Abstract
While DNA inside the cells is predominantly canonical right-handed double helix, guanine-rich DNAs have potential to fold into four-stranded structures that contain stacks of G-quartets (G4 DNA quadruplex). Genome sequencing has revealed G4 sequences tend to localize at the gene control regions, especially in the promoters of oncogenes. A growing body of evidence indicates that G4 DNA quadruplexes might have important regulatory roles in genome function, highlighting the need for techniques to detect genome-wide folding of DNA into this structure. Potassium permanganate in vivo treatment of cells results in oxidizing of nucleotides in single-stranded DNA regions that accompany G4 DNA quadruplexes formation, providing an excellent probe for the conformational state of DNA inside the living cells. Here, we describe a permanganate-based methodology to detect G4 DNA quadruplex, genome-wide. This methodology combined with high-throughput sequencing provides a snapshot of the DNA conformation over the whole genome in vivo.
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References
Zaytseva O, Quinn LM (2018) DNA conformation regulates gene expression: the MYC promoter and beyond. Bioessays 40:e1700235. https://doi.org/10.1002/bies.201700235
Kouzine F, Levens D (2007) Supercoil-driven DNA structures regulate genetic transactions. Front Biosci 12:4409–4423
van Holde K, Zlatanova J (1994) Unusual DNA structures, chromatin and transcription. Bioessays 16(1):59–68. https://doi.org/10.1002/bies.950160110
Qin Y, Hurley LH (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie 90(8):1149–1171. https://doi.org/10.1016/j.biochi.2008.02.020
Murat P, Balasubramanian S (2014) Existence and consequences of G-quadruplex structures in DNA. Curr Opin Genet Dev 25:22–29. https://doi.org/10.1016/j.gde.2013.10.012
Brooks TA, Kendrick S, Hurley L (2010) Making sense of G-quadruplex and i-motif functions in oncogene promoters. FEBS J 277(17):3459–3469. https://doi.org/10.1111/j.1742-4658.2010.07759.x
Guilbaud G, Murat P, Recolin B, Campbell BC, Maiter A, Sale JE, Balasubramanian S (2017) Local epigenetic reprogramming induced by G-quadruplex ligands. Nat Chem 9(11):1110–1117. https://doi.org/10.1038/nchem.2828
Kendrick S, Muranyi A, Gokhale V, Hurley LH, Rimsza LM (2017) Simultaneous drug targeting of the promoter MYC G-quadruplex and BCL2 i-motif in diffuse large B-cell lymphoma delays tumor growth. J Med Chem 60(15):6587–6597. https://doi.org/10.1021/acs.jmedchem.7b00298
Schaffitzel C, Berger I, Postberg J, Hanes J, Lipps HJ, Pluckthun A (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc Natl Acad Sci U S A 98(15):8572–8577. https://doi.org/10.1073/pnas.141229498
Biffi G, Tannahill D, McCafferty J, Balasubramanian S (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem 5(3):182–186. https://doi.org/10.1038/nchem.1548
Lam EY, Beraldi D, Tannahill D, Balasubramanian S (2013) G-quadruplex structures are stable and detectable in human genomic DNA. Nat Commun 4:1796. https://doi.org/10.1038/ncomms2792
Hansel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, Di Antonio M, Pike J, Kimura H, Narita M, Tannahill D, Balasubramanian S (2016) G-quadruplex structures mark human regulatory chromatin. Nat Genet 48(10):1267–1272. https://doi.org/10.1038/ng.3662
Bui CT, Rees K, Cotton RG (2003) Permanganate oxidation reactions of DNA: perspective in biological studies. Nucleosides Nucleotides Nucleic Acids 22(9):1835–1855. https://doi.org/10.1081/NCN-120023276
Giardina C, Perez-Riba M, Lis JT (1992) Promoter melting and TFIID complexes on drosophila genes in vivo. Genes Dev 6(11):2190–2200
Johnston BH, Rich A (1985) Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution. Cell 42(3):713–724
Kouzine F, Wojtowicz D, Baranello L, Yamane A, Nelson S, Resch W, Kieffer-Kwon KR, Benham CJ, Casellas R, Przytycka TM, Levens D (2017) Permanganate/S1 nuclease footprinting reveals non-B DNA structures with regulatory potential across a mammalian genome. Cell Syst 4(3):344–356 e347. https://doi.org/10.1016/j.cels.2017.01.013
Kouzine F, Wojtowicz D, Yamane A, Resch W, Kieffer-Kwon KR, Bandle R, Nelson S, Nakahashi H, Awasthi P, Feigenbaum L, Menoni H, Hoeijmakers J, Vermeulen W, Ge H, Przytycka TM, Levens D, Casellas R (2013) Global regulation of promoter melting in naive lymphocytes. Cell 153(5):988–999. https://doi.org/10.1016/j.cell.2013.04.033
Huppert JL, Balasubramanian S (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33(9):2908–2916. https://doi.org/10.1093/nar/gki609
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923
Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25(14):1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Anders S, Pyl PT, Huber W (2015) HTSeq—a python framework to work with high-throughput sequencing data. Bioinformatics 31(2):166–169. https://doi.org/10.1093/bioinformatics/btu638
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Kouzine, F., Wojtowicz, D., Yamane, A., Casellas, R., Przytycka, T.M., Levens, D.L. (2019). In Vivo Chemical Probing for G-Quadruplex Formation. In: Yang, D., Lin, C. (eds) G-Quadruplex Nucleic Acids. Methods in Molecular Biology, vol 2035. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9666-7_23
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DOI: https://doi.org/10.1007/978-1-4939-9666-7_23
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