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
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.