Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra.
Methods Mol Biol
; 2770: 227-261, 2024.
Article
in En
| MEDLINE
| ID: mdl-38351457
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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
DNA Breaks, Double-Stranded
/
Homologous Recombination
Language:
En
Journal:
Methods Mol Biol
Journal subject:
BIOLOGIA MOLECULAR
Year:
2024
Document type:
Article
Affiliation country:
France
Country of publication:
United States