Landscape of G-quadruplex DNA structural regions in breast cancer
Open accessAbstract
Response and resistance to anticancer therapies vary due to intertumor and intratumor heterogeneity 1. Here, we map differentially enriched G-quadruplex (G4) DNA structure-forming regions (∆G4Rs) in 22 breast cancer patient-derived tumor xenograft (PDTX) models. ∆G4Rs are associated with the promoters of highly amplified genes showing high expression, and with somatic single-nucleotide variants. Differences in ΔG4R landscapes reveal seven transcription factor programs across PDTXs. ∆G4R abundance and locations stratify PDTXs into at least three G4-based subtypes. ∆G4Rs in most PDTXs (14 of 22) were found to associate with more than one breast cancer subtype, which we also call an integrative cluster (IC)2. This suggests the frequent coexistence of multiple breast cancer states within a PDTX model, the majority of which display aggressive triple-negative IC10 gene activity. Short-term cultures of PDTX models with increased ∆G4R levels are more sensitive to small molecules targeting G4 DNA. Thus, G4 landscapes reveal additional IC-related intratumor heterogeneity in PDTX biopsies, improving breast cancer stratification and potentially identifying new treatment strategies.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
G4-associated intratumor heterogeneity exists in breast cancer patient-derived tumor xenografts beyond current classifications.
“as a recent study revealed G4-associated intratumor heterogeneity in breast cancer patient-derived tumor xenografts beyond current classifications (90).”
From G-quadruplex-mediated genomic instability drives SNVs in cancer (2024) · cites this paper as [90]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
METABRIC Group, Curtis, C., Shah, S. P., Chin, S.-F., Turashvili, G., Rueda, O. M., Dunning, M. J., Speed, D., Lynch, A. G., Samarajiwa, S., et al. (2012) · Nature · doi:10.1038/nature10983 · Cited by 6,097 · see citing works
Self-citationQuantitative visualization of DNA G-quadruplex structures in human cells
Biffi, G., Tannahill, D., McCafferty, J., & Balasubramanian, S. (2013) · Nature Chemistry · doi:10.1038/nchem.1548 · Cited by 2,152 · see citing works
Self-citationPereira, B., Chin, S., Rueda, O. M., Vollan, H. K. M., Provenzano, E., Bardwell, H. A., Pugh, M., Jones, L. R., Russell, R., Sammut, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms11479 · Cited by 1,712 · see citing works
Self-citationPioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589 · see citing works
G-quadruplexes and their regulatory roles in biology
Rhodes, D., & Lipps, H. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv862 · Cited by 1,494 · see citing works
Epigenetic plasticity and the hallmarks of cancer
Flavahan, W. A., Gaskell, E., & Bernstein, B. E. (2017) · Science · doi:10.1126/science.aal2380 · Cited by 1,340 · see citing works
The regulation and functions of DNA and RNA G-quadruplexes
Varshney, D., Spiegel, J., Zyner, K. G., Tannahill, D., & Balasubramanian, S. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0236-x · Cited by 1,265 · see citing works
Self-citationHigh-throughput sequencing of DNA G-quadruplex structures in the human genome
Chambers, V. S., Marsico, G., Boutell, J. M., Antonio, M. D., Smith, G. P., & Balasubramanian, S. (2015) · Nature Biotechnology · doi:10.1038/nbt.3295 · Cited by 1,238 · see citing works
Self-citationG-quadruplex structures mark human regulatory chromatin
Hänsel-Hertsch, R., Beraldi, D., Lensing, S. V., Marsico, G., Zyner, K., Parry, A., Di Antonio, M., Pike, J., Kimura, H., Narita, M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3662 · Cited by 964 · see citing works
Self-citationDNA G-quadruplexes in the human genome: detection, functions and therapeutic potential
Hänsel‐Hertsch, R., Antonio, M. D., & Balasubramanian, S. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.3 · Cited by 882 · see citing works
Self-citationChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
Oki, S., Ohta, T., Shioi, G., Hatanaka, H., Ogasawara, O., Okuda, Y., Kawaji, H., Nakaki, R., Sese, J., & Meno, C. (2018) · The EMBO Reports · doi:10.15252/embr.201846255 · Cited by 763 · see citing works
CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours
Xu, H., Antonio, M. D., McKinney, S. E., Mathew, V., Ho, B., O’Neil, N. J., Santos, N. D., Silvester, J., Wei, V., Garcia, J., et al. (2017) · Nature Communications · doi:10.1038/ncomms14432 · Cited by 574 · see citing works
Self-citationPaeschke, K., Capra, J. A., & Zakian, V. A. (2011) · Cell · doi:10.1016/j.cell.2011.04.015 · Cited by 566 · see citing works
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Khan, A., & Mathelier, A. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1708-7 · Cited by 537 · see citing works
Rodriguez, R., Müller, S., Yeoman, J. A., Trentesaux, C., Riou, J.-F., & Balasubramanian, S. (2008) · Journal of the American Chemical Society · doi:10.1021/ja805615w · Cited by 517 · see citing works
Self-citationChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions
Schmidt, D., Wilson, M. D., Spyrou, C., Brown, G. D., Hadfield, J., & Odom, D. T. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.001 · Cited by 515 · see citing works
Quantitative ChIP-Seq normalization reveals global modulation of the epigenome
Orlando, D. A., Chen, M. W., Brown, V. E., Solanki, S., Choi, Y. J., Olson, E. R., Fritz, C. C., Bradner, J. E., & Guenther, M. G. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.018 · Cited by 503 · see citing works
Scheinin, I., Sie, D., Bengtsson, H. L., van de Wiel, M. A., Olshen, A. B., van Thuijl, H. F., Essen, H. F. H. V., Eijk, P. P., Rustenburg, F., Meijer, G. A., et al. (2014) · Genome Research · doi:10.1101/gr.175141.114 · Cited by 491 · see citing works
Whole genome experimental maps of DNA G-quadruplexes in multiple species
Marsico, G., Chambers, V. S., Sahakyan, A. B., McCauley, P., Boutell, J. M., Antonio, M. D., & Balasubramanian, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz179 · Cited by 435 · see citing works
Self-citationBruna, A., Rueda, O. M., Greenwood, W., Batra, A. S., Callari, M., Batra, R. N., McNamara, K. L., Sandoval, J. L., Cassidy, J. W., Vidaković, A. T., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.041 · Cited by 433 · see citing works
Self-citationDynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups
Rueda, O. M., Sammut, S., Seoane, J. A., Chin, S., Caswell-Jin, J. L., Callari, M., Batra, R. N., Pereira, B., Bruna, A., Ali, H. R., et al. (2019) · Nature · doi:10.1038/s41586-019-1007-8 · Cited by 412 · see citing works
Self-citationDistinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites
Gertz, J., Savic, D., Varley, K. E., Partridge, E. C., Safi, A., Jain, P., Cooper, G. M., Reddy, T. E., Crawford, G. E., & Myers, R. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.08.037 · Cited by 363 · see citing works
Hänsel‐Hertsch, R., Spiegel, J., Marsico, G., Tannahill, D., & Balasubramanian, S. (2018) · Nature Protocols · doi:10.1038/nprot.2017.150 · Cited by 335 · see citing works
Self-citationDisruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA
Cheung, I. K., Schertzer, M. J., Rose, A. M., & Lansdorp, P. M. (2002) · Nature Genetics · doi:10.1038/ng928 · Cited by 270 · see citing works
DNA G-quadruplex structures mold the DNA methylome
Mao, S.-Q., Ghanbarian, A. T., Spiegel, J., Cuesta, S. M., Beraldi, D., Antonio, M. D., Marsico, G., Hänsel‐Hertsch, R., Tannahill, D., & Balasubramanian, S. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0131-8 · Cited by 268 · see citing works
Self-citationTargeting BRCA1 and BRCA2 Deficiencies with G-Quadruplex-Interacting Compounds
Zimmer, J., Tacconi, E. M. C., Folio, C., Badie, S., Porru, M., Klare, K., Tumiati, M., Markkanen, E., Halder, S., Ryan, A., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2015.12.004 · Cited by 261 · see citing works
DNA secondary structures and epigenetic determinants of cancer genome evolution
De, S., & Franziska Michor, A. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2089 · Cited by 248 · see citing works
Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer Tissues
Biffi, G., Tannahill, D., Miller, J., Howat, W. J., & Balasubramanian, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102711 · Cited by 223 · see citing works
Self-citationG-Quadruplex DNA as a Molecular Target for Induced Synthetic Lethality in Cancer Cells
McLuckie, K. I. E., Antonio, M. D., Zecchini, H. I., Xian, J., Caldas, C., Krippendorff, B., Tannahill, D., Lowe, C., & Balasubramanian, S. (2013) · Journal of the American Chemical Society · doi:10.1021/ja404868t · Cited by 172 · see citing works
Self-citationPAVIS: a tool for Peak Annotation and Visualization
Huang, W., Loganantharaj, R., Schroeder, B., Fargo, D. C., & Li, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt520 · Cited by 157 · see citing works
DSBCapture: in situ capture and sequencing of DNA breaks
Lensing, S. V., Marsico, G., Hänsel‐Hertsch, R., Lam, E. Y. N., Tannahill, D., & Balasubramanian, S. (2016) · Nature Methods · doi:10.1038/nmeth.3960 · Cited by 155 · see citing works
Self-citationNoncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis
Georgakopoulos-Soares, I., Morganella, S., Jain, N., Hemberg, M., & Nik-Zainal, S. (2018) · Genome Research · doi:10.1101/gr.231688.117 · Cited by 146 · see citing works
G-quadruplex ligands exhibit differential G-tetrad selectivity.
Le, D., di Antonio, M., Chan, L. M., & Balasubramanian, S. (2015) · Chemical Communications · doi:10.1039/c5cc02252e · Cited by 90 · see citing works
Self-citationBouwman, B. A. M., & Crosetto, N. (2018) · Genes · doi:10.3390/genes9120632 · Cited by 54 · see citing works
Chin, S., Santonja, Á., Grzelak, M., Ahn, S., Sammut, S., Clifford, H., Rueda, O. M., Pugh, M., Goldgraben, M. A., Bardwell, H. A., et al. (2018) · Experimental and Molecular Pathology · doi:10.1016/j.yexmp.2018.03.006 · Cited by 31 · see citing works
Self-citation
Flagged first, then by citations
1 of the 37 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
G-quadruplexes: a promising target for cancer therapy
Kosiol, N., Juranek, S., Brossart, P., Heine, A., & Paeschke, K. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01328-4 · Cited by 540 · see citing works
Aggregation-Induced Emission (AIE), Life and Health
Wang, H., Li, Q., Alam, P., Bai, H., Bhalla, V., Bryce, M. R., Cao, M., Chen, C., Chen, S., Chen, X., et al. (2023) · ACS Nano · doi:10.1021/acsnano.3c03925 · Cited by 398 · see citing works
Self-citationZou, Z., Ohta, T., Miura, F., & Oki, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac199 · Cited by 350 · see citing works
DNA G-quadruplex structures: more than simple roadblocks to transcription?
Robinson, J., Raguseo, F., Nuccio, S. P., Liano, D., & Antonio, M. D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab609 · Cited by 312 · see citing works
G-quadruplexes are transcription factor binding hubs in human chromatin
Spiegel, J., Cuesta, S. M., Adhikari, S., Hänsel-Hertsch, R., Tannahill, D., & Balasubramanian, S. (2021) · Genome Biology · doi:10.1186/s13059-021-02324-z · Cited by 231 · see citing works
Self-citationLago, S., Nadai, M., Cernilogar, F. M., Kazerani, M., Domíniguez Moreno, H., Schotta, G., & Richter, S. N. (2021) · Nature Communications · doi:10.1038/s41467-021-24198-2 · Cited by 269 · see citing works
Genome-wide mapping of G-quadruplex structures with CUT&Tag
Lyu, J., Shao, R., Yung, P. Y. K., & Elsässer, S. J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1073 · Cited by 225 · see citing works
Chemical profiling of DNA G-quadruplex-interacting proteins in live cells
Zhang, X., Spiegel, J., Cuesta, S. M., Adhikari, S., & Balasubramanian, S. (2021) · Nature Chemistry · doi:10.1038/s41557-021-00736-9 · Cited by 154 · see citing works
Self-citationG-quadruplex DNA structure is a positive regulator of MYC transcription
Esain-Garcia, I., Kirchner, A., Melidis, L., Tavares, R. D. C. A., Dhir, S., Simeone, A., Yu, Z., Madden, S. K., Hermann, R., Tannahill, D., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2320240121 · Cited by 147 · see citing works
Self-citationG-quadruplex DNA structures in human stem cells and differentiation
Zyner, K. G., Simeone, A., Flynn, S. M., Doyle, C., Marsico, G., Adhikari, S., Portella, G., Tannahill, D., & Balasubramanian, S. (2022) · Nature Communications · doi:10.1038/s41467-021-27719-1 · Cited by 122 · see citing works
Self-citationPromoter G-quadruplex folding precedes transcription and is controlled by chromatin
Shen, J., Varshney, D., Simeone, A., Zhang, X., Adhikari, S., Tannahill, D., & Balasubramanian, S. (2021) · Genome biology · doi:10.1186/s13059-021-02346-7 · Cited by 118 · see citing works
Self-citationLigand-induced native G-quadruplex stabilization impairs transcription initiationPreprint
Li, C., Wang, H., Yin, Z., Fang, P., Xiao, R., Xiang, Y., Wang, W., Li, Q., Huang, B., Huang, J., et al. (2021) · Genome Research · doi:10.1101/gr.275431.121 · Cited by 115 · see citing works
Sun, Y. J., Lu, Y., Bian, M., Yang, Z., Ma, X., & Liu, W. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.113098 · Cited by 117 · see citing works
Xu, D., Li, Y., Yin, S., & Huang, F. (2024) · Chemical Society Reviews · doi:10.1039/d3cs00926b · Cited by 108 · see citing works
Identifying G-Quadruplex-DNA-Disrupting Small Molecules
Mitteaux, J., Lejault, P., Wojciechowski, F., Joubert, A., Boudon, J., Desbois, N., Gros, C. P., Hudson, R. H. E., Boulé, J.-B., Granzhan, A., et al. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c04426 · Cited by 107 · see citing works
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNAPreprint
Hudecova, I., Smith, C. G., Hänsel‐Hertsch, R., Chilamakuri, C. S. R., Morris, J. A., Vijayaraghavan, A., Heider, K., Chandrananda, D., Cooper, W. N., Gale, D. G., et al. (2021) · Genome Research · doi:10.1101/gr.275691.121 · Cited by 96 · see citing works
Self-citationHow to untie G-quadruplex knots and why?
Lejault, P., Mitteaux, J., Sperti, F. R., & Monchaud, D. (2021) · Cell chemical biology · doi:10.1016/j.chembiol.2021.01.015 · Cited by 96 · see citing works
Structural Basis of Pyridostatin and Its Derivatives Specifically Binding to G-Quadruplexes
Liu, L., Ma, T., Zeng, Y., Liu, W., & Mao, Z. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c04775 · Cited by 94 · see citing works
Single-cell mapping of DNA G-quadruplex structures in human cancer cells
Hui, W. W. I., Simeone, A., Zyner, K. G., Tannahill, D., & Balasubramanian, S. (2021) · Scientific Reports · doi:10.1038/s41598-021-02943-3 · Cited by 85 · see citing works
Self-citationG-quadruplex binders as cytostatic modulators of innate immune genes in cancer cells
Miglietta, G., Russo, M. V., Duardo, R. C., & Capranico, G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab500 · Cited by 72 · see citing works
The Relevance of G-Quadruplexes for DNA Repair
Linke, R., Limmer, M., Juranek, S., Heine, A., & Paeschke, K. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222212599 · Cited by 64 · see citing works
Metal Ion Signaling in Biomedicine
Rodriguez, R., Müller, S., Colombeau, L., Solier, S., Sindikubwabo, F., & Cañeque, T. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00577 · Cited by 66 · see citing works
Pramanik, S., Chen, Y., Song, H., Khutsishvili, I., Marky, L. A., Ray, S., Natarajan, A., Singh, P. K., & Bhakat, K. K. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac172 · Cited by 60 · see citing works
G-quadruplex resolution: From molecular mechanisms to physiological relevance
Sato, K., & Knipscheer, P. (2023) · DNA repair · doi:10.1016/j.dnarep.2023.103552 · Cited by 64 · see citing works
Deiana, M., Castán, J. M. A., Josse, P., Kahsay, A. G., Sánchez, D. P., Morice, K., Gillet, N., Ravindranath, R., Patel, A. K., Sengupta, P., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad365 · Cited by 63 · see citing works
Wang, W.-M., Li, D.-D., Xu, Q.-Q., Cheng, J., Yu, Z., Li, G.-Y., Qiao, S., Pan, J.-S., Wang, H., Shi, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45353-5 · Cited by 56 · see citing works
Evolution of Diverse Strategies for Promoter Regulation
Brázda, V., Bartas, M., & Bowater, R. P. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.04.003 · Cited by 54 · see citing works
Hańczyc, P., Rajchel-Mieldzioć, P., Feng, B., & Fita, P. (2021) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c01254 · Cited by 50 · see citing works
R-Loops and R-Loop-Binding Proteins in Cancer Progression and Drug Resistance
Elsakrmy, N., & Cui, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24087064 · Cited by 44 · see citing works
DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions
Rocher, V., Genais, M., Nassereddine, E., & Mourad, R. (2021) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1009308 · Cited by 37 · see citing works
Wang, K., Liu, Y., Li, Y., Dickerhoff, J., Li, J., Yang, M.-H., Yang, D., & Kong, L. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c00435 · Cited by 43 · see citing works
Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions
Poggi, L., & Richard, G.-F. (2020) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00110-20 · Cited by 43 · see citing works
Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription
Feng, Y., Tao, S., Zhang, P., Sperti, F. R., Liu, G., Cheng, X., Zhang, T., Yu, H., Wang, X., Chen, C., et al. (2021) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiab566 · Cited by 40 · see citing works
An Upstream G-Quadruplex DNA Structure Can Stimulate Gene Transcription
Chen, Y., Simeone, A., Melidis, L., Cuesta, S. M., Tannahill, D., & Balasubramanian, S. (2024) · ACS Chemical Biology · doi:10.1021/acschembio.3c00775 · Cited by 39 · see citing works
Self-citationONQUADRO: a database of experimentally determined quadruplex structures
Zok, T., Kraszewska, N., Miskiewicz, J., Pielacinska, P., Zurkowski, M., & Szachniuk, M. (2021) · Nucleic Acids Res. · doi:10.1093/nar/gkab1118 · Cited by 36 · see citing works
Antariksa, N. F., & Antonio, M. D. (2024) · Accounts of Chemical Research · doi:10.1021/acs.accounts.4c00574 · Cited by 36 · see citing works
RNA transcripts regulate G-quadruplex landscapes through G-loop formation
Sato, K., Lyu, J., van den Berg, J., Braat, D., Cruz, V. M., Luzón, C. N., Schimmel, J., Esteban-Jurado, C., Alemany, M., Dreyer, J., et al. (2025) · Science · doi:10.1126/science.adr0493 · Cited by 37 · see citing works
Hu, M.-H. (2021) · Analytica Chimica Acta · doi:10.1016/j.aca.2021.338600 · Cited by 35 · see citing works
Insights from Binding on Quadruplex Selective Carbazole Ligands
Müller, D., Saha, P., Panda, D., Dash, J., & Schwalbe, H. (2021) · Chemistry · doi:10.1002/chem.202101866 · Cited by 21 · see citing works
Monsen, R. C., Chua, E. Y. D., Hopkins, J. B., Chaires, J. B., & Trent, J. O. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad014 · Cited by 33 · see citing works
Persistent epigenetic memory of SARS-CoV-2 mRNA vaccination in monocyte-derived macrophages
Simonis, A., Theobald, S. J., Koch, A. E., Mummadavarapu, R., Mudler, J. M., Pouikli, A., Göbel, U., Acton, R., Winter, S., Albus, A., et al. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00093-6 · Cited by 33 · see citing works
Self-citationSelective, Disruptive Luminescent Ru(II) Polypyridyl Probes of G-Quadruplex
Holden, L., Gkika, K. S., Burke, C. S., Long, C., & Keyes, T. (2023) · Inorganic Chemistry · doi:10.1021/acs.inorgchem.2c03903 · Cited by 23 · see citing works
Yuan, J., Tu, J.-L., Liu, G., Chen, X., Huang, Z.-S., Chen, S.-B., & Tan, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac245 · Cited by 31 · see citing works
Jiang, X., Tu, F., Wei, L., Wang, B.-Z., Yuan, H., Yuan, J., Rao, Y., Huang, S., Li, Q., Ou, T., et al. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c01058 · Cited by 31 · see citing works
Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch
Zhang, X., Dhir, S., Melidis, L., Chen, Y., Yu, Z., Simeone, A., Spiegel, J., Adhikari, S., & Balasubramanian, S. (2025) · Nature Chemistry · doi:10.1038/s41557-025-01792-1 · Cited by 31 · see citing works
Self-citationStructured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids
Neidle, S. (2021) · Pharmaceuticals · doi:10.3390/ph15010007 · Cited by 29 · see citing works
Wang, Y., Chen, N., Pan, Z., Ye, Z., Yuan, J., Zeng, Y.-X., Long, W.-W., Bian, W., Li, X., Lu, Y., et al. (2022) · Chemical Engineering Journal · doi:10.1016/j.cej.2022.135977 · Cited by 30 · see citing works
BG-flow, a new flow cytometry tool for G-quadruplex quantification in fixed cells
Magis, A. D., Kastl, M., Brossart, P., Heine, A., & Paeschke, K. (2021) · BMC Biology · doi:10.1186/s12915-021-00986-6 · Cited by 29 · see citing works
G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes
Barshai, M., Aubert, A., & Orenstein, Y. (2021) · IEEE/ACM Transactions on Computational Biology & Bioinformatics · doi:10.1109/tcbb.2021.3073595 · Cited by 22 · see citing works
Biomimetic, Smart, and Multivalent Ligands for G-Quadruplex Isolation and Bioorthogonal Imaging
Sperti, F. R., Charbonnier, T., Lejault, P., Zell, J., Bernhard, C., Valverde, I. E., & Monchaud, D. (2021) · ACS Chemical Biology · doi:10.1021/acschembio.1c00111 · Cited by 28 · see citing works
A Phenotypic Approach to the Discovery of Potent G-Quadruplex Targeted Drugs
Neidle, S. (2024) · Molecules · doi:10.3390/molecules29153653 · Cited by 27 · see citing works
DNA G-Quadruplexes as Targets for Natural Product Drug Discovery
Wang, K.-B., Wang, Y., Dickerhoff, J., & Yang, D.-Z. (2024) · Engineering · doi:10.1016/j.eng.2024.03.015 · Cited by 24 · see citing works
Saczuk, K., Dudek, M., Matczyszyn, K., & Deiana, M. (2024) · Nanoscale Horizons · doi:10.1039/d4nh00186a · Cited by 26 · see citing works
G-Quadruplex Assembly by Ribosomal DNA: Emerging Roles in Disease Pathogenesis and Cancer Biology
Datta, A., Pollock, K. J., Kormuth, K. A., & Brosh, R. M. (2021) · Cytogenetic and Genome Research · doi:10.1159/000516394 · Cited by 26 · see citing works
Dai, Y., Teng, X., & Li, J. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202111132 · Cited by 26 · see citing works
G-quadruplexes in helminth parasites
Cantara, A., Luo, Y., Dobrovolná, M., Bohálová, N., Fojta, M., Verga, D., Guittat, L., Cucchiarini, A., Savrimoutou, S., Häberli, C., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac129 · Cited by 19 · see citing works
Nuccio, S. P., Cadoni, E., Nikoloudaki, R., Galli, S., Ler, A.-J., Sanchez-Cabanillas, C., Maher, T. E., Fan, E., Guneri, D., Flint, G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-67074-z · Cited by 22 · see citing works
G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data
Barshai, M., Engel, B., Haim, I., & Orenstein, Y. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010948 · Cited by 23 · see citing works
Liu, Y., Li, J., Zhang, Y., Wang, Y., Chen, J.-N., Bian, Y., Xia, Y., Yang, M., Zheng, K., Wang, K., et al. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c05214 · Cited by 24 · see citing works
Saczuk, K., Cottini, M. V., Dudek, M., Mazur, L. M., Sánchez, D. P., López‐Pacios, L., Kassem, A., Matczyszyn, K., Nogueira, J. J., Monnereau, C., et al. (2025) · Nanoscale Horizons · doi:10.1039/d5nh00237k · Cited by 22 · see citing works
Ruan, H., Gu, W., Xia, W., Gong, Y. Q., Zhou, X., Chen, W., & Xiong, J. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.778132 · Cited by 22 · see citing works
EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database
Qian, S. H., Shi, M., Xiong, Y.-L., Zhang, Y., Zhang, Z.-H., Song, X., Deng, X.-Y., & Chen, Z. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad966 · Cited by 22 · see citing works
Xu, Y.-Z., Jenjaroenpun, P., Wongsurawat, T., Byrum, S. D., Shponka, V., Tannahill, D., Chavez, E. A., Hung, S. S., Steidl, C., Balasubramanian, S., et al. (2020) · NAR Cancer · doi:10.1093/narcan/zcaa029 · Cited by 22 · see citing works
Self-citationG-quadruplex-mediated genomic instability drives SNVs in cancer
Richl, T., Kuper, J., & Kisker, C. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae098 · Cited by 20 · see citing works
Feng, Y.-L., He, Z., Luo, Z., Sperti, F., Valverde, I. E., Zhang, W.-L., & Monchaud, D. (2023) · iScience · doi:10.1016/j.isci.2023.106846 · Cited by 17 · see citing works
Li, G., Su, G., Wang, Y., Wang, W., Shi, J., Li, D., & Sui, G. (2023) · Communications Biology · doi:10.1038/s42003-023-05015-6 · Cited by 20 · see citing works
Lu, Z., Xie, S., Su, H., Han, S., Huang, H., & Zhou, X. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae126 · Cited by 20 · see citing works
Knop, J., Mukherjee, S., Oliva, R., Möbitz, S., & Winter, R. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c07192 · Cited by 20 · see citing works
Volná, A., Bartas, M., Nezval, J., Špunda, V., Pečínka, P., & Červeň, J. (2021) · BioTech · doi:10.3390/biotech10040020 · Cited by 20 · see citing works
Robinson, J., Flint, G., Garner, I., Galli, S., Maher, T. E., Kuimova, M. K., Vilar, R., McNeish, I. A., Brown, R. E., Keun, H. C., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03654-y · Cited by 19 · see citing works
Li, H., Cao, H.-W., Lang, X., Chen, Y., & Wang, M. (2022) · Journal of Materials Chemistry B · doi:10.1039/d2tb01316a · Cited by 19 · see citing works
Prediction of G4 formation in live cells with epigenetic data: a deep learning approach
Korsakova, A., & Phan, A. (2023) · bioRxiv · doi:10.1093/nargab/lqad071 · Cited by 14 · see citing works
Zhang, X., Wang, J., & Hu, M.-H. (2024) · ACS Pharmacology & Translational Science · doi:10.1021/acsptsci.4c00234 · Cited by 19 · see citing works
Self-citationNovel Roles of G-quadruplexes on Enhancers in human chromatinPreprint
Hou, Y., Guo, Y., Dong, S., & Yang, T. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.12.451993 · Cited by 18 · see citing works
Platella, C., Napolitano, E., Riccardi, C., Musumeci, D., & Montesarchio, D. (2022) · ChemistryOpen · doi:10.1002/open.202200090 · Cited by 11 · see citing works
Froux, A., D’Anna, L., Rainot, A., Neybecker, C., Spinello, A., Bonsignore, R., Rouget, R., Harlé, G., Terenzi, A., Monari, A., et al. (2024) · Inorganic Chemistry Frontiers · doi:10.1039/d4qi01394h · Cited by 17 · see citing works
Lorenzatti, A., Piga, E. J., Gismondi, M., Binolfi, A., Margarit, E., Calcaterra, N., & Armas, P. (2022) · bioRxiv · doi:10.1093/nar/gkad948 · Cited by 14 · see citing works
Ketkar, A., Smith, L., Johnson, C., Richey, A., Berry, M., Hartman, J. H., Maddukuri, L., Reed, M. R., Gunderson, J. E. C., Leung, J. W. C., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab041 · Cited by 15 · see citing works
Precise detection of G-quadruplexs in living systems: principles, applications, and perspectives
Li, H., Jin, Z., Gao, S., Kuang, S., Lei, C., & Nie, Z. (2025) · Chemical Science · doi:10.1039/d5sc00918a · Cited by 15 · see citing works
Solution structures and effects of a platinum compound successively bound MYC G-quadruplex
Liu, W.-T., Zhu, B., Liu, L.-Y., Xia, X., Jang, J., Dickerhoff, J., Yang, D.-Z., & Mao, Z.-W. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae649 · Cited by 11 · see citing works
An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks
Elimelech-Zohar, K., & Orenstein, Y. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad252 · Cited by 15 · see citing works
Ahmed, A. A., & Neidle, S. (2020) · Molecules · doi:10.3390/molecules25225407 · Cited by 14 · see citing works
Huang, X., He, Z., Zhou, K., Zhi, H., & Yang, J. (2021) · The Analyst · doi:10.1039/d1an01603b · Cited by 14 · see citing works
Wang, X., & Hu, M.-H. (2023) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2023.134075 · Cited by 14 · see citing works
Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox
Kretzmann, J. A., Irving, K. L., Smith, N. M., & Evans, C. W. (2021) · NAR Cancer · doi:10.1093/narcan/zcab048 · Cited by 14 · see citing works
Bartosik, A. R., Hou, P., Tang, S., Vaughn, J. P., Smaldino, P. J., Ratan, A., Mayo, M. W., & Wang, Y. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf621 · Cited by 13 · see citing works
Targeting KRAS Regulation with PolyPurine Reverse Hoogsteen Oligonucleotides
Psaras, A., Valiuska, S., Noé, V., Ciudad, C., & Brooks, T. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23042097 · Cited by 14 · see citing works
Lahnsteiner, A., Craig, S. J. C., Kamali, K., Weissensteiner, B., McGrath, B. C., Risch, A., & Makova, K. D. (2024) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2023.12.003 · Cited by 13 · see citing works
DNA 5mC methylation inhibits the formation of G-quadruplex structures in the genome
Niu, K., Xiang, L., Zhang, X., Li, X., Yao, T., Li, J., Zhang, C., Liu, J., Peng, Y., Xu, G., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03678-4 · Cited by 13 · see citing works
Self-citationStitch, M., Avagliano, D., Graczyk, D., Clark, I. P., González, L., Towrie, M., & Quinn, S. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c06099 · Cited by 5 · see citing works
Neupane, A., Chariker, J. H., & Rouchka, E. C. (2023) · Genes · doi:10.3390/genes14122125 · Cited by 12 · see citing works
Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR
Flynn, S. M., Dhir, S., Herka, K., Doyle, C., Melidis, L., Simeone, A., Hui, W. W. I., Tavares, R. D. C. A., Schoenfelder, S., Tannahill, D., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03377-6 · Cited by 11 · see citing works
Self-citationPlatella, C., Capasso, D., Riccardi, C., Musumeci, D., DellaGreca, M., & Montesarchio, D. (2021) · Organic & Biomolecular Chemistry · doi:10.1039/d1ob01995c · Cited by 12 · see citing works
Brázda, V., Bohálová, N., & Bowater, R. (2021) · Gene · doi:10.1016/j.gene.2021.146058 · Cited by 12 · see citing works
Liu, T., Wu, Y., Qin, L., Luo, Q., Li, W., Cheng, Y., Tu, Y., & You, H. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c03031 · Cited by 12 · see citing works
Yam, V., & Law, A. S.-Y. (2020) · Journal of the Chinese Chemical Society (Taipei) · doi:10.1002/jccs.202000536 · Cited by 8 · see citing works
Cui, Y., Liu, H., Ming, Y., Zhang, Z., Liu, L., & Liu, R. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad024 · Cited by 10 · see citing works
A non-B DNA binding peptidomimetic channel alters cellular functions
Paul, R., Dutta, D., Mukhopadhyay, T. K., Müller, D., Lala, B., Datta, A., Schwalbe, H., & Dash, J. (2024) · Nature Communications · doi:10.1038/s41467-024-49534-0 · Cited by 10 · see citing works
Maurizio, I., Ruggiero, E., Zanin, I., Conflitti, M., Nicoletto, G., Provvedi, R., & Richter, S. N. (2025) · Nature Communications · doi:10.1038/s41467-025-62485-4 · Cited by 10 · see citing works
Identification and functional characterization of G-quadruplexes in plants
Ma, X., Feng, Y., Luo, Z., & Zhang, W. (2022) · Trends in Plant Science · doi:10.1016/j.tplants.2022.03.015 · Cited by 10 · see citing works
- Authors
- Hänsel-Hertsch, R., Simeone, A., Shea, A., Hui, W. W. I., Zyner, K. G., Marsico, G., Rueda, O. M., Bruna, A., Martin, A., Zhang, X., Adhikari, S., Tannahill, D., Caldas, C., & Balasubramanian, S.
- Affiliations
- University of Cambridge (GB)
- Institute of Cancer Research (GB)
- Corresponding author
- Balasubramanian, Shankar
- ORCID
- Venue
- Nature Genetics
- Published
- 2020-08-03
- Volume
- 52
- Issue
- 9
- Pages
- 878-883
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W3047068833
- Cited by
- 223
- References
- 37
- Citations by year
- 2026: 24 · 2025: 35 · 2024: 42 · 2023: 39 · 2022: 27 · 2021: 48 · 2020: 8
- FWCI
- 9.97
- Type
- journal article
- Language
- en
- Open access
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Cancer Research UK (C9681/A18618, C9681/A29214, C14303/A17197)
- Wellcome Trust (209441/z/17/z)
- University of Cologne | Center for Molecular Medicine Cologne, University of Cologne (2635020301)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- G-quadruplex, breast cancer, patient-derived xenografts, intratumoral heterogeneity, triple-negative breast cancer, gene amplification, somatic single nucleotide variants, tumor stratification, drug sensitivity
- MeSH terms
- Breast Neoplasms, DNA, Female, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Transcription Factors, G-Quadruplexes
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
