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Article

DNA G-Quadruplexes Contribute to CTCF Recruitment

1
Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
2
Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
3
A.V. Topchiev Institute of Petrochemical Synthesis RAS, 119071 Moscow, Russia
4
WCRC Russia “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
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Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
6
Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia
*
Authors to whom correspondence should be addressed.
Academic Editor: Amelia Casamassimi
Int. J. Mol. Sci. 2021, 22(13), 7090; https://doi.org/10.3390/ijms22137090
Received: 4 June 2021 / Revised: 25 June 2021 / Accepted: 25 June 2021 / Published: 30 June 2021
G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome. G4s bound CTCF with Kd values similar to that of the control duplex, while respective i-motifs exhibited no affinity for CTCF. Using ChIP-qPCR assays, we showed that G4-stabilizing ligands enhance CTCF occupancy at a G4-prone site in STAT3 gene. In view of the reportedly increased CTCF affinity for hypomethylated DNA, we next questioned whether G4s also facilitate CTCF recruitment to CGIs via protecting CpG sites from methylation. Bioinformatics analysis of previously published data argued against such a possibility. Finally, we questioned whether G4s facilitate CTCF recruitment by affecting chromatin structure. We showed that three architectural chromatin proteins of the high mobility group colocalize with G4s in the genome and recognize parallel-stranded or mixed-topology G4s in vitro. One of such proteins, HMGN3, contributes to the association between G4s and CTCF according to our bioinformatics analysis. These findings support both direct and indirect roles of G4s in CTCF recruitment. View Full-Text
Keywords: G-quadruplex; chromatin remodeling; CpG methylation; CTCF; HMG proteins G-quadruplex; chromatin remodeling; CpG methylation; CTCF; HMG proteins
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MDPI and ACS Style

Tikhonova, P.; Pavlova, I.; Isaakova, E.; Tsvetkov, V.; Bogomazova, A.; Vedekhina, T.; Luzhin, A.V.; Sultanov, R.; Severov, V.; Klimina, K.; Kantidze, O.L.; Pozmogova, G.; Lagarkova, M.; Varizhuk, A. DNA G-Quadruplexes Contribute to CTCF Recruitment. Int. J. Mol. Sci. 2021, 22, 7090. https://doi.org/10.3390/ijms22137090

AMA Style

Tikhonova P, Pavlova I, Isaakova E, Tsvetkov V, Bogomazova A, Vedekhina T, Luzhin AV, Sultanov R, Severov V, Klimina K, Kantidze OL, Pozmogova G, Lagarkova M, Varizhuk A. DNA G-Quadruplexes Contribute to CTCF Recruitment. International Journal of Molecular Sciences. 2021; 22(13):7090. https://doi.org/10.3390/ijms22137090

Chicago/Turabian Style

Tikhonova, Polina, Iulia Pavlova, Ekaterina Isaakova, Vladimir Tsvetkov, Alexandra Bogomazova, Tatjana Vedekhina, Artem V. Luzhin, Rinat Sultanov, Vjacheslav Severov, Ksenia Klimina, Omar L. Kantidze, Galina Pozmogova, Maria Lagarkova, and Anna Varizhuk. 2021. "DNA G-Quadruplexes Contribute to CTCF Recruitment" International Journal of Molecular Sciences 22, no. 13: 7090. https://doi.org/10.3390/ijms22137090

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