Human genomic DNA is widely interspersed with i-motif structures
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.
Authors
- Daniel Christ (ORCID: https://orcid.org/0000-0002-7313-3977)
- Cristian David Peña Martinez (ORCID: https://orcid.org/0000-0003-1048-6158)
- Nicole M. Smith (ORCID: https://orcid.org/0000-0002-5519-8152)
- Brian Gloss (ORCID: https://orcid.org/0000-0001-7695-4394)
- Romain Rouet (ORCID: https://orcid.org/0000-0003-4210-9613)
- Emanuela Ruggiero (ORCID: https://orcid.org/0000-0003-0989-4074)
- Maja Marušič (ORCID: https://orcid.org/0000-0001-6595-193X)
- Ohan Mazigi
- Cameron W. Evans (ORCID: https://orcid.org/0000-0003-2312-9803)
- Marcel E. Dinger (ORCID: https://orcid.org/0000-0003-4423-934X)
- Sarah Kummerfeld (ORCID: https://orcid.org/0000-0002-0089-2358)
- Tracy M. Bryan (ORCID: https://orcid.org/0000-0002-7990-5501)
- Irene Zanin (ORCID: https://orcid.org/0000-0003-2095-4170)
- Janez Plavec (ORCID: https://orcid.org/0000-0003-1570-8602)
- Sara N. Richter (ORCID: https://orcid.org/0000-0002-5446-9029)
- Jake Y. Henry (ORCID: https://orcid.org/0000-0003-0435-3308)
- Jessica A. Kretzmann (ORCID: https://orcid.org/0000-0002-8680-7766)
- Mahdi Zeraati (ORCID: https://orcid.org/0000-0002-7198-5738)
Institutions
- The University of Sydney (AU)
- Garvan Institute of Medical Research (AU)
- University of Padua (IT)
- Children's Medical Research Institute (AU)
- The University of Western Australia (AU)
- UNSW Sydney (AU)
- St Vincent's Clinic (AU)
- National Institute of Chemistry (SI)
Publication Details
- Journal
- The EMBO Journal
- Published
- 2024-08-29
- DOI
- https://doi.org/10.1038/s44318-024-00210-5
- Citations
- 33
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 7.25
Funders
- Children's Medical Research
- Medical Research Council
- National Health and Medical Research Council