Live-cell epigenome manipulation by synthetic histone acetylation catalyst system

Abstract

Chemical modifications of histones, such as lysine acetylation and ubiquitination, play pivotal roles in epigenetic regulation of gene expression. Methods to alter the epigenome thus hold promise as tools for elucidating epigenetic mechanisms and as therapeutics. However, an entirely chemical method to introduce histone modifications in living cells without genetic manipulation is unprecedented. Here, we developed a chemical catalyst, PEG-LANA-DSSMe 11, that binds with nucleosome’s acidic patch and promotes regioselective, synthetic histone acetylation at H2BK120 in living cells. The size of polyethylene glycol in the catalyst was a critical determinant for its in-cell metabolic stability, binding affinity to histones, and high activity. The synthetic acetylation promoted by 11 without genetic manipulation competed with and suppressed physiological H2B ubiquitination, a mark regulating chromatin functions, such as transcription and DNA damage response. Thus, the chemical catalyst will be a useful tool to manipulate epigenome for unraveling epigenetic mechanisms in living cells.

Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism

“…However, cellular deacetylases can act quickly on these sites resulting in deacetylation, a problem that most likely also applies to other types of acylations. Recently, Fujiwara et al (2021) demonstrated that site-specific acylations can also be introduced in vivo via a protease-resistant nucleosome-binding catalyst and a cellpermeable acetyl donor. Subsequent development of this exiting method might enable us to study the effects of histone acylations on nucleosome assembly in vivo.…”

Targeted Protein Acetylation in Cells Using Heterobifunctional Molecules

“…Thus, the ability to selectively induce acetylation of targeted proteins overcomes many of these challenges. Toward this end, chemical-based approaches have yielded ligand-directed acetyl-donating reagents for stoichiometric, nonenzymatic transfer of acyl groups to lysine residues on specific proteins like androgen receptor, histone H2B, , dihydrofolate reductase, , and phosphoglycerate mutase 1 . Though capable of targeting endogenous POIs, such reagents are “single use”, allowing for the transfer of one acetyl group per molecule and, further, are limited to proteins with available ligands that bind within proximity to targeted recipient lysine residues.…”

Targeted Protein Acetylation in Cells Using Heterobifunctional Molecules

“…Thus, the ability to selectively induce acetylation of targeted proteins overcomes many of these challenges. Towards this end, ‘all-chemical’ based approaches have yielded ligand-directed acetyl-donating reagents for stoichiometric, non-enzymatic transfer of acyl groups to lysine residues on specific proteins like androgen receptor 48 , histone H2B 49–50 , dihydrofolate reductase 51–52 , and phosphoglycerate mutase 1 53 . Though capable of targeting endogenous POIs, such reagents are ‘single use,’ allowing for the transfer of one acetyl group per molecule and, further, are limited to proteins with available ligands that bind within proximity to targeted recipient lysine residues.…”