Non-canonical DNA secondary structures (non-B DNA), such as G-quadruplexes and triplex DNA, are mutation hotspots and genome regulators contributing to disease and evolution. Yet they remain poorly characterized in vivo in completely sequenced genomes. Many non-B DNA structures induce single-stranded DNA (ssDNA) formation. Here, using Permanganate/S1 footprinting with Direct Adapter Ligation and Sequencing (PDAL-Seq) across 14 cell lines, we generated comparative ssDNA profiles for human and six non-human ape telomere-to-telomere (T2T) genomes. Newly resolved satellite arrays displayed high ssDNA levels, implicating non-B DNA in satellite expansion and function. Hidden Markov Models applied to PDAL-Seq data revealed conserved active genomic regions enriched in non-B DNA and exhibiting elevated replication initiation, gene expression, and/or recombination. Human-specific ssDNA states correlated with nervous system genes, whereas cancer and embryonic cells showed increased ssDNA in transposable elements. This comprehensive ssDNA analysis across ape T2T genomes uncovers conserved and species-specific DNA structural dynamics central to genome regulation in differentiated, embryonic, and cancer cells.
Jacob Sieg is a postdoc of Makova Lab in the Department of Biology. Jacob’s current research in Makova Lab uses a combination of experimental and computational approaches to characterize the role of non-canonical DNA secondary structures in primate genomes. Before joining Makova Lab, Jacob studied RNA biochemistry. His Ph.D. thesis work with Dr. Philip Bevilacqua updated thermodynamic models that describe RNA secondary structures to better reflect the cellular environment. His undergraduate thesis work focused on drug targeting RNA thermometers in bacteria.