A3A-ssDNA-seq Raw sequence reads (Mus musculus)

Dynamic and fragile single stranded (ss) DNA, a template for RNA transcription, DNA replication, and DNA repair, is distributed widely in genomes of prokaryotes and eukaryotes. Here, we introduce an APOBEC3A (A3A) deamination-assisted ssDNA sequencing approach (A3A-ssDNA-seq), which is characterized by its extraordinary specificity and high reaction efficiency of cytosine deamination within genomics ssDNA regions under mild and un-denaturing conditions. Thus the resolution of genome-wide mapping of ssDNA is higher, reaching near single nucleotide, using the approach than the reported capturing-mediated enrichment method. Using the approach, we identified genome-wide R-loop structure and demonstrated an association of the structure with gene transcription regulation. We found that the fragile ssDNA is widely distributed in the genome of mouse embryonic stem cells, accounting for 0.6-1.4%, which is significantly higher than the previously reported. These data suggest that the approach enables us precisely identifying ssDNA and R-loop genome-widely.