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

Area of Science:

• Genomics
• Molecular Biology
• DNA Structure

Background:

• Single-stranded DNA (ssDNA) transiently forms during DNA processes.
• ssDNA can adopt alternative conformations like cruciforms, triplexes, and quadruplexes.
• The presence and stability of ssDNA regions in the human genome are not well understood.

Purpose of the Study:

• To identify and characterize stable single-stranded DNA (ssDNA) regions in the human genome.
• To investigate the types and genomic locations of non-B DNA structures.
• To explore the relationship between these structures and genome instability.

Main Methods:

• Utilized S1-END-seq to convert ssDNA regions into DNA double-strand breaks.
• Processed breaks for high-throughput sequencing to map ssDNA regions.
• Analyzed sequence data to identify non-B DNA structures and their genomic context.

Main Results:

• Identified two predominant non-B DNA structures: cruciform DNA and DNA triplexes (H-DNA).
• Cruciform DNA is associated with expanded (TA)n repeats in microsatellite unstable cancer cell lines.
• H-DNA, formed by homopurine/homopyrimidine mirror repeats, is enriched during replication and conserved across cell lines.
• H-DNA formation can be modulated, and triplex-forming repeats are mutagenesis hotspots.

Conclusions:

• Dynamic DNA secondary structures, including cruciforms and H-DNA, exist stably in the human genome.
• These structures are associated with specific repeat sequences and are enriched during replication.
• The identified non-B DNA structures contribute to elevated genome instability and mutagenesis.