Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region

• Published in: Nature communications 2024-08, Vol.15 (1), p.7119-11
• Main Authors: Guneri, Dilek, Alexandrou, Effrosyni, El Omari, Kamel, Dvořáková, Zuzana, Chikhale, Rupesh V., Pike, Daniel T. S., Waudby, Christopher A., Morris, Christopher J., Haider, Shozeb, Parkinson, Gary N., Waller, Zoë A. E.
• Format: Article
• Language: English
• Subjects: 101/6; 13; 13/106; 38; 49; 631/535/1266; 631/57/2272/2273; 631/92/147; 639/638/92/147; Animals; Base Sequence; Crystal structure; Crystallography, X-Ray; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; DNA structure; Drug development; Dynamic structural analysis; G-Quadruplexes; Gene expression; Gene sequencing; Genes, Reporter; Humanities and Social Sciences; Humans; Insulin; Insulin - chemistry; Insulin - genetics; Models, Molecular; multidisciplinary; Nucleic Acid Conformation; Nucleotide Motifs; Nucleotide sequence; Polymorphism, Genetic; Promoter Regions, Genetic; Science; Science (multidisciplinary); Tandem Repeat Sequences - genetics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50553-0

The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA in the promoter of the insulin gene that regulates transcription of insulin. This region is known to form the alternative DNA structures, i-motifs and G-quadruplexes. Individuals have different sequence variants of tandem repeats and although previous work investigated the effects of some variants on G-quadruplex formation, there is not a clear picture of the relationship between the sequence diversity, the DNA structures formed, and the functional effects on insulin gene expression. Here we show that different sequence variants of the insulin linked polymorphic region form different DNA structures in vitro. Additionally, reporter genes in cellulo indicate that insulin expression may change depending on which DNA structures form. We report the crystal structure and dynamics of an intramolecular i-motif, which reveal sequences within the loop regions forming additional stabilising interactions that are critical to formation of stable i-motif structures. The outcomes of this work reveal the detail in formation of stable i-motif DNA structures, with potential for rational based drug design for compounds to target i-motif DNA. DNA sequences from the insulin-linked polymorphic region can form non-canonical structures. Here, the authors present a structural investigation into the relationship between native sequence variants and the different structures they form.