Genome-wide profiling of endogenous single-stranded DNA using SSiNGLe-P1 method

Endogenous single-stranded DNA (essDNA) can form in a mammalian genome as the result of a variety of molecular processes and can both play important roles inside the cell as well as have detrimental consequences to genome integrity — much of which remains to be fully understood. Here we established SSiNGLe-P1 approach based on limited digestion by P1 endonuclease for high-throughput genome-wide identification of essDNA regions in human cells. We applied this method to profile essDNA in both the mitochondrial and nuclear genomes. In the mitochondrial genome, the profiles of essDNA provide new evidence to support the strand-displacement model of mitochondrial DNA replication. In the nuclear genome, essDNAs were found to be enriched in certain types of functional genomic elements, particularly, origins of DNA replication, R-loops, and to a lesser degree, in promoters. Furthermore, many of the essDNA regions identified by SSiNGLe-P1 have not been annotated and thus represent yet unknown functional elements. Established a next-generation sequencing based approach for identification of endogenous single-stranded DNA