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Human genomic DNA is widely interspersed with i-motif structures

Affiliations
  • 1Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia.
  • 2St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia.
  • 3School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia.
  • 4School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia.
  • 5Department of Molecular Medicine, University of Padua, 35121, Padua, Italy.
  • 6Slovenian NMR Centre, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia.
  • 7Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2145, Australia.
  • 8Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia.
  • 9Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia. d.christ@garvan.org.au.
  • 10St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia. d.christ@garvan.org.au.

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August 29, 2024

Abstract

DNA i-motif structures are formed in the nuclei of human cells and are believed to provide critical genomic regulation. While the existence, abundance, and distribution of i-motif structures in human cells has been demonstrated and studied by immunofluorescent staining, and more recently NMR and CUT&Tag, the abundance and distribution of such structures in human genomic DNA have remained unclear. Here we utilise high-affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in the purified genomic DNA of human MCF7, U2OS and HEK293T cells. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach aimed to identify DNA sequences capable of i-motif formation on a genome-wide scale, revealing that such sequences are widely distributed throughout the human genome and are common in genes upregulated in G0/G1 cell cycle phases. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA and a foundational resource for future studies of their genomic, structural, and molecular roles.

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