Histone proteins are decorated with a combinatorially and numerically diverse set of biochemical modifications. Different histone modification patterns strongly correlate and even define the functional states of many genomic loci and therefore have deep importance in our understanding of cell biology and disease. Traditional methods to study these modifications and the enzymes that regulate them can be laborious, time consuming, and cumbersome. Using yeast surface display, we established a versatile and scalable platform, REMY: Rapid interrogation of Epigenomic Modifications using Yeast. REMY enables efficient characterization of the enzymes that create histone modifications without the need for recombinant protein production.<br/>As proof-of-concept, we first used REMY to rapidly profile the histone H3 and H4 N-terminal tail residue writing specificities of the human histone acetyltransferase, p300. Subsequently, a large panel of commercially available anti-acetylation antibodies was screened for their specificities, identifying many suitable and unsuitable reagents. Finally, using site-specific histone mutations, this platform enabled the efficient mapping of the large binary crosstalk space between acetylated residues on histones H3 and H4 and uncovered residue interdependencies affecting p300 activity. These results show that using yeast surface display to study histone modifications can not only advance our understanding of the natural proteins that regulate chromatin biology, but also enable us to engineer advanced epigenomic enzymes for use in transcriptional control and cellular engineering.

REMY: A rapid and facile method to map the specificities of epigenomic enzymes

ACS Spring 2022

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