Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier
Abstract DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/C...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-46479-2 |
| _version_ | 1797247132169666560 |
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| author | Zhiqian Li Lang You Anita Hermann Ethan Bier |
| author_facet | Zhiqian Li Lang You Anita Hermann Ethan Bier |
| author_sort | Zhiqian Li |
| collection | DOAJ |
| description | Abstract DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events. |
| first_indexed | 2024-04-24T19:53:50Z |
| format | Article |
| id | doaj.art-67b65bace54b4cb5b428d75c581ef7a6 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T19:53:50Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-67b65bace54b4cb5b428d75c581ef7a62024-03-24T12:25:46ZengNature PortfolioNature Communications2041-17232024-03-0115111910.1038/s41467-024-46479-2Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifierZhiqian Li0Lang You1Anita Hermann2Ethan Bier3Department of Cell and Developmental Biology, University of California, San DiegoDepartment of Cell and Developmental Biology, University of California, San DiegoDepartment of Cell and Developmental Biology, University of California, San DiegoDepartment of Cell and Developmental Biology, University of California, San DiegoAbstract DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.https://doi.org/10.1038/s41467-024-46479-2 |
| spellingShingle | Zhiqian Li Lang You Anita Hermann Ethan Bier Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier Nature Communications |
| title | Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier |
| title_full | Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier |
| title_fullStr | Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier |
| title_full_unstemmed | Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier |
| title_short | Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier |
| title_sort | developmental progression of dna double strand break repair deciphered by a single allele resolution mutation classifier |
| url | https://doi.org/10.1038/s41467-024-46479-2 |
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