Hypoxia-Driven Histone Modifications Govern Gene Regulation for Mature Eye Lens Formation

Purpose: Evidence suggests that the hypoxic environment of the lens regulates the expression of genes required for lens formation and function. Here, we tested the hypothesis that hypoxia regulates these genes through the induction of specific histone modifications. Methods: Global levels of hypoxia-induced histone modifications were determined in cultured day 13 chick lenses exposed to 1% oxygen. The genome-wide localizations of H3K27ac and H3K4me3 were identified by cleavage under target and release using nuclease analysis and mapped to within 5 kb of the transcriptional start sites of genes activated or repressed by hypoxia identified by RNA sequencing. The requirement for these histone modifications for hypoxia-induced gene expression was determined using inhibitors of histone writers and erasers. Results: The levels of activating modifications H3K4me3, H3K9ac, H3K14ac, and H3K27ac in hypoxia-treated lenses increased, whereas levels of repressive modifications H3K9me3 and H3K27me3 remained unchanged. Hypoxia-specific H3K4me3 and/or H3K27ac regions were detected within 5 kb of the transcriptional start sites of more than 900 fiber cell genes with increased expression upon hypoxia exposure and 350 genes with decreased expression. The inhibition of histone writers and erasers resulted in altered levels of key fiber cell genes upon hypoxia exposure. Conclusions: These results provide evidence that hypoxia-induced histone modifications regulate the genes required for mature lens formation and provide a framework for understanding the role of hypoxia-specific histone modifications in the regulation of genes in more complex tissues.