Chromatin context-dependent regulation and epigenetic manipulation of prime editing

Xiaoyi Li; Wei Chen; Beth K Martin; Diego Calderon; Choli Lee; Junhong Choi; Florence M Chardon; Troy A McDiarmid; Riza M Daza; Haedong Kim; Jean-Benoît Lalanne; Jenny F Nathans; David S Lee; Jay Shendure

doi:10.1016/j.cell.2024.03.020

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

Cell. 2024 Apr 5:S0092-8674(24)00311-8. doi: 10.1016/j.cell.2024.03.020. Online ahead of print.

Authors

Affiliations

¹ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address: xyli10@uw.edu.
² Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA.
³ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
⁴ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
⁵ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.
⁶ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
⁷ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA; Seattle Hub for Synthetic Biology, Seattle, WA 98109, USA. Electronic address: shendure@uw.edu.

PMID: 38608704
DOI: 10.1016/j.cell.2024.03.020

Abstract

We set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing, a precise genome engineering tool. Using a highly sensitive method for mapping the genomic locations of randomly integrated reporters, we discover massive position effects, exemplified by editing efficiencies ranging from ∼0% to 94% for an identical target site and edit. Position effects on prime editing efficiency are well predicted by chromatin marks, e.g., positively by H3K79me2 and negatively by H3K9me3. Next, we developed a multiplex perturbational framework to assess the interaction of trans-acting factors with the cis-chromatin environment on editing outcomes. Applying this framework to DNA repair factors, we identify HLTF as a context-dependent repressor of prime editing. Finally, several lines of evidence suggest that active transcriptional elongation enhances prime editing. Consistent with this, we show we can robustly decrease or increase the efficiency of prime editing by preceding it with CRISPR-mediated silencing or activation, respectively.

Keywords: DNA damage repair; cis x trans interactions; cis-chromatin effect; epigenome editing; genome engineering; prime editing.

Abstract

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