Precise epigenomic editing with a SunTag-based modular epigenetic toolkit

ABSTRACT

Epigenetic regulation is a crucial factor controlling gene expression. Here, we report our CRISPR/dCas9-based modular epigenetic toolkit that enables gene-specific modulation of epigenetic architecture. By modifying the SunTag framework of dCas9 tagged with five GCN4 moieties, each epigenetic writer is bound to scFv and target-specific sgRNA, and this system is able to modify multiple epigenetic marks in a target-specific manner. We successfully demonstrated that this system is efficient in modifying individual histone post-translational modifications. We display its utility as a tool to understand the contributions of specific histone marks on gene expression by screening a large promoter region and identifying differential outcomes with high base-pair resolution. This epigenetic toolkit can be easily altered with a large variety of epigenetic effectors and is a useful tool for researchers to use in understanding gene-specific epigenetic changes and their relation to gene expression.

KEYWORDS:

• Epigenetics
• histone post-translational modifications
• epigenome editing
• CRISPR
• epigenetic writers

Acknowledgments

Authors would like to acknowledge the efforts by Ms. Siyona Mishra and Ms. Annlisa Simon for their help in maintaining eukaryotic cells and bacterial cultures. The authors also thank Dr. Sambuddha Basu and Dr. Goun Je for their valuable input in study design.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors’ contributions

SGT and YSK conceived the study and designed all the experiments. SGT created all modular epigenetic toolkit system. LA, SGT, IHJ, AS, and MBF performed the experiments. MC and HNH performed bioinformatics analysis. LA SGT, HNH, AS, MBF, and YSK wrote the manuscript. All authors read and approved the final manuscript. YSK supervised the entire project.

Availability of data and materials

All supporting data are included in the manuscript and supplementary files. All vectors described will be deposited at Addgene and will be available under a Uniform Materials Transfer Agreement.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15592294.2022.2106646

Additional information

Funding

The authors acknowledge the funding from NIH vide grant nos. 5R01NS100919-01A1 and 1R01NS101461-01A1.