Abstract
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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Acknowledgments
We thank Cyril Noël and Alizée Bardon (SeBiMER, Ifremer, Plouzané) for their help regarding Singularity images building. The authors acknowledge the bioinformatic service of IGH for providing computational resources for the early developments and the Pôle de Calcul et de Données Marines (PCDM; http://www.ifremer.fr/pcdm) for providing DATARMOR computational resources on which hotSSDS and hotSSDS-extra pipelines development have been completed.
We also thank Paola Sanna, Akbar Zainu, Mathilde Biot, Frédéric Baudat, Corinne Grey (de Massy team) and Miao Tian (Mochizuki team) from IGH for their feedback on the pipeline and their critical tests; Attila Toth, Arkasarathi Gope, Andreas Petzold, and Christin Richter from TU Dresden for their tests and helpful comments.
BdM was funded by ERC (European Research Council (ERC) Executive Agency under the European Union’s Horizon 2020 research and innovation program (Grant Agreement no. 883605)) and MSD Avenir.
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Auffret, P., de Massy, B., Clément, J.A.J. (2024). Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra. In: Barchi, M., De Felici, M. (eds) Germ Cell Development. Methods in Molecular Biology, vol 2770. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3698-5_16
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DOI: https://doi.org/10.1007/978-1-0716-3698-5_16
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