. Analysis of transcription factor-occupied loci indicated partial overlap between retinal progenitor transcriptional networks and Polycomb-marked regions. At the Pitx2 locus, EZH2 and H3K27me3 occupancy coincided with a distal enhancer that is accessible and transcriptionally competent in the developing retina.<h4>Conclusions</h4>These findings provide a genome-wide characterization of EZH2 occupancy in the developing mouse retina and support a model in which EZH2-mediated repression is associated with reduced transcription from chromatin that otherwise displays features of transcriptional competence. This work offers a framework for understanding how Polycomb-associated chromatin states intersect with retinal transcriptional programs to maintain lineage-appropriate gene expression.