DNA and RNA can adopt various secondary structures. Four-stranded G-quadruplex (G4) structures form through self-recognition of guanines into stacked tetrads, and considerable biophysical and structural evidence exists for G4 formation in vitro. Computational studies and sequencing methods have revealed the prevalence of G4 sequence motifs at gene regulatory regions in various genomes, including in humans. Experiments using chemical, molecular and cell biology methods have demonstrated that G4s exist in chromatin DNA and in RNA, and have linked G4 formation with key biological processes ranging from transcription and translation to genome instability and cancer. In this Review, we first discuss the identification of G4s and evidence for their formation in cells using chemical biology, imaging and genomic technologies. We then discuss possible functions of DNA G4s and their interacting proteins, particularly in transcription, telomere biology and genome instability. Roles of RNA G4s in RNA biology, especially in translation, are also discussed. Furthermore, we consider the emerging relationships of G4s with chromatin and with RNA modifications. Finally, we discuss the connection between G4 formation and synthetic lethality in cancer cells, and recent progress towards considering G4s as therapeutic targets in human diseases.
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Bang, I. Untersuchungen über die Guanylsäure. Biochemische 26, 293–311 (1910).
Gellert, M., Lipsett, M. N. & Davies, D. R. Helix formation by guanylic acid. Proc. Natl Acad. Sci. USA 48, 2013–2018 (1962).
Sen, D. & Gilbert, W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334, 364–366 (1988). This paper is an early demonstration of a G4 comprising stacked tetrads with interconnecting loop sequences performed using chemical mapping and providing biological insight.
Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K. & Neidle, S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 34, 5402–5415 (2006).
Kwok, C. K. & Merrick, C. J. G-Quadruplexes: prediction, characterization, and biological application. Trends Biotechnol. 35, 997–1013 (2017).
Lane, A. N., Chaires, J. B., Gray, R. D. & Trent, J. O. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 36, 5482–5515 (2008).
Lerner, L. K. & Sale, J. E. Replication of G Quadruplex DNA. Genes 10, 95 (2019).
Maizels, N. G4-associated human diseases. EMBO Rep. 16, 910–922 (2015).
Neidle, S. Quadruplex nucleic acids as novel therapeutic targets. J. Med. Chem. 59, 5987–6011 (2016).
Mergny, J. L. & Lacroix, L. UV melting of G-quadruplexes. Curr. Protoc. Nucleic Acid Chem. 37, 17.1.1–17.1.15 (2009).
Huppert, J. L. & Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908–2916 (2005). This work presents the earliest computational predictions showing that sequences encoding G4s are widespread in the human genome.
Todd, A. K., Johnston, M. & Neidle, S. Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res. 33, 2901–2907 (2005).
Huppert, J. L. & Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35, 406–413 (2007).
Eddy, J. & Maizels, N. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res. 34, 3887–3896 (2006).
Varizhuk, A. et al. The expanding repertoire of G4 DNA structures. Biochimie 135, 54–62 (2017).
Stegle, O., Payet, L., Mergny, J. L., MacKay, D. J. & Leon, J. H. Predicting and understanding the stability of G-quadruplexes. Bioinformatics 25, i374–i382 (2009).
Bedrat, A., Lacroix, L. & Mergny, J. L. Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res. 44, 1746–1759 (2016).
Belmonte-Reche, E. & Morales, J. C. G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool. NAR Genom. Bioinform. 2, 1–12 (2020).
Sahakyan, A. B. et al. Machine learning model for sequence-driven DNA G-quadruplex formation. Sci. Rep. 7, 14535 (2017).
Garant, J. M., Perreault, J. P. & Scott, M. S. Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. Bioinformatics 33, 3532–3537 (2017).
Woodford, K. J., Howell, R. M. & Usdin, K. A novel K+-dependent DNA synthesis arrest site in a commonly occurring sequence motif in eukaryotes. J. Biol. Chem. 269, 27029–27035 (1994).
Han, H., Hurley, L. H. & Salazar, M. A DNA polymerase stop assay for G-quadruplex-interactive compounds. Nucleic Acids Res. 27, 537–542 (1999).
Kwok, C. K. & Balasubramanian, S. Targeted detection of G-quadruplexes in cellular RNAs. Angew. Chem. Int. Ed. Engl. 54, 6751–6754 (2015).
Chambers, V. S. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 877–881 (2015).
Marsico, G. et al. Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 47, 3862–3874 (2019).
Guo, J. U. & Bartel, D. P. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science 353, aaf5371 (2016).
Kwok, C. K., Marsico, G., Sahakyan, A. B., Chambers, V. S. & Balasubramanian, S. rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. Nat. Methods 13, 841–844 (2016).
Kouzine, F. et al. Permanganate/S1 nuclease footprinting reveals non-B DNA structures with regulatory potential across a mammalian genome. Cell Syst. 4, 344–356 (2017).
Williamson, J. R., Raghuraman, M. K. & Cech, T. R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell 59, 871–880 (1989).
Wilkinson, K. A., Merino, E. J. & Weeks, K. M. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 1, 1610–1616 (2006).
Kwok, C. K., Sahakyan, A. B. & Balasubramanian, S. Structural analysis using SHALiPE to reveal RNA G-quadruplex formation in human precursor microRNA. Angew. Chem. Int. Ed. Engl. 55, 8958–8961 (2016).
Kwok, C. K., Marsico, G. & Balasubramanian, S. Detecting RNA G-quadruplexes (rG4s) in the transcriptome. Cold Spring Harb. Perspect. Biol. 10, a032284 (2018).
Schaffitzel, C. et al. In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl Acad. Sci. USA 98, 8572–8577 (2001).
Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182–186 (2013). This work is the first demonstration of G4s in human cells by imaging using a structure-specific antibody.
Henderson, A. et al. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res. 42, 860–869 (2014).
Liu, H. Y. et al. Conformation selective antibody enables genome profiling and leads to discovery of parallel G-quadruplex in human telomeres. Cell Chem. Biol. 23, 1261–1270 (2016).
Biffi, G., Di Antonio, M., Tannahill, D. & Balasubramanian, S. Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells. Nat. Chem. 6, 75–80 (2014).
Wang, Y. et al. G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma. Nat. Commun. 10, 943 (2019).
Zhang, M. et al. Mammalian CST averts replication failure by preventing G-quadruplex accumulation. Nucleic Acids Res. 47, 5243–5259 (2019).
Wu, W. et al. HERC2 facilitates BLM and WRN helicase complex interaction with RPA to suppress G-quadruplex DNA. Cancer Res. 78, 6371–6385 (2018).
Xu, H. et al. CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours. Nat. Commun. 8, 14432 (2017).
Kazemier, H. G., Paeschke, K. & Lansdorp, P. M. Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA. Nucleic Acids Res. 45, 5913–5919 (2017).
Rodriguez, R. et al. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat. Chem. Biol. 8, 301–310 (2012).
Lefebvre, J., Guetta, C., Poyer, F., Mahuteau-Betzer, F. & Teulade-Fichou, M. P. Copper–alkyne complexation responsible for the nucleolar localization of quadruplex nucleic acid drugs labeled by click reactions. Angew. Chem. Int. Ed. Engl. 56, 11365–11369 (2017).
Shivalingam, A. et al. The interactions between a small molecule and G-quadruplexes are visualized by fluorescence lifetime imaging microscopy. Nat. Commun. 6, 8178 (2015).
Hansel-Hertsch, R. et al. G-quadruplex structures mark human regulatory chromatin. Nat. Genet. 48, 1267–1272 (2016). This paper presents the first maps of G4s generated in an endogenous chromatin context using G4 ChIP-seq and demonstrating G4 enrichment in active promoters linked with elevated transcription.
Hansel-Hertsch, R., Spiegel, J., Marsico, G., Tannahill, D. & Balasubramanian, S. Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing. Nat. Protoc. 13, 551–564 (2018).
Law, M. J. et al. ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell 143, 367–378 (2010).
Gray, L. T., Vallur, A. C., Eddy, J. & Maizels, N. G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD. Nat. Chem. Biol. 10, 313–318 (2014).
Paeschke, K., Capra, J. A. & Zakian, V. A. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell 145, 678–691 (2011). This paper presents genetic experiments in yeast showing that the helicase Pif1 resolves G4s in vivo to prevent replication-fork stalling and DNA breaks.
Gotz, S., Pandey, S., Bartsch, S., Juranek, S. & Paeschke, K. A novel G-quadruplex binding protein in yeast-Slx9. Molecules 24, 1774 (2019).
Kanoh, Y. et al. Rif1 binds to G quadruplexes and suppresses replication over long distances. Nat. Struct. Mol. Biol. 22, 889–897 (2015).
Meyer, C. A. & Liu, X. S. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat. Rev. Genet. 15, 709–721 (2014).
Herdy, B. et al. Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts. Nucleic Acids Res. 46, 11592–11604 (2018).
Murat, P. et al. RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs. Genome Biol. 19, 229 (2018).
Sauer, M. et al. DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. Nat. Commun. 10, 2421 (2019).
Joachimi, A., Benz, A. & Hartig, J. S. A comparison of DNA and RNA quadruplex structures and stabilities. Bioorg. Med. Chem. 17, 6811–6815 (2009).
Bugaut, A. & Balasubramanian, S. A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry 47, 689–697 (2008).
Hazel, P., Huppert, J., Balasubramanian, S. & Neidle, S. Loop-length-dependent folding of G-quadruplexes. J. Am. Chem. Soc. 126, 16405–16415 (2004).
Sen, D. & Gilbert, W. A sodium–potassium switch in the formation of four-stranded G4-DNA. Nature 344, 410–414 (1990).
Zoroddu, M. A. et al. The essential metals for humans: a brief overview. J. Inorg. Biochem. 195, 120–129 (2019).
Selvam, S., Koirala, D., Yu, Z. & Mao, H. Quantification of topological coupling between DNA superhelicity and G-quadruplex formation. J. Am. Chem. Soc. 136, 13967–13970 (2014).
Shrestha, P. et al. Confined space facilitates G-quadruplex formation. Nat. Nanotechnol. 12, 582–588 (2017).
Fry, M. & Loeb, L. A. Human werner syndrome DNA helicase unwinds tetrahelical structures of the fragile X syndrome repeat sequence d(CGG)n. J. Biol. Chem. 274, 12797–12802 (1999).
Mohaghegh, P., Karow, J. K., Brosh, R. M. Jr, Bohr, V. A. & Hickson, I. D. The Bloom’s and Werner’s syndrome proteins are DNA structure-specific helicases. Nucleic Acids Res. 29, 2843–2849 (2001).
Creacy, S. D. et al. G4 resolvase 1 binds both DNA and RNA tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex G4-DNA and G4-RNA resolving activity in HeLa cell lysates. J. Biol. Chem. 283, 34626–34634 (2008).
Chatterjee, S. et al. Mechanistic insight into the interaction of BLM helicase with intra-strand G-quadruplex structures. Nat. Commun. 5, 5556 (2014).
Chen, M. C. et al. Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 558, 465–469 (2018). This work presents the first X-ray crystallography structure of a G4-resolving helicase bound to a G4, proposing a structural mechanism for G4 unfolding.
Tippana, R., Hwang, H., Opresko, P. L., Bohr, V. A. & Myong, S. Single-molecule imaging reveals a common mechanism shared by G-quadruplex-resolving helicases. Proc. Natl Acad. Sci. USA 113, 8448–8453 (2016).
Tippana, R., Chen, M. C., Demeshkina, N. A., Ferre-D’Amare, A. R. & Myong, S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat. Commun. 10, 1855 (2019).
Byrd, A. K. & Raney, K. D. Structure and function of Pif1 helicase. Biochem. Soc. Trans. 45, 1159–1171 (2017).
Wu, Y., Shin-ya, K. & Brosh, R. M. Jr FANCJ helicase defective in Fanconia anemia and breast cancer unwinds G-quadruplex DNA to defend genomic stability. Mol. Cell Biol. 28, 4116–4128 (2008).
Benhalevy, D. et al. The human CCHC-type zinc finger nucleic acid-binding protein binds G-rich elements in target mRNA coding sequences and promotes translation. Cell Rep. 18, 2979–2990 (2017).
Pietras, Z. et al. Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria. Nat. Commun. 9, 2558 (2018).
Ray, S., Bandaria, J. N., Qureshi, M. H., Yildiz, A. & Balci, H. G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding. Proc. Natl Acad. Sci. USA 111, 2990–2995 (2014).
Zaug, A. J., Podell, E. R. & Cech, T. R. Human POT1 disrupts telomeric G-quadruplexes allowing telomerase extension in vitro. Proc. Natl Acad. Sci. USA 102, 10864–10869 (2005).
Gonzalez, V., Guo, K., Hurley, L. & Sun, D. Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein. J. Biol. Chem. 284, 23622–23635 (2009).
Niu, K. et al. Identification of LARK as a novel and conserved G-quadruplex binding protein in invertebrates and vertebrates. Nucleic Acids Res. 47, 7306–7320 (2019).
Serikawa, T. et al. Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5′ UTR of tumor-associated mRNAs. Biochimie 144, 169–184 (2018).
Kouzine, F., Liu, J., Sanford, S., Chung, H. J. & Levens, D. The dynamic response of upstream DNA to transcription-generated torsional stress. Nat. Struct. Mol. Biol. 11, 1092–1100 (2004).
Duquette, M. L., Handa, P., Vincent, J. A., Taylor, A. F. & Maizels, N. Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes. Dev. 18, 1618–1629 (2004).
Chen, L. et al. R-ChIP using inactive RNase H reveals dynamic coupling of R-loops with transcriptional pausing at gene promoters. Mol. Cell 68, 745–757 (2017).
Gehring, K., Leroy, J. L. & Gueron, M. A tetrameric DNA structure with protonated cytosine.cytosine base pairs. Nature 363, 561–565 (1993).
Zeraati, M. et al. I-motif DNA structures are formed in the nuclei of human cells. Nat. Chem. 10, 631–637 (2018).
Cui, Y., Kong, D., Ghimire, C., Xu, C. & Mao, H. Mutually exclusive formation of G-quadruplex and i-motif is a general phenomenon governed by steric hindrance in duplex DNA. Biochemistry 55, 2291–2299 (2016).
Hoffmann, R. F. et al. Guanine quadruplex structures localize to heterochromatin. Nucleic Acids Res. 44, 152–163 (2016).
Sen, D. & Poon, L. C. RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean? Crit. Rev. Biochem. Mol. Biol. 46, 478–492 (2011).
Gray, L. T. et al. G-quadruplexes sequester free heme in living cells. Cell Chem. Biol. 26, 1681–1691 (2019).
Fouquerel, E. et al. Targeted and persistent 8-oxoguanine base damage at telomeres promotes telomere loss and crisis. Mol. Cell 75, 117–130 (2019).
Fleming, A. M., Zhu, J., Ding, Y. & Burrows, C. J. 8-Oxo-7,8-dihydroguanine in the context of a gene promoter G-quadruplex is an on–off switch for transcription. ACS Chem. Biol. 12, 2417–2426 (2017).
Shay, J. W. & Wright, W. E. Telomeres and telomerase: three decades of progress. Nat. Rev. Genet. 20, 299–309 (2019).
Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D. & Lipps, H. J. Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat. Struct. Mol. Biol. 12, 847–854 (2005).
de Lange, T. T-loops and the origin of telomeres. Nat. Rev. Mol. Cell Biol. 5, 323–329 (2004).
Biffi, G., Tannahill, D. & Balasubramanian, S. An intramolecular G-quadruplex structure is required for binding of telomeric repeat-containing RNA to the telomeric protein TRF2. J. Am. Chem. Soc. 134, 11974–11976 (2012).
Smith, J. S. et al. Rudimentary G-quadruplex-based telomere capping in Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 18, 478–485 (2011).
Takahama, K. et al. Regulation of telomere length by G-quadruplex telomere DNA- and TERRA-binding protein TLS/FUS. Chem. Biol. 20, 341–350 (2013).
Takahama, K., Kino, K., Arai, S., Kurokawa, R. & Oyoshi, T. Identification of Ewing’s sarcoma protein as a G-quadruplex DNA- and RNA-binding protein. FEBS J. 278, 988–998 (2011).
Vannier, J. B., Pavicic-Kaltenbrunner, V., Petalcorin, M. I., Ding, H. & Boulton, S. J. RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity. Cell 149, 795–806 (2012).
Sfeir, A. et al. Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication. Cell 138, 90–103 (2009).
Zahler, A. M., Williamson, J. R., Cech, T. R. & Prescott, D. M. Inhibition of telomerase by G-quartet DNA structures. Nature 350, 718–720 (1991). This paper is the earliest demonstration that the activity of telomerase can be affected by a G4 structure in its telomere DNA substrate, suggesting that G4s might regulate telomere elongation.
Moye, A. L. et al. Telomeric G-quadruplexes are a substrate and site of localization for human telomerase. Nat. Commun. 6, 7643 (2015).
Zhang, M. L. et al. Yeast telomerase subunit Est1p has guanine quadruplex-promoting activity that is required for telomere elongation. Nat. Struct. Mol. Biol. 17, 202–209 (2010).
Hwang, H., Buncher, N., Opresko, P. L. & Myong, S. POT1–TPP1 regulates telomeric overhang structural dynamics. Structure 20, 1872–1880 (2012).
Jansson, L. I. et al. Telomere DNA G-quadruplex folding within actively extending human telomerase. Proc. Natl Acad. Sci. USA 116, 9350–9359 (2019).
Booy, E. P. et al. The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary. Nucleic Acids Res. 40, 4110–4124 (2012).
Sun, D. et al. Inhibition of human telomerase by a G-quadruplex-interactive compound. J. Med. Chem. 40, 2113–2116 (1997).
Neidle, S. Human telomeric G-quadruplex: the current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS J. 277, 1118–1125 (2010).
Clynes, D. et al. Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX. Nat. Commun. 6, 7538 (2015).
Gowan, S. M., Heald, R., Stevens, M. F. & Kelland, L. R. Potent inhibition of telomerase by small-molecule pentacyclic acridines capable of interacting with G-quadruplexes. Mol. Pharmacol. 60, 981–988 (2001).
Simonsson, T., Pecinka, P. & Kubista, M. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 26, 1167–1172 (1998).
Siddiqui-Jain, A., Grand, C. L., Bearss, D. J. & Hurley, L. H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA 99, 11593–11598 (2002). This study of the G4 structure in the MYC promoter shows that a small-molecule G4 ligand can inhibit transcription.
Cogoi, S. & Xodo, L. E. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res. 34, 2536–2549 (2006).
Bejugam, M. et al. Trisubstituted isoalloxazines as a new class of G-quadruplex binding ligands: small molecule regulation of c-kit oncogene expression. J. Am. Chem. Soc. 129, 12926–12927 (2007).
Marchetti, C. et al. Targeting multiple effector pathways in pancreatic ductal adenocarcinoma with a G-quadruplex-binding small molecule. J. Med. Chem. 61, 2500–2517 (2018).
Kumar, P. et al. Zinc-finger transcription factors are associated with guanine quadruplex motifs in human, chimpanzee, mouse and rat promoters genome-wide. Nucleic Acids Res. 39, 8005–8016 (2011).
Hou, Y. et al. Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure. Epigenetics 14, 894–911 (2019).
Thakur, R. K. et al. Metastases suppressor NM23–H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression. Nucleic Acids Res. 37, 172–183 (2009).
Borgognone, M., Armas, P. & Calcaterra, N. B. Cellular nucleic-acid-binding protein, a transcriptional enhancer of c-Myc, promotes the formation of parallel G-quadruplexes. Biochem. J. 428, 491–498 (2010).
Raiber, E. A., Kranaster, R., Lam, E., Nikan, M. & Balasubramanian, S. A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro. Nucleic Acids Res. 40, 1499–1508 (2012).
Li, P. T. et al. Expression of the human telomerase reverse transcriptase gene is modulated by quadruplex formation in its first exon due to DNA methylation. J. Biol. Chem. 292, 20859–20870 (2017).
Agarwal, T., Roy, S., Kumar, S., Chakraborty, T. K. & Maiti, S. In the sense of transcription regulation by G-quadruplexes: asymmetric effects in sense and antisense strands. Biochemistry 53, 3711–3718 (2014).
Holder, I. T. & Hartig, J. S. A matter of location: influence of G-quadruplexes on Escherichia coli gene expression. Chem. Biol. 21, 1511–1521 (2014).
Belotserkovskii, B. P., Soo Shin, J. H. & Hanawalt, P. C. Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter. Nucleic Acids Res. 45, 6589–6599 (2017).
Eddy, J. et al. G4 motifs correlate with promoter-proximal transcriptional pausing in human genes. Nucleic Acids Res. 39, 4975–4983 (2011).
Du, Z., Zhao, Y. & Li, N. Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription. Genome Res. 18, 233–241 (2008).
Wanrooij, P. H. et al. A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop. Nucleic Acids Res. 40, 10334–10344 (2012).
Zheng, K. W. et al. Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Nucleic Acids Res. 41, 5533–5541 (2013).
Puget, N., Miller, K. M. & Legube, G. Non-canonical DNA/RNA structures during transcription-coupled double-strand break repair: roadblocks or bona fide repair intermediates? DNA Repair. 81, 102661 (2019).
Techer, H., Koundrioukoff, S., Nicolas, A. & Debatisse, M. The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat. Rev. Genet. 18, 535–550 (2017).
De, S. & Michor, F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat. Struct. Mol. Biol. 18, 950–955 (2011).
Georgakopoulos-Soares, I., Morganella, S., Jain, N., Hemberg, M. & Nik-Zainal, S. Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis. Genome Res. 28, 1264–1271 (2018).
Kruisselbrink, E. et al. Mutagenic capacity of endogenous G4 DNA underlies genome instability in FANCJ-defective C. elegans. Curr. Biol. 18, 900–905 (2008).
Castillo Bosch, P. et al. FANCJ promotes DNA synthesis through G-quadruplex structures. EMBO J. 33, 2521–2533 (2014).
Lemmens, B., van Schendel, R. & Tijsterman, M. Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers. Nat. Commun. 6, 8909 (2015).
Paeschke, K. et al. Pif1 family helicases suppress genome instability at G-quadruplex motifs. Nature 497, 458–462 (2013).
Piazza, A. et al. Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae. Nucleic Acids Res. 38, 4337–4348 (2010).
Piazza, A. et al. Non-canonical G-quadruplexes cause the hCEB1 minisatellite instability in Saccharomyces cerevisiae. eLife 6, e26884 (2017).
Piazza, A. et al. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites. EMBO J. 34, 1718–1734 (2015).
van Wietmarschen, N. et al. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat. Commun. 9, 271 (2018).
Pladevall-Morera, D. et al. Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability. Nucleic Acids Res. 47, 8004–8018 (2019).
Zyner, K. G. et al. Genetic interactions of G-quadruplexes in humans. eLife 8, e46793 (2019).
Muller, S. et al. Pyridostatin analogues promote telomere dysfunction and long-term growth inhibition in human cancer cells. Org. Biomol. Chem. 10, 6537–6546 (2012).
Sanz, L. A. et al. Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals. Mol. Cell 63, 167–178 (2016).
Ginno, P. A., Lim, Y. W., Lott, P. L., Korf, I. & Chedin, F. GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res. 23, 1590–1600 (2013).
De Magis, A. et al. DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells. Proc. Natl Acad. Sci. USA 116, 816–825 (2019).
Nguyen, D. T. et al. The chromatin remodelling factor ATRX suppresses R-loops in transcribed telomeric repeats. EMBO Rep. 18, 914–928 (2017).
Schaeffer, C. et al. The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif. EMBO J. 20, 4803–4813 (2001).
Kumari, S., Bugaut, A., Huppert, J. L. & Balasubramanian, S. An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol. 3, 218–221 (2007).
Shahid, R., Bugaut, A. & Balasubramanian, S. The BCL-2 5′ untranslated region contains an RNA G-quadruplex-forming motif that modulates protein expression. Biochemistry 49, 8300–8306 (2010).
Lammich, S. et al. Translational repression of the disintegrin and metalloprotease ADAM10 by a stable G-quadruplex secondary structure in its 5′-untranslated region. J. Biol. Chem. 286, 45063–45072 (2011).
Khateb, S., Weisman-Shomer, P., Hershco-Shani, I., Ludwig, A. L. & Fry, M. The tetraplex (CGG)n destabilizing proteins hnRNP A2 and CBF-A enhance the in vivo translation of fragile X premutation mRNA. Nucleic Acids Res. 35, 5775–5788 (2007).
Kumari, S., Bugaut, A. & Balasubramanian, S. Position and stability are determining factors for translation repression by an RNA G-quadruplex-forming sequence within the 5′ UTR of the NRAS proto-oncogene. Biochemistry 47, 12664–12669 (2008).
Huppert, J. L., Bugaut, A., Kumari, S. & Balasubramanian, S. G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 36, 6260–6268 (2008).
Hinnebusch, A. G. The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779–812 (2014).
Wolfe, A. L. et al. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 513, 65–70 (2014). This study presents a comprehensive investigation into the control of translation by the helicase eIF4A–RNA G4 interactions in the 5′ UTR of mRNAs.
Modelska, A. et al. The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death Dis. 6, e1603 (2015).
Bonnal, S. et al. A single internal ribosome entry site containing a G quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons. J. Biol. Chem. 278, 39330–39336 (2003).
Koukouraki, P. & Doxakis, E. Constitutive translation of human alpha-synuclein is mediated by the 5′-untranslated region. Open. Biol. 6, 160022 (2016).
Morris, M. J., Negishi, Y., Pazsint, C., Schonhoft, J. D. & Basu, S. An RNA G-quadruplex is essential for cap-independent translation initiation in human VEGF IRES. J. Am. Chem. Soc. 132, 17831–17839 (2010).
Bhattacharyya, D., Diamond, P. & Basu, S. An independently folding RNA G-quadruplex domain directly recruits the 40S ribosomal subunit. Biochemistry 54, 1879–1885 (2015).
Cammas, A. et al. Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation. RNA Biol. 12, 320–329 (2015).
Wu, Y. et al. Stabilization of VEGF G-quadruplex and inhibition of angiogenesis by quindoline derivatives. Biochim. Biophys. Acta 1840, 2970–2977 (2014).
Endoh, T., Kawasaki, Y. & Sugimoto, N. Suppression of gene expression by G-quadruplexes in open reading frames depends on G-quadruplex stability. Angew. Chem. Int. Ed. Engl. 52, 5522–5526 (2013).
Mirihana Arachchilage, G., Hetti Arachchilage, M., Venkataraman, A., Piontkivska, H. & Basu, S. Stable G-quadruplex enabling sequences are selected against by the context-dependent codon bias. Gene 696, 149–161 (2019).
Hagerman, R. J. et al. Fragile X syndrome. Nat. Rev. Dis. Prim. 3, 17065 (2017).
Agarwala, P., Pandey, S., Mapa, K. & Maiti, S. The G-quadruplex augments translation in the 5′ untranslated region of transforming growth factor β2. Biochemistry 52, 1528–1538 (2013).
Serikawa, T., Eberle, J. & Kurreck, J. Effects of genomic disruption of a guanine quadruplex in the 5′ UTR of the Bcl-2 mRNA in melanoma cells. FEBS Lett. 591, 3649–3659 (2017).
Bhattacharyya, D. et al. Engineered domain swapping indicates context dependent functional role of RNA G-quadruplexes. Biochimie 137, 147–150 (2017).
Endoh, T. & Sugimoto, N. Conformational dynamics of the RNA G-quadruplex and its effect on translation efficiency. Molecules 24, 1613 (2019).
Bugaut, A., Murat, P. & Balasubramanian, S. An RNA hairpin to G-quadruplex conformational transition. J. Am. Chem. Soc. 134, 19953–19956 (2012).
Subramanian, M. et al. G-quadruplex RNA structure as a signal for neurite mRNA targeting. EMBO Rep. 12, 697–704 (2011).
Darnell, J. C. et al. Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function. Cell 107, 489–499 (2001).
Valentin-Vega, Y. A. et al. Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation. Sci. Rep. 6, 25996 (2016).
Chalupnikova, K. et al. Recruitment of the RNA helicase RHAU to stress granules via a unique RNA-binding domain. J. Biol. Chem. 283, 35186–35198 (2008).
Fay, M. M., Anderson, P. J. & Ivanov, P. ALS/FTD-associated C9ORF72 repeat RNA promotes phase transitions in vitro and in cells. Cell Rep. 21, 3573–3584 (2017).
Khong, A. et al. The stress granule transcriptome reveals principles of mRNA accumulation in stress granules. Mol. Cell 68, 808–820 (2017).
Tao, E. W., Cheng, W. Y., Li, W. L., Yu, J. & Gao, Q. Y. tiRNAs: a novel class of small noncoding RNAs that helps cells respond to stressors and plays roles in cancer progression. J. Cell Physiol. 235, 683–690 (2020).
Lyons, S. M., Achorn, C., Kedersha, N. L., Anderson, P. J. & Ivanov, P. YB-1 regulates tiRNA-induced stress granule formation but not translational repression. Nucleic Acids Res. 44, 6949–6960 (2016).
Lyons, S. M., Gudanis, D., Coyne, S. M., Gdaniec, Z. & Ivanov, P. Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nat. Commun. 8, 1127 (2017).
Ivanov, P. et al. G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. Proc. Natl Acad. Sci. USA 111, 18201–18206 (2014).
Conlon, E. G. et al. The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains. eLife 5, e17820 (2016).
Huang, H., Zhang, J., Harvey, S. E., Hu, X. & Cheng, C. RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF. Genes. Dev. 31, 2296–2309 (2017).
Didiot, M. C. et al. The G-quartet containing FMRP binding site in FMR1 mRNA is a potent exonic splicing enhancer. Nucleic Acids Res. 36, 4902–4912 (2008).
Marcel, V. et al. G-quadruplex structures in TP53 intron 3: role in alternative splicing and in production of p53 mRNA isoforms. Carcinogenesis 32, 271–278 (2011).
Ribeiro, M. M. et al. G-quadruplex formation enhances splicing efficiency of PAX9 intron 1. Hum. Genet. 134, 37–44 (2015).
Fisette, J. F., Montagna, D. R., Mihailescu, M. R. & Wolfe, M. S. A G-rich element forms a G-quadruplex and regulates BACE1 mRNA alternative splicing. J. Neurochem. 121, 763–773 (2012).
Zhang, J., Harvey, S. E. & Cheng, C. A high-throughput screen identifies small molecule modulators of alternative splicing by targeting RNA G-quadruplexes. Nucleic Acids Res. 47, 3667–3679 (2019).
Kharel, P., Balaratnam, S., Beals, N. & Basu, S. The role of RNA G-quadruplexes in human diseases and therapeutic strategies. Wiley Interdiscip. Rev. RNA 11, e1568 (2020).
Cree, S. L. et al. DNA G-quadruplexes show strong interaction with DNA methyltransferases in vitro. FEBS Lett. 590, 2870–2883 (2016).
Mao, S. Q. et al. DNA G-quadruplex structures mold the DNA methylome. Nat. Struct. Mol. Biol. 25, 951–957 (2018).
Saha, D. et al. Epigenetic suppression of human telomerase (hTERT) is mediated by the metastasis suppressor NME2 in a G-quadruplex-dependent fashion. J. Biol. Chem. 292, 15205–15215 (2017).
Hussain, T. et al. Transcription regulation of CDKN1A (p21/CIP1/WAF1) by TRF2 is epigenetically controlled through the REST repressor complex. Sci. Rep. 7, 11541 (2017).
Sarkies, P. et al. FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA. Nucleic Acids Res. 40, 1485–1498 (2012).
Sarkies, P., Reams, C., Simpson, L. J. & Sale, J. E. Epigenetic instability due to defective replication of structured DNA. Mol. Cell 40, 703–713 (2010). This paper presents genetic experiments that provide the first demonstration of a link between G4s and cellular epigenetic inheritance.
Papadopoulou, C., Guilbaud, G., Schiavone, D. & Sale, J. E. Nucleotide pool depletion induces G-quadruplex-dependent perturbation of gene expression. Cell Rep. 13, 2491–2503 (2015).
Guilbaud, G. et al. Local epigenetic reprogramming induced by G-quadruplex ligands. Nat. Chem. 9, 1110–1117 (2017).
Mirihana Arachchilage, G., Dassanayake, A. C. & Basu, S. A potassium ion-dependent RNA structural switch regulates human pre-miRNA 92b maturation. Chem. Biol. 22, 262–272 (2015).
Pandey, S., Agarwala, P., Jayaraj, G. G., Gargallo, R. & Maiti, S. The RNA stem-loop to G-quadruplex equilibrium controls mature microRNA production inside the cell. Biochemistry 54, 7067–7078 (2015).
Pandolfini, L. et al. METTL1 promotes let-7 microRNA processing via m7G methylation. Mol. Cell 74, 1278–1290.e9 (2019).
Chan, K. L. et al. Structural analysis reveals the formation and role of RNA G-quadruplex structures in human mature microRNAs. Chem. Commun. 54, 10878–10881 (2018).
Rouleau, S., Glouzon, J. S., Brumwell, A., Bisaillon, M. & Perreault, J. P. 3′ UTR G-quadruplexes regulate miRNA binding. RNA 23, 1172–1179 (2017).
Wang, X. et al. Targeting of polycomb repressive complex 2 to RNA by short repeats of consecutive guanines. Mol. Cell 65, 1056–1067.e5 (2017).
Fleming, A. M., Nguyen, N. L. B. & Burrows, C. J. Colocalization of m6A and G-quadruplex-forming sequences in viral RNA (HIV, Zika, hepatitis B, and SV40) suggests topological control of adenosine N 6-methylation. ACS Cent. Sci. 5, 218–228 (2019).
Sahakyan, A. B., Murat, P., Mayer, C. & Balasubramanian, S. G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition. Nat. Struct. Mol. Biol. 24, 243–247 (2017).
Hegyi, H. Enhancer–promoter interaction facilitated by transiently forming G-quadruplexes. Sci. Rep. 5, 9165 (2015).
Silverman, R. B. & Holladay, M. W. The Organic Chemistry of Drug Design and Drug Action 3rd edn (Academic, 2015).
Neidle, S. Quadruplex nucleic acids as targets for anticancer therapeutics. Nat. Rev. Chem. 1, 0041 (2017).
Neidle, S. & Parkinson, G. Telomere maintenance as a target for anticancer drug discovery. Nat. Rev. Drug. Discov. 1, 383–393 (2002).
Salvati, E. et al. PARP1 is activated at telomeres upon G4 stabilization: possible target for telomere-based therapy. Oncogene 29, 6280–6293 (2010).
Biffi, G., Tannahill, D., Miller, J., Howat, W. J. & Balasubramanian, S. Elevated levels of G-quadruplex formation in human stomach and liver cancer tissues. PLOS ONE 9, e102711 (2014).
O’Neil, N. J., Bailey, M. L. & Hieter, P. Synthetic lethality and cancer. Nat. Rev. Genet. 18, 613–623 (2017).
Zimmer, J. et al. Targeting BRCA1 and BRCA2 deficiencies with G-quadruplex-interacting compounds. Mol. Cell 61, 449–460 (2016).
McLuckie, K. I. et al. G-quadruplex DNA as a molecular target for induced synthetic lethality in cancer cells. J. Am. Chem. Soc. 135, 9640–9643 (2013).
Parkinson, G. N., Lee, M. P. & Neidle, S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417, 876–880 (2002).
The Balasubramanian laboratory is supported by Cancer Research UK core and programme award funding (C14303/A17197; C9681/A18618), S.B. is a Senior Investigator of the Wellcome Trust (099232/Z/12/Z) and D.V. is a Herchel Smith postdoctoral fellow. J.S. gratefully acknowledges EU H2020 Framework Programme funding (H2020-MSCA-IF-2016, ID: 747297-QAPs).
S.B. is a founder and shareholder of Cambridge Epigenetix Ltd.
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- Circular dichroism
A spectroscopic technique to investigate structure based on the interaction of plane-polarized light with a structurally asymmetric molecule.
- Bayesian predictions
Statistical methods to infer probabilities for a hypothesis, which can be updated when new information becomes available.
The proportion of G bases in a sequence, that is, G-richness.
The under-representation or over-representation of G bases in a sequence.
- Polytene chromosomes
Giant chromosomes found in particular tissues of various eukaryotes, which are formed following several rounds of DNA replication without cell division.
- Fragile telomeres
Aberrant or discontinuous appearance of telomere chromatin in metaphase chromosomes, identified by fluorescence in situ hybridization and indicative of telomere replication defects.
- Common fragile sites
Specific chromosomal regions that are intrinsically hard to replicate and preferentially form chromatin gaps or breaks during metaphase following replication stress.
- Stress granules
Cytoplasmic membraneless bodies of proteins and RNAs that appear in response to conditions of cellular stress.
- CpG island
A genomic region with CG:GC content higher than 60%.
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Varshney, D., Spiegel, J., Zyner, K. et al. The regulation and functions of DNA and RNA G-quadruplexes. Nat Rev Mol Cell Biol (2020). https://doi.org/10.1038/s41580-020-0236-x
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