synapsis: A Bioconductor package to automate the analysis of meiotic double-strand break repair and crossover formation

Abstract

Immunofluorescent staining is commonly used to generate images to characterise cytological phenotypes. The manual quantification of DNA double-strand breaks and their repair intermediates during meiosis using image data requires a series of subjective steps, from image selection to the counting of particular events per nucleus. Here we describe synapsis, a Bioconductor package, which includes a set of functions to automate the process of identifying meiotic nuclei and quantifying key double-strand break formation and repair events in a rapid, scalable and reproducible workflow, and compare it to manual user quantification. The software can be extended for other applications in meiosis research, such as incorporating machine learning approaches to categorise meiotic substages.

Fancm regulates meiotic double-strand break repair pathway choice in mammals

“…Image analysis was performed using Fiji (ImageJ-win64) [127] with a macro developed by Boekhout et al [128], synapsis [129] and manual counts. For cell scoring, the following criteria were used to classify the prophase stage: (i) leptotene: Short, discontinuous SYCP3 signals.…”