High resolution mapping of sister chromatid exchanges in single cells using DNA template strand sequencing

Current single cell sequencing techniques mask DNA rearrangements such as sister chromatid exchanges (SCE), the accumulation of which is a sensitive indicator of genomic instability. Here we show that sequencing only parental DNA template strands (Strand-Seq) in single murine embryonic stem cells (mES) maps SCE events with orders of magnitude greater resolution than previously possible. On average, mES cells exhibit 8 SCEs per cell that were detected at a resolution of up to 23 bp, with a median of 6 kb. Strikingly, sequencing 62 single ES cells by Strand-Seq predicts that the mm9 assembly of the mouse reference genome contains at least 17 incorrectly oriented segments totaling nearly 1% of the genome. These mis-oriented contigs and fragments have persisted through several iterations of the mouse reference genome and have been difficult to detect using conventional sequencing techniques. The ability to map genomic rearrangements and fine tune reference genomes by Strand-Seq dramatically expands the scope of single cell sequencing.