Chromatin context-dependent regulation and epigenetic manipulation of prime editing.

Publisher: Cell Press Country of Publication: United States NLM ID: 0413066 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1097-4172 (Electronic) Linking ISSN: 00928674 NLM ISO Abbreviation: Cell Subsets: MEDLINE

Publication: Cambridge, Ma : Cell Press
Original Publication: Cambridge, MIT Press.

Chromatin*/metabolism ; Chromatin*/genetics ; CRISPR-Cas Systems*/genetics ; Epigenesis, Genetic* ; Gene Editing*/methods; Humans ; Histones/metabolism ; Transcription Factors/metabolism ; Histone Code

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.
Competing Interests: Declaration of interests J.S. is an SAB member, consultant and/or co-founder of Prime Medicine, Cajal Neuroscience, Guardant Health, Maze Therapeutics, Camp4 Therapeutics, Phase Genomics, Adaptive Biotechnologies, Scale Biosciences, Sixth Street Capital, and Pacific Biosciences. University of Washington has filed a provisional patent application based on this work on which J.S., X.L., W.C., and J.C. are co-inventors.
(Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Update of: bioRxiv. 2023 Apr 12;:. (PMID: 37090511)

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F32 HG011817 United States HG NHGRI NIH HHS; K99 HG012973 United States HG NHGRI NIH HHS; R01 HG010632 United States HG NHGRI NIH HHS; UM1 HG011966 United States HG NHGRI NIH HHS

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

0 (Chromatin)
0 (Histones)
0 (Transcription Factors)

Date Created: 20240412 Date Completed: 20240510 Latest Revision: 20240529

20240529

PMC11088515

10.1016/j.cell.2024.03.020

38608704