Abstract
G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC.
Recommended Citation
Y. P. Bhavsar-Jog et al., "Co-Localization of Dna I-Motif-Forming Sequences and 5-Hydroxymethyl-Cytosines in Human Embryonic Stem Cells," Molecules, vol. 24, no. 19, article no. 3619, MDPI, Oct 2019.
The definitive version is available at https://doi.org/10.3390/molecules24193619
Department(s)
Chemistry
Publication Status
Open Access
Keywords and Phrases
Cytosine-rich DNA; DNA nanomaterials; DNA secondary structures
International Standard Serial Number (ISSN)
1420-3049
Document Type
Article - Journal
Document Version
Final Version
File Type
text
Language(s)
English
Rights
© 2024 The Authors, All rights reserved.
Creative Commons Licensing
This work is licensed under a Creative Commons Attribution 4.0 License.
Publication Date
08 Oct 2019
PubMed ID
31597270
Comments
National Institutes of Health, Grant 1R15CA173667-01A1