Programmable Human Histone Phosphorylation and Gene Activation Using a CRISPR/Cas9-Based Chromatin Kinase

Histone phosphorylation is a ubiquitous post-translational modification that allows eukaryotic cells to rapidly respond to environmental stimuli. Despite correlative evidence linking histone phosphorylation to changes in gene expression, the lack of targeted technologies has hindered the ability to establish the causal role of this key epigenomic modification within native chromatin. To address this technological gap, we built a programmable chromatin kinase, called dCas9-dMSK1, by directly fusing nuclease-null CRISPR/Cas9 to a hyperactive, truncated variant of the human MSK1 histone kinase. Targeting dCas9-dMSK1 to human promoters results in increased target histone phosphorylation and gene activation and demonstrates that hyperphosphorylation of histone H3 serine 28 (H3S28ph) in particular plays a causal role in the transactivation of human promoters. Furthermore, we use dCas9-dMSK1 to show that H3S28ph influences the acetylation status of histone H3 lysine 27 (H3K27ac) coincident with the activation of targeted human promoters. In addition, we uncover new mediators of resistance to the BRAF V600E inhibitor PLX-4720 in human melanoma cells using genome-scale screening with dCas9-dMSK1. Collectively, our findings enable a new way to reshape human chromatin using CRISPR/Cas9-based epigenome editing and establish the causal link between histone phosphorylation and human gene activation.