{"ID": "PMID:36107780", "lab": {"display_title": "External Lab", "@type": ["Lab", "Item"], "uuid": "d3412190-317a-4837-823f-3892b9f641a4", "title": "External Lab", "status": "current", "@id": "/labs/external-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.d3412190-317a-4837-823f-3892b9f641a4"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/36107780", "tags": ["4dn-external-reuse"], "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "description": "Funding source is from outside 4DN.", "center_title": "External", "project": "External", "center": "External", "name": "external-award", "display_title": "EXTERNAL AWARD", "status": "current", "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Double-strand break toxicity is chromatin context independent.", "status": "current", "aliases": ["4dn-dcic-lab:PMID:36107780"], "authors": ["Friskes A", "Koob L", "Krenning L", "Severson TM", "Koeleman ES", "Vergara X", "Schubert M", "van den Berg J", "Evers B", "Manjon AG", "Joosten S", "Kim Y", "Zwart W", "Medema RH"], "journal": "Nucleic acids research", "abstract": "Cells respond to double-strand breaks (DSBs) by activating DNA damage response  pathways, including cell cycle arrest. We have previously shown that a single  double-strand break generated via CRISPR/Cas9 is sufficient to delay cell cycle  progression and compromise cell viability. However, we also found that the  cellular response to DSBs can vary, independent of the number of lesions. This  implies that not all DSBs are equally toxic, and raises the question if the  location of a single double-strand break could influence its toxicity. To  systematically investigate if DSB-location is a determinant of toxicity we  performed a CRISPR/Cas9 screen targeting 6237 single sites in the human genome.  Next, we developed a data-driven framework to design CRISPR/Cas9 sgRNA (crRNA)  pools targeting specific chromatin features. The chromatin context was defined  using ChromHMM states, Lamin-B1 DAM-iD, DNAseI hypersensitivity, and  RNA-sequencing data. We computationally designed 6 distinct crRNA pools, each  containing 10 crRNAs targeting the same chromatin state. We show that the  toxicity of a DSB is highly similar across the different ChromHMM states. Rather,  we find that the major determinants of toxicity of a sgRNA are cutting efficiency  and off-target effects. Thus, chromatin features have little to no effect on the  toxicity of a single CRISPR/Cas9-induced DSB.", "date_created": "2024-02-13T22:04:48.188115+00:00", "published_by": "External", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-15T16:03:14.379714+00:00"}, "date_published": "2022-09-23", "public_release": "2024-03-15", "schema_version": "2", "project_release": "2024-03-15", "exp_sets_used_in_pub": [{"uuid": "849f6d64-560c-43e3-999f-40973e5e004b", "display_title": "4DNESHGTQ73M", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESHGTQ73M/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/publications/3a03fb4c-e4f5-45a4-83b4-0bfdc5fcd5e0/", "@type": ["Publication", "Item"], "uuid": "3a03fb4c-e4f5-45a4-83b4-0bfdc5fcd5e0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Friskes A et al. (2022) PMID:36107780", "external_references": [], "short_attribution": "Friskes A et al. (2022)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}