• 1.

    Flavahan, W. A., Gaskell, E. & Bernstein, B. E. Epigenetic plasticity and the hallmarks of cancer. Science 357, eaal2380 (2017).

    Article  Google Scholar 

  • 2.

    Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).

    CAS  Article  Google Scholar 

  • 3.

    Rhodes, D. & Lipps, H. J. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 43, 8627–8637 (2015).

    CAS  Article  Google Scholar 

  • 4.

    Varshney, D., Spiegel, J., Zyner, K., Tannahill, D. & Balasubramanian, S. The regulation and functions of DNA and RNA G-quadruplexes. Nat. Rev. Mol. Cell Biol. https://doi.org/10.1038/s41580-020-0236-x (2020).

  • 5.

    Marsico, G. et al. Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 47, 3862–3874 (2019).

    CAS  Article  Google Scholar 

  • 6.

    Hänsel-Hertsch, R. et al. G-quadruplex structures mark human regulatory chromatin. Nat. Genet. 48, 1267–1272 (2016).

    Article  Google Scholar 

  • 7.

    Hänsel-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).

    Article  Google Scholar 

  • 8.

    Hänsel-Hertsch, R., Di Antonio, M. & Balasubramanian, S. DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential. Nat. Rev. Mol. Cell Biol. 18, 279–284 (2017).

    Article  Google Scholar 

  • 9.

    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).

    CAS  Article  Google Scholar 

  • 10.

    Cheung, I., Schertzer, M., Rose, A. & Lansdorp, P. M. Disruption of dog-1 in Caenorhabditis elegans triggers deletions upstream of guanine-rich DNA. Nat. Genet. 31, 405–409 (2002).

    CAS  Article  Google Scholar 

  • 11.

    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).

    CAS  Article  Google Scholar 

  • 12.

    Lensing, S. V. et al. DSBCapture: in situ capture and sequencing of DNA breaks. Nat. Methods 13, 855–857 (2016).

    CAS  Article  Google Scholar 

  • 13.

    Bouwman, B. A. M. & Crosetto, N. Endogenous DNA double-strand breaks during DNA transactions: emerging insights and methods for genome-wide profiling. Genes (Basel) 9, 632 (2018).

    Article  Google Scholar 

  • 14.

    De, S. & Michor, F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat. Struct. Mol. Biol. 18, 950–955 (2011).

    CAS  Article  Google Scholar 

  • 15.

    Chambers, V. S. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 1–7 (2015).

    Article  Google Scholar 

  • 16.

    Pereira, B. et al. The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes. Nat. Commun. 7, 11479 (2016).

    CAS  Article  Google Scholar 

  • 17.

    Bruna, A. et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell 167, 260–274.e22 (2016).

    CAS  Article  Google Scholar 

  • 18.

    Rueda, O. M. et al. Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups. Nature 567, 399–404 (2019).

    CAS  Article  Google Scholar 

  • 19.

    Orlando, D. A. et al. Quantitative ChIP–Seq normalization reveals global modulation of the epigenome. Cell Rep. 9, 1163–1170 (2014).

    CAS  Article  Google Scholar 

  • 20.

    Scheinin, I. et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 24, 2022–2032 (2014).

    CAS  Article  Google Scholar 

  • 21.

    Mao, S.-Q. et al. DNA G-quadruplex structures mold the DNA methylome. Nat. Struct. Mol. Biol. 25, 951–957 (2018).

    CAS  Article  Google Scholar 

  • 22.

    Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227–2241 (2011).

    CAS  Article  Google Scholar 

  • 23.

    Gertz, J. et al. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol. Cell 52, 25–36 (2013).

    CAS  Article  Google Scholar 

  • 24.

    Oki, S. et al. ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP–seq data. EMBO Rep. 19, e46255 (2018).

    Article  Google Scholar 

  • 25.

    Rodriguez, R. et al. A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres. J. Am. Chem. Soc. 130, 15758–15759 (2008).

    CAS  Article  Google Scholar 

  • 26.

    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).

    CAS  Article  Google Scholar 

  • 27.

    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).

    Article  Google Scholar 

  • 28.

    McLuckie, K. I. E. et al. G-quadruplex DNA as a molecular target for induced synthetic lethality in cancer cells. J. Am. Chem. Soc. 135, 9640–9643 (2013).

    CAS  Article  Google Scholar 

  • 29.

    Zimmer, J. et al. Targeting BRCA1 and BRCA2 deficiencies with G-quadruplex-interacting compounds. Mol. Cell 61, 449–460 (2016).

    CAS  Article  Google Scholar 

  • 30.

    Schmidt, D. et al. ChIP–seq: using high-throughput sequencing to discover protein–DNA interactions. Methods 48, 240–248 (2009).

    CAS  Article  Google Scholar 

  • 31.

    Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182–186 (2013).

    CAS  Article  Google Scholar 

  • 32.

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).

  • 33.

    Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

    CAS  Article  Google Scholar 

  • 34.

    Khan, A. & Mathelier, A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics 18, 287 (2017).

    Article  Google Scholar 

  • 35.

    Chin, S.-F. et al. Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Exp. Mol. Pathol. 104, 161–169 (2018).

    CAS  Article  Google Scholar 

  • 36.

    Huang, W., Loganantharaj, R., Schroeder, B., Fargo, D. & Li, L. PAVIS: a tool for peak annotation and visualization. Bioinformatics 29, 3097–3099 (2013).

    CAS  Article  Google Scholar 

  • 37.

    Le, D. D., Di Antonio, M., Chan, L. K. M. & Balasubramanian, S. G-quadruplex ligands exhibit differential G-tetrad selectivity. Chem. Commun. (Camb.) 51, 8048–8050 (2015).

    CAS  Article  Google Scholar 

  • Source