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An immune-inspired spatiotemporal switch for precise CRISPR genome editing with reduced off-target effects and chromosomal translocations

ABSTRACT: Off-target mutations and chromosomal translocations are a fundamental obstacle to precise CRISPR-Cas9 genome editing—a challenge strikingly analogous to that faced by activation-induced cytidine deaminase (AID), which must introduce targeted DNA deamination at the immunoglobulin heavy chain (IgH) locus for antibody diversification while avoiding genome-wide collateral damage. In B cells, AID has evolved a C-terminal nuclear export signal (NES) that constitutively sequesters it in the cytoplasm, restricting genomic access to the brief mitotic window when the nuclear envelope breaks down. This spatiotemporal confinement ensures efficient on-target editing while strictly limiting off-target deamination across the genome. Inspired by this evolutionarily refined immune regulatory mechanism, we engineered a Cas9 variant fused to AID’s NES, confining its nuclear access to mitosis. This confinement preserves on-target editing efficiency while dramatically reducing off-target mutations and chromosomal translocations. This principle extends naturally to cytosine base editors (CBEs): AID-nCas9-UGI already harbors an endogenous NES within its AID component, functioning as a built-in specificity safeguard. Notably, the occurrence of efficient mitotic editing within condensed chromatin challenges the long-held assumption that mitotic chromatin is refractory to CRISPR-based editing. These results establish spatiotemporal restriction of nuclear access as a broadly applicable strategy for enhancing the precision of CRISPR-based genome editing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE345607 | GEO | 2026/09/05

REPOSITORIES: GEO

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Project description:The antibody gene mutator AID promiscuously damages oncogenes and B cell identity genes leading to chromosomal translocations and tumorigenesis. Why non-immunoglobulin loci are susceptible to AID activity is unknown. Here we study AID-mediated lesions in the context of nuclear architecture and the B cell regulome. We show that AID targets are not randomly distributed across the genome, but are predominantly clustered within super-enhancers. Unexpectedly, in these domains AID deaminates highly active promoters and eRNA+ enhancers interconnected in some instances over megabases of linear chromatin. Using genome editing we demonstrate that 3D-linked targets cooperate to recruit AID-mediated breaks. Furthermore, a comparison of hypermutation in mouse B cells, AID-induced kataegis in human lymphomas, and translocations in MEFs reveals that AID damages different genes in different cell types. Yet, in all cases, the targets are predominantly associated with topological complex, highly transcribed super-enhancers, demonstrating that these compartments are key mediators of AID recruitment. Examination of AID activity in human cells via Single Nucleotide Variant discovery in H3K4me3 ChIP-seq data from 26 MSH2-/-; AIDtg; UGItg, 18 AICDA-/- and 2 unmodified RAMOS clonal populations. Examination of PolII mediated long-range interactions via Chia-PET of RAMOS cells (2 sample). Identification of super-enhancers from H3K27Ac ChIP-Seq data from activated B cells (3 replicates and 1 input control) and RAMOS cells (1 sample and 1 input control), 2 preparations of naive and 2 of germinal center (GC) B cells from human tonsilectomy samples. Mapping of regulatory elements in RAMOS based on H3K4me1 (1 sample) and Nipbl (2 replicates) ChIP-Seq. RNA expression analyses of activated B cells from 3 WT and 3 Il4raU/U mice and RAMOS cells (3 replicates). Mapping of long-range interactions by 4C in activated B cells from a WT and an Il4raU/U mouse with the IL4ra and Il21r locus, respectively, as a viewpoint. Mapping of Super-Enhancers in activated B cells from Il4raU/U and WT control mice (2 samples).

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An immune-inspired spatiotemporal switch for precise CRISPR genome editing with reduced off-target effects and chromosomal translocations

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