Time to move over histone methylation, the potent activating power of programmable histone phosphorylation joins the dCas9 epigenome editing toolbox and shows how it takes histone acetylation along for the ride.
A rather active team of researchers led by Isaac B. Hilton (Rice University, Houston, TX, USA) knew that phosphorylation represents one of the most common post-translational modifications but also that we lacked a dCas9-based epigenome editing tool for robust locus-specific histone phosphorylation. To solve this powerful problem without resorting to brute force, the team deftly fused dCas9 to a hyperactive human histone kinase (dMSK1) to provide a veritable epigenetic powerhouse – the first programmable chromatin kinase (dCas9-dMSK1).
Li and Colleagues took an activating approach in this new study – so let’s hear all the details!
- dCas9-dMSK1 induces phosphorylation on H3S10 and H3S28 in normal human kidney cells and on in vitro-assembled human histone octamers, with H3S28ph being the major target modification
- dCas9-dMSK1 (with the help of specific guide RNAs) efficiently and specifically activates gene expression at both natural (BMP2 and GDF6) and non-natural (OCT4 and MYOD) MSK1 target genes
- dCas9-dMSK1 binds to proximal promoter regions, increases H3S28ph levels, and activates gene expression
- ChIP-seq and RNA-seq showed that dCas9-MSK1 has negligible off-target effects
- Cas9-dMSK1-mediated H3S28ph prompts an increase in H3K27 acetylation levels to induce OCT4 and MYOD gene expression, while histone acetylase inhibition reduces the efficacy of dCas9-dMSK1-mediated promoter activation
- Fascinatingly, dCas9-dMSK1 combined with a genome-scale gRNA library aids the discovery of genes whose overexpression results in resistance to the BRAF V600E inhibitor PLX-4720 in human melanoma cells
- Of the top ten hits, three genes have been linked to BRAF (EPDR1, AFF2, and ERC2), while TRAT1, LACC1, AGL, TDRP, MIPOL1, and LELP1 represent novel melanoma resistance-associated genes
Overall, this sturdy new study provides a killer combo of epigenetic insight – the team describes dCas9-dMSK1 as an efficient epigenome editing tool and causally link histone phosphorylation (H3S28ph, in particular) to human promoter activation through functional crosstalk with histone acetylation. Additionally, the authors also demonstrate the potential of their new advance to allow a better understanding of disease pathology and, potentially, promote the development of new treatment approaches.
First author Li notes that this research “tells us that chemical modifications on histones talk to each other, and we can show it happening at specific spots in the human genome, and that’s linked to a gene turning on, so this allows us to synthetically control them.” Lead author Isaac B. Hilton concludes that “Getting these technologies into patients is a long process, but tools like this are the first step and can pave the way towards understanding how normal cellular processes unfortunately go awry in human diseases.”
For more on how epigenome editors can use dCas9-dMSK1 to provide the potent power of programmable histone phosphorylation, see Nature Communications, February 2021.