Nature geneticsJul 8, 2026

Finding important lysine sites in mammal histone H3 using advanced CRISPR editing

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Updated Jul 10, 2026

Abstract

A high-throughput CRISPR prime editing platform was developed to enable precise mutagenesis of histone H3 genes.

Key residues H3K4, H3K9, H3K14, H3K18, and H3K79 are identified, where mutations reduce fitness in mouse embryonic stem cells.
H3K56, previously associated with genome stability in other species, plays a similar role in mammalian cells.
Analysis of double mutants reveals functional interactions between histone residues, with specific combinations impairing stem cell self-renewal and altering gene expression.
A functional map of histone H3 lysines in mammals is established, contributing to the understanding of chromatin regulation.

Simplified

Histone post-translational modifications are fundamental to genome regulation, yet dissecting the functions of individual histone marks in mammals remains challenging due to the presence of multiple histone gene copies. Here we develop a high-throughput clustered regularly interspaced short palindromic repeats (CRISPR) prime editing platform enabling precise, reversible and combinatorial mutagenesis of canonical and noncanonical histone H3 genes within their native genomic context. Using systematic lysine-to-arginine substitutions benchmarked against synonymous controls, we identify key residues, including H3K4, H3K9, H3K14, H3K18 and H3K79, whose mutation compromises fitness in mouse embryonic stem cells. We further show that H3K56, linked to genome stability in yeast and Drosophila, has a conserved role in mammalian cells. Through analysis of selected double mutants, we uncover functional crosstalk across residues, with combinations such as H3K27R + H3K36R impairing stem cell self-renewal and altering transcription. Altogether, this study establishes a functional map of histone H3 lysines in mammals and provides a broadly applicable platform for systematic dissection of chromatin regulation.

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Finding important lysine sites in mammal histone H3 using advanced CRISPR editing

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