High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

Area of Science:

• Genomics
• Molecular Biology
• Genetics

Background:

• Detecting structural rearrangements, especially error-free sister-chromatid exchanges, in single cells is a significant challenge in genomics.
• Existing methods lack the scalability and resolution needed to comprehensively map mitotic crossover events and genome instability.

Purpose of the Study:

• To introduce sci-L3-Strand-seq, a scalable single-cell sequencing method for mapping mitotic crossovers and genome instability.
• To develop a computational framework for analyzing multifaceted single-cell genotype data, including strandedness and copy number.

Main Methods:

• sci-L3-Strand-seq: a combinatorial indexing and linear amplification method for DNA template strand sequencing.
• Computational analysis of strandedness, digital copy number counting, and haplotype-aware chromosome segmentation.
• Quantification of error-free and mutational crossovers across thousands of single cells.

Main Results:

• Successfully quantified error-free and mutational crossover rates in thousands of cells.
• Enabled exploration of genomic and epigenomic feature enrichment patterns.
• Revealed insights into the temporal order of genome instability events through clonal lineage mapping.

Conclusions:

• sci-L3-Strand-seq provides a cost-effective platform for large-scale single-cell analysis of structural variations and genome instability.
• The method facilitates the study of DNA repair mechanisms and has potential applications in cancer evolution research and large-scale mutational screens.