S1-END-seq reveals DNA secondary structures in human cells

Gabriel Matos-Rodrigues, Niek van Wietmarschen, Wei Wu, Veenu Tripathi, Natasha C. Koussa, Raphael Pavani, William J. Nathan, Elsa Callen, Frida Belinky, Ashraf Mohammed, Marek Napierala, Karen Usdin, Aseem Z. Ansari, Sergei M. Mirkin, André Nussenzweig

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


DNA becomes single stranded (ssDNA) during replication, transcription, and repair. Transiently formed ssDNA segments can adopt alternative conformations, including cruciforms, triplexes, and quadruplexes. To determine whether there are stable regions of ssDNA in the human genome, we utilized S1-END-seq to convert ssDNA regions to DNA double-strand breaks, which were then processed for high-throughput sequencing. This approach revealed two predominant non-B DNA structures: cruciform DNA formed by expanded (TA)n repeats that accumulate in microsatellite unstable human cancer cell lines and DNA triplexes (H-DNA) formed by homopurine/homopyrimidine mirror repeats common across a variety of cell lines. We show that H-DNA is enriched during replication, that its genomic location is highly conserved, and that H-DNA formed by (GAA)n repeats can be disrupted by treatment with a (GAA)n-binding polyamide. Finally, we show that triplex-forming repeats are hotspots for mutagenesis. Our results identify dynamic DNA secondary structures in vivo that contribute to elevated genome instability.

Original languageEnglish (US)
Pages (from-to)3538-3552.e5
JournalMolecular cell
Issue number19
StatePublished - Oct 6 2022
Externally publishedYes


  • cruciforms
  • DNA secondary structures
  • END-seq
  • Friederichs ataxia
  • genome instability
  • H-DNA
  • mutations
  • non B-DNA
  • triplexes

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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