Human genomic DNA is widely interspersed with i-motif structures

Cristian David Peña Martinez; Mahdi Zeraati; Romain Rouet; Ohan Mazigi; Jake Y Henry; Brian Gloss; Jessica A Kretzmann; Cameron W Evans; Emanuela Ruggiero; Irene Zanin; Maja Marušič; Janez Plavec; Sara N Richter; Tracy M Bryan; Nicole M Smith; Marcel E Dinger; Sarah Kummerfeld; Daniel Christ

doi:10.1038/s44318-024-00210-5

Human genomic DNA is widely interspersed with i-motif structures

EMBO J. 2024 Oct;43(20):4786-4804. doi: 10.1038/s44318-024-00210-5. Epub 2024 Aug 29.

Authors

Cristian David Peña Martinez^{1

2}, Mahdi Zeraati^{1

2

3}, Romain Rouet^{1

2}, Ohan Mazigi^{1

2}, Jake Y Henry^{1

2}, Brian Gloss^{1

2}, Jessica A Kretzmann⁴, Cameron W Evans⁴, Emanuela Ruggiero⁵, Irene Zanin⁵, Maja Marušič⁶, Janez Plavec⁶, Sara N Richter⁵, Tracy M Bryan⁷, Nicole M Smith⁴, Marcel E Dinger^{1

2

8}, Sarah Kummerfeld^{1

2}, Daniel Christ^{9

10}

Affiliations

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

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.

Keywords: Antibody; DNA Quadruplex Structures; Immunoprecipitation; i-motif; iMab.

MeSH terms

DNA* / chemistry
DNA* / genetics
DNA* / metabolism
Genome, Human*
HEK293 Cells
Humans
MCF-7 Cells
Nucleic Acid Conformation
Nucleotide Motifs*

Substances

DNA

Grants and funding

1157744/DHAC | National Health and Medical Research Council (NHMRC)