Computational Tools for the Analysis of Meiotic Prophase I Images
Computational Tools for the Analysis of Meiotic Prophase I Images
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DOI：
10.1101/2023.11.15.567191
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发表时间：
2024-03
期刊：
影响因子：
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通讯作者：
James H. Crichton;I. Adams
中科院分区：
文献类型：
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作者：
James H. Crichton;I. Adams
前期I是减数分裂的一个显著阶段，在此期间同源染色体配对并通过减数分裂重组交换DNA。减数分裂染色体扩散的荧光显微镜是研究这一过程的核心工具，染色体轴蛋白被可视化为延伸的细丝，重组蛋白定位在焦点图案上。染色体配对和重组是一个动态过程，在某些减数分裂细胞核中可存在数百个重组灶。由于减数分裂细胞核可以在细胞核内和细胞核之间表现出染色模式的显著变化，特别是在突变体中，图像的手动分析对一致性、记录和再现性提出了挑战。在这里，我们分享一个互补的计算工具，可用于部分自动化减数分裂图像的定量分析的组合。1)分割轴向和局灶染色模式，自动测量染色体轴长并计数相关轴（和非轴相关的）重组灶; 2）量化沿沿着染色体轴的灶位置以研究空间调节; 3）模拟核内或沿着染色体轴的灶的随机分布以统计学研究观察到的灶-轴关联和灶-灶关联; 4）染色体轴接近度的定量以研究与染色体联会/不联会的关系; 5）聚焦轴距离的定量和方向。这些工具共同提供了一个框架，用于对减数分裂图像进行常规记录和分析，并开辟了在此初始输出的基础上进行更详细分析的途径。
Prophase I is a remarkable stage of meiotic division during which homologous chromosomes pair together and exchange DNA by meiotic recombination. Fluorescence microscopy of meiotic chromosome spreads is a central tool in the study of this process, with chromosome axis proteins being visualised as extended filaments upon which recombination proteins localise in focal patterns. Chromosome pairing and recombination are dynamic processes, and hundreds of recombination foci can be present in some meiotic nuclei. As meiotic nuclei can exhibit significant variations in staining patterns within and between nuclei, particularly in mutants, manual analysis of images presents challenges for consistency, documentation, and reproducibility. Here we share a combination of complementary computational tools which can be used to partially automate the quantitative analysis of meiotic images. 1) The segmentation of axial and focal staining patterns, to automatically measure chromosome axis length and count axis-associated (and non-axis associated) recombination foci; 2) Quantification of focus position along chromosome axes to investigate spatial regulation; 3) Simulation of random distributions of foci within the nucleus or along the chromosome axes to statistically investigate observed foci-axis associations and foci-foci associations; 4) Quantification of chromosome axis proximity to investigate relationships with chromosome synapsis/asynapsis; 5) Quantification of and orientation of focus-axis distances. Together these tools provide a framework to perform routine documentation and analysis of meiotic images, as well as opening up routes to build on this initial output and perform more detailed analyses.