Mapping Meiotic DNA Breaks: Two Fully-Automated Pipelines to Analyze Single-Strand DNA Sequencing Data, hotSSDS and hotSSDS-extra.
Pauline AuffretBernard de MassyJulie A J ClémentPublished in: Methods in molecular biology (Clifton, N.J.) (2024)
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.
Keyphrases
- circulating tumor
- single molecule
- high resolution
- cell free
- genome wide
- high throughput
- single cell
- machine learning
- circulating tumor cells
- electronic health record
- dna damage
- gene expression
- nucleic acid
- big data
- mass spectrometry
- dna methylation
- transcription factor
- copy number
- high intensity
- oxidative stress
- dna repair
- high density
- high speed
- tandem mass spectrometry
- liquid chromatography