References
References
[1] Capra, John A., Katrin Paeschke, Mona Singh, and Virginia A. Zakian. 2010. “G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces Cerevisiae.” PLoS Computational Biology 6 (7): e1000861.
https://doi.org/10.1371/journal.pcbi.1000861.
[2] Marzano, Simona, Gabriella Pinto, Anna Di Porzio, Jussara Amato, Antonio Randazzo, Angela Amoresano, and Bruno Pagano. 2025. “Identifying G-Quadruplex-Interacting Proteins in Cancer-Related Gene Promoters.” Communications Chemistry 8 (1): 64.
https://doi.org/10.1038/s42004-025-01462-w.
[3] Raguseo, Federica, Yiran Wang, Jessica Li, Marija Petrić Howe, Rubika Balendra, Anouk Huyghebaert, Devkee M. Vadukul, et al. 2023. “The ALS/FTD-Related C9orf72 Hexanucleotide Repeat Expansion Forms RNA Condensates through Multimolecular G-Quadruplexes.” Nature Communications 14 (1): 8272.
https://doi.org/10.1038/s41467-023-43872-1.
[4] Ishiguro, Akira. 2026. “Impact of G-Quadruplex RNA Oxidation on Its Conformational Dynamics and Interaction with ALS-Associated TDP-43.” Scientific Reports 16 (1).
https://doi.org/10.1038/s41598-026-39767-y.
[5] Beaudoin, Jean-Denis, and Jean-Pierre Perreault. 2010. “5’-UTR G-Quadruplex Structures Acting as Translational Repressors.” Nucleic Acids Research 38 (20): 7022–36.
https://doi.org/10.1093/nar/gkq557.
[6] Figueiredo, Joana, Jean-Louis Mergny, and Carla Cruz. 2024. “G-Quadruplex Ligands in Cancer Therapy: Progress, Challenges, and Clinical Perspectives.” Life Sciences 340 (122481): 122481.
https://doi.org/10.1016/j.lfs.2024.122481.
[7] Romano, Francesca, Anna Di Porzio, Nunzia Iaccarino, Gelsomina Riccardi, Ritamaria Di Lorenzo, Sonia Laneri, Bruno Pagano, Jussara Amato, and Antonio Randazzo. 2023. “G-Quadruplexes in Cancer-Related Gene Promoters: From Identification to Therapeutic Targeting.” Expert Opinion on Therapeutic Patents 33 (11): 745–73.
https://doi.org/10.1080/13543776.2023.2271168.
[8] “GEO Accession Viewer.” n.d. Nih.gov. Accessed April 14, 2026.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152216.
[9] Hänsel-Hertsch, Robert, Angela Simeone, Abigail Shea, Winnie W. I. Hui, Katherine G. Zyner, Giovanni Marsico, Oscar M. Rueda, et al. 2020. “Landscape of G-Quadruplex DNA Structural Regions in Breast Cancer.” Nature Genetics 52 (9): 878–83.
https://doi.org/10.1038/s41588-020-0672-8.
[10] Calabrese, David R., Xiang Chen, Elena C. Leon, Snehal M. Gaikwad, Zaw Phyo, William M. Hewitt, Stephanie Alden, et al. 2018. “Chemical and Structural Studies Provide a Mechanistic Basis for Recognition of the MYC G-Quadruplex.” Nature Communications 9 (1): 4229.
https://doi.org/10.1038/s41467-018-06315-w.
[11] Kumar, Niti, Ashok Patowary, Sridhar Sivasubbu, Michael Petersen, and Souvik Maiti. 2008. “Silencing C-MYC Expression by Targeting Quadruplex in P1 Promoter Using Locked Nucleic Acid Trap.” Biochemistry 47 (50): 13179–88.
https://doi.org/10.1021/bi801064j.
[12] Siddiqui-Jain, Adam, Cory L. Grand, David J. Bearss, and Laurence H. Hurley. 2002. “Direct Evidence for a G-Quadruplex in a Promoter Region and Its Targeting with a Small Molecule to Repress c-MYC Transcription.” Proceedings of the National Academy of Sciences of the United States of America 99 (18): 11593–98.
https://doi.org/10.1073/pnas.182256799.
[13] Raudvere, Uku, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, and Jaak Vilo. 2019. “G:Profiler: A Web Server for Functional Enrichment Analysis and Conversions of Gene Lists (2019 Update).” Nucleic Acids Research 47 (W1): W191–98.
https://doi.org/10.1093/nar/gkz369.
[14] Barcia, Giulia, Matthew R. Fleming, Aline Deligniere, Valeswara-Rao Gazula, Maile R. Brown, Maeva Langouet, Haijun Chen, et al. 2012. “De Novo Gain-of-Function KCNT1 Channel Mutations Cause Malignant Migrating Partial Seizures of Infancy.” Nature Genetics 44 (11): 1255–59.
https://doi.org/10.1038/ng.2441.
[15] Giubellino, Alessio, Terrence R. Burke Jr, and Donald P. Bottaro. 2008. “Grb2 Signaling in Cell Motility and Cancer.” Expert Opinion on Therapeutic Targets 12 (8): 1021–33.
https://doi.org/10.1517/14728222.12.8.1021.
[16] Doni Jayavelu, Naresh, Ajay Jajodia, Arpit Mishra, and R. David Hawkins. 2020. “Candidate Silencer Elements for the Human and Mouse Genomes.” Nature Communications 11 (1): 1061.
https://doi.org/10.1038/s41467-020-14853-5.
[17] Bretones, Gabriel, M. Dolores Delgado, and Javier León. 2015. “Myc and Cell Cycle Control.” Biochimica et Biophysica Acta 1849 (5): 506–16.
https://doi.org/10.1016/j.bbagrm.2014.03.013.
[18] Hnisz, Denes, Brian J. Abraham, Tong Ihn Lee, Ashley Lau, Violaine Saint-André, Alla A. Sigova, Heather A. Hoke, and Richard A. Young. 2013. “Super-Enhancers in the Control of Cell Identity and Disease.” Cell 155 (4): 934–47.
https://doi.org/10.1016/j.cell.2013.09.053.
[19] Kim, Baek Gil, Sung Hwan Lee, Yeonsue Jang, Suki Kang, Chang Moo Kang, and Nam Hoon Cho. 2024. “Differentially Expressed Genes Associated with High Metabolic Tumor Volume Served as Diagnostic Markers and Potential Therapeutic Targets for Pancreatic Cancer.” Journal of Translational Medicine 22 (1): 453.
https://doi.org/10.1186/s12967-024-05181-z.
[20] Li, Changchang, Nanhui Wu, Xiaoqiong Lin, Qiaochu Zhou, and Mingyuan Xu. 2024. “Integrated Transcriptomic and Immunological Profiling Reveals New Diagnostic and Prognostic Models for Cutaneous Melanoma.” Frontiers in Pharmacology 15: 1389550.
https://doi.org/10.3389/fphar.2024.1389550.
[21] Xiang, Ying, Kai Yan, Qian Zheng, Haiqiang Ke, Jie Cheng, Wenjun Xiong, Xin Shi, et al. 2019. “Histone Demethylase KDM4B Promotes DNA Damage by Activating Long Interspersed Nuclear Element-1.” Cancer Research 79 (1): 86–98.
https://doi.org/10.1158/0008-5472.CAN-18-1310.
[22] Vacic, Vladimir, Shane McCarthy, Dheeraj Malhotra, Fiona Murray, Hsun-Hua Chou, Aine Peoples, Vladimir Makarov, et al. 2011. “Duplications of the Neuropeptide Receptor Gene VIPR2 Confer Significant Risk for Schizophrenia.” Nature 471 (7339): 499–503.
https://doi.org/10.1038/nature09884.
[23] Qiu, Le, Fei Wang, Sheng Liu, and Xu-Lin Chen. 2014. “Current Understanding of Tyrosine Kinase BMX in Inflammation and Its Inhibitors.” Burns & Trauma 2 (3): 121–24.
https://doi.org/10.4103/2321-3868.135483.
[24] Kunvariya, Aditi D., Shivani A. Dave, Zeal J. Modi, Paresh K. Patel, and Sneha R. Sagar. 2023. “Exploration of Multifaceted Molecular Mechanism of Angiotensin-Converting Enzyme 2 (ACE2) in Pathogenesis of Various Diseases.” Heliyon 9 (5): e15644.
https://doi.org/10.1016/j.heliyon.2023.e15644.
[25] Vaish, Vivek, Joohwee Kim, and Minsub Shim. 2017. “Jagged-2 (JAG2) Enhances Tumorigenicity and Chemoresistance of Colorectal Cancer Cells.” Oncotarget 8 (32): 53262–75.
https://doi.org/10.18632/oncotarget.18391.
[26] Boyer, Laurie A., Tong Ihn Lee, Megan F. Cole, Sarah E. Johnstone, Stuart S. Levine, Jacob P. Zucker, Matthew G. Guenther, et al. 2005. “Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells.” Cell 122 (6): 947–56.
https://doi.org/10.1016/j.cell.2005.08.020.
[27] Hansen, Tyler J., and Emily Hodges. 2022. “ATAC-STARR-Seq Reveals Transcription Factor-Bound Activators and Silencers within Chromatin-Accessible Regions of the Human Genome.” Genome Research 32 (8): 1529–41.
https://doi.org/10.1101/gr.276766.122.
[28] Fiskerstrand, Torunn, Dorra H’mida-Ben Brahim, Stefan Johansson, Abderrahim M’zahem, Bjørn Ivar Haukanes, Nathalie Drouot, Julian Zimmermann, et al. 2010. “Mutations in ABHD12 Cause the Neurodegenerative Disease PHARC: An Inborn Error of Endocannabinoid Metabolism.” American Journal of Human Genetics 87 (3): 410–17.
https://doi.org/10.1016/j.ajhg.2010.08.002.
[29] Antonarakis, Stylianos E., Brian G. Skotko, Michael S. Rafii, Andre Strydom, Sarah E. Pape, Diana W. Bianchi, Stephanie L. Sherman, and Roger H. Reeves. 2020. “Down Syndrome.” Nature Reviews. Disease Primers 6 (1): 9.
https://doi.org/10.1038/s41572-019-0143-7.
[30] Dang, Chi V. 2012. “MYC on the Path to Cancer.” Cell 149 (1): 22–35.
https://doi.org/10.1016/j.cell.2012.03.003.
[31] Feng, Yu Chen, Xiao Ying Liu, Liu Teng, Qiang Ji, Yongyan Wu, Jin Ming Li, Wei Gao, et al. 2020. “C-Myc Inactivation of P53 through the Pan-Cancer lncRNA MILIP Drives Cancer Pathogenesis.” Nature Communications 11 (1): 4980.
https://doi.org/10.1038/s41467-020-18735-8.
[32] Raiber, Eun-Ang, Ramon Kranaster, Enid Lam, Mehran Nikan, and Shankar Balasubramanian. 2012. “A Non-Canonical DNA Structure Is a Binding Motif for the Transcription Factor SP1 in Vitro.” Nucleic Acids Research 40 (4): 1499–1508.
https://doi.org/10.1093/nar/gkr882.