Triplexes are Dynamic DNA Secondary Structures Formed in vivo and Linked to Genome Instability [END-seq]

Numerous indirect, genetic approaches in various experimental systems have implicated dynamic alternative non-B DNA structures in human physiology and disease. Nevertheless, direct detection of dynamic DNA structures in vivo remains a challenge. To address this problem, we developed a new methods to visualize ssDNA containing alternative DNA structures. We described an uncharted landscape of dynamic alternative DNA structures formed by DNA cruciform and DNA triplexes (H-DNA) that contribute to genome instability. We used a combinatorial approach of END-seq, S1-END-seq and P1-END-seq to detect alternative DNA structures in vivo in human cells