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 required for comprehensive analysis of mitotic events.

Purpose of the Study:

• To introduce sci-L3-Strand-seq, a novel combinatorial indexing method for DNA template strand sequencing.
• To provide a scalable and cost-effective platform for mapping mitotic crossover (CO) and genome instability events in millions of single cells.

Main Methods:

• Developed sci-L3-Strand-seq, a method combining combinatorial indexing and linear amplification for DNA template strand sequencing.
• Created a computational framework to analyze single-cell genotype data, including strandedness, copy number, and haplotype information.
• Systematically distinguished seven types of mitotic CO outcomes.

Main Results:

• Quantified error-free and mutational crossover rates in thousands of single cells using sci-L3-Strand-seq.
• Explored enrichment patterns of genomic and epigenomic features associated with crossovers.
• Measured subtle phenotypes and mapped clonal lineages to understand genome instability.
• Provided insights into the temporal order of genome instability events and cancer evolution.

Conclusions:

• Sci-L3-Strand-seq offers a powerful, scalable platform for studying DNA repair and structural variations at single-cell resolution.
• The method enables exploration of genomic and epigenomic features and facilitates large-scale mutational screens.
• It has the potential to dissect complex processes like cancer evolution by mapping clonal lineages and instability events.