Histone H3 proline 16 hydroxylation regulates mammalian gene expression [CUT&RUN]

Histone posttranslational modifications (PTMs) are important for regulating various DNA-templated processes. Emerging evidence suggests a critical involvement of the previously less-explored histone PTMs in gene activity regulation. Here, we report the existence of a new histone PTM in the mammalian cells, hydroxylation of H3 proline 16 (H3P16-OH) catalyzed by EglN2, a proline hydroxylase. We show that EglN2-mediated H3P16-OH enhances direct binding of Lysine-Specific Demethylase 5A (KDM5A) with its substrate, H3 lysine 4 trimethylation (H3K4me3), resulting in enhanced chromatin recruitment of KDM5A and decrease of H3K4me3 at target genes. Genome-wide mapping by CUT&RUN in multiple mammalian cell models reveals a functional connection between EglN2, H3P16-OH, KDM5A and H3K4me3. Integrated analysis with RNA-Seq also identifies distinct subsets of genes that are regulated through H3P16-OH in different cell lines. This study therefore demonstrates a new player of the “histone code” by revealing a role of H3P16-OH in regulating gene expression in mammalian cells. Overall design: Genome-wide mapping by CUT&RUN or spike-in CUT&RUN in multiple mammalian cell models reveals a functional connection between EglN2, H3P16-OH, KDM5A and H3K4me3. A faction of Drosophila chromatin was added to these human cells as spike-in controls.