Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra - Archive ouverte HAL Accéder directement au contenu
Chapitre D'ouvrage Année : 2024

Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra

Résumé

Molecular approaches are required to detect DNA double-strand break (DSB) events and to map and quantify them at high resolution. One of the most popular molecular methods in the field of meiotic recombination is the ChIP-SSDS (Chromatin immuno-precipitation and single-strand DNA sequencing). Here, we present two fully-automated Nextflow-based pipelines to analyze the sequencing data generated by this method. The first one identifies highly reproducible DSB sites, while the second provides a characterization of recovered DSB sites, including the description of the hotspot distribution and intensity along the genome and the overlap with specific regions such as gene features or known DSB hotspots. Finally, we discuss limitations/advantages and key points to consider when applying this method to specific genotypes or unconventional species.
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Dates et versions

hal-04474446 , version 1 (23-02-2024)

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Citer

Pauline Auffret, Bernard de Massy, Julie Clément. Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra. Germ Cell Development, 2770, Springer US, pp.227-261, 2024, Methods in Molecular Biology, 978-1-0716-3698-5. ⟨10.1007/978-1-0716-3698-5_16⟩. ⟨hal-04474446⟩
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