References
Bochman, M. L., Paeschke, K. & Zakian, V. A. DNA secondary structures: stability and function of G-quadruplex structures. Nat. Rev. Genet. 13, 770–780 (2012).
Hansel-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).
CAS PubMed Google Scholar
Mao, S. Q. et al. DNA G-quadruplex structures mold the DNA methylome. Nat. Struct. Mol. Biol. 25, 951–957 (2018).
Huppert, J. L. & Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908–2916 (2005).
Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182–186 (2013).
Henderson, A. et al. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res. 42, 860–869 (2014).
CAS PubMed Google Scholar
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).
CAS PubMed Google Scholar
Soldatenkov, V. A., Vetcher, A. A., Duka, T. & Ladame, S. First evidence of a functional interaction between DNA quadruplexes and poly(ADP-ribose) polymerase-1. ACS Chem. Biol. 3, 214–219 (2008).
CAS PubMed Google Scholar
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).
Paramasivam, M. et al. Protein hnRNP A1 and its derivative Up1 unfold quadruplex DNA in the human KRAS promoter: implications for transcription. Nucleic Acids Res. 37, 2841–2853 (2009).
See AlsoTranscription factor YY1: structure, function, and therapeutic implications in cancer biologyThe Role of Transcription Factor YY1 in the Biology of CancerOnline Mendelian Inheritance in Man (OMIM)Nach rassistischem Gesang von Party-Gästen auf Sylt: Arbeitgeber kündigen Mitarbeitenden fristlosWilliams, P., Li, L., Dong, X. & Wang, Y. Identification of SLIRP as a G quadruplex-binding protein. J. Am. Chem. Soc. 139, 12426–12429 (2017).
Gordon, S., Akopyan, G., Garban, H. & Bonavida, B. Transcription factor YY1: structure, function, and therapeutic implications in cancer biology. Oncogene 25, 1125–1142 (2006).
CAS PubMed Google Scholar
Deng, Z., Cao, P., Wan, M. M. & Sui, G. Yin Yang 1: a multifaceted protein beyond a transcription factor. Transcription 1, 81–84 (2010).
Wu, S. et al. A YY1–INO80 complex regulates genomic stability through hom*ologous recombination-based repair. Nat. Struct. Mol. Biol. 14, 1165–1172 (2007).
Weintraub, A. S. et al. YY1 is a structural regulator of enhancer-promoter loops. Cell 171, 1573–1588.e28 (2017).
Maru, Y., Afar, D. E., Witte, O. N. & Shibuya, M. The dimerization property of glutathione S-transferase partially reactivates Bcr-Abl lacking the oligomerization domain. J. Biol. Chem. 271, 15353–15357 (1996).
CAS PubMed Google Scholar
Han, F. X., Wheelhouse, R. T. & Hurley, L. H. Interactions of TMPyP4 and TMPyP2 with quadruplex DNA. Structural basis for the differential effects on telomerase inhibition. J. Am. Chem. Soc. 121, 3561–3570 (1999).
CAS Google Scholar
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).
Houbaviy, H. B., Usheva, A., Shenk, T. & Burley, S. K. Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proc. Natl Acad. Sci. USA 93, 13577–13582 (1996).
Whitfield, T. W. et al. Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 13, R50 (2012).
Chambers, V. S. et al. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 33, 877–881 (2015).
Muller, S., Kumari, S., Rodriguez, R. & Balasubramanian, S. Small-molecule-mediated G-quadruplex isolation from human cells. Nat. Chem. 2, 1095–1098 (2010).
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).
Lee, G. R. Role of YY1 in long-range chromosomal interactions regulating Th2 cytokine expression. Transcription 5, e27976 (2014).
Liu, H. et al. Yin Yang 1 is a critical regulator of B-cell development. Genes Dev. 21, 1179–1189 (2007).
Mumbach, M. R. et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat. Methods 13, 919–922 (2016).
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).
Lopez-Perrote, A. et al. Structure of Yin Yang 1 oligomers that cooperate with RuvBL1-RuvBL2 ATPases. J. Biol. Chem. 289, 22614–22629 (2014).
Shi, Y., Seto, E., Chang, L. S. & Shenk, T. Transcriptional repression by YY1, a human GLI-Kruppel-related protein, and relief of repression by adenovirus E1A protein. Cell 67, 377–388 (1991).
CAS PubMed Google Scholar
Merkenschlager, M. & Nora, E. P. CTCF and cohesin in genome folding and transcriptional gene regulation. Annu. Rev. Genomics Hum. Genet. 17, 17–43 (2016).
CAS PubMed Google Scholar
Tang, Z. et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163, 1611–1627 (2015).
Parelho, V. et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422–433 (2008).
CAS PubMed Google Scholar
Khachigian, L. M. The Yin and Yang of YY1 in tumor growth and suppression. Int. J. Cancer 143, 460–465 (2018).
CAS PubMed Google Scholar
Shi, J., Hao, A., Zhang, Q. & Sui, G. The role of YY1 in oncogenesis and its potential as a drug target in cancer therapies. Curr. Cancer Drug Targets 15, 145–157 (2015).
CAS PubMed Google Scholar
Rhodes, D. & Lipps, H. J. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 43, 8627–8637 (2015).
Favicchio, R., Dragan, A. I., Kneale, G. G. & Read, C. M. Fluorescence spectroscopy and anisotropy in the analysis of DNA–protein interactions. Methods Mol. Biol. 543, 589–611 (2009).
CAS PubMed Google Scholar
Li, L., Miao, W., Huang, M., Williams, P. & Wang, Y. Integrated genomic and proteomic analyses reveal novel mechanisms of the methyltransferase SETD2 in renal cell carcinoma development. Mol. Cell. Proteom. 18, 437–447 (2019).
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP–seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).
CAS PubMed Google Scholar
Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
Matsuda, K. et al. ChIP–seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network. Development 144, 1948–1958 (2017).
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997v2 (2013).
Wolff, J. et al. Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization. Nucleic Acids Res. 46, W11–W16 (2018).
Gertz, J. et al. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol. Cell 52, 25–36 (2013).
CAS PubMed Google Scholar
