Review Article

G-四链体在线粒体中的潜在作用

卷 26, 期 16, 2019

页: [2918 - 2932] 页: 15

弟呕挨: 10.2174/0929867325666180228165527

价格: $65

摘要

富含鸟嘌呤(G)核苷酸的一些DNA或RNA序列可采用称为G-四链体(G4)的非常规构象。 在核基因组中,G4基序与基因组不稳定性和基因表达缺陷有关,但它们越来越被认为是调节结构。 最近的研究表明,G4结构可以在线粒体基因组(mtDNA)中形成,潜在的G4形成序列与mtDNA缺失的起源有关。 然而,关于G4结构在线粒体中的调节作用知之甚少。 在这篇简短的综述中,我们将根据来自细胞核的证据,探索G4结构调节线粒体功能的可能性。

关键词: G-四链体,mtDNA,线粒体基因表达,线粒体基因组不稳定性,mtDNA缺失,mtDNA消耗,G4配体。

[1]
Burge, S.; Parkinson, G.N.; Hazel, P.; Todd, A.K.; Neidle, S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res., 2005, 34(19), 5402-5415. [http://dx.doi.org/10.1093/nar/gkl655]. [PMID: 17012276].
[2]
Sen, D.; Gilbert, W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature, 1988, 334(6180), 364-366. [http://dx.doi.org/10.1038/334364a0]. [PMID: 3393228].
[3]
Sen, D.; Gilbert, W. A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature, 1990, 344(6265), 410-414. [http://dx.doi.org/10.1038/344410a0]. [PMID: 2320109].
[4]
Hazel, P.; Parkinson, G.N.; Neidle, S. Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex. J. Am. Chem. Soc., 2006, 128(16), 5480-5487. [http://dx.doi.org/10.1021/ja058577+]. [PMID: 16620121].
[5]
Karsisiotis, A.I.; Hessari, N.M.; Novellino, E.; Spada, G.P.; Randazzo, A.; Webba da Silva, M. Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism. Angew. Chem. Int. Ed. Engl., 2011, 50(45), 10645-10648. [http://dx.doi.org/10.1002/anie.201105193]. [PMID: 21928459].
[6]
Lane, A.N.; Chaires, J.B.; Gray, R.D.; Trent, J.O. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res., 2008, 36(17), 5482-5515. [http://dx.doi.org/10.1093/nar/gkn517]. [PMID: 18718931].
[7]
Harkness, R.W. V; Mittermaier, A.K. G-quadruplex dynamics. Biochim. Biophys. Acta. Proteins Proteomics, 2017, 1865(11 Pt B), 1544-1554. [http://dx.doi.org/10.1016/j.bbapap.2017.06.012]. [PMID: 28642152].
[8]
Huppert, J.L.; Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res., 2005, 33(9), 2908-2916. [http://dx.doi.org/10.1093/nar/gki609]. [PMID: 15914667].
[9]
Bedrat, A.; Lacroix, L.; Mergny, J.L. Re-evaluation of G-quadruplex propensity with G4 Hunter. Nucleic Acids Res., 2016, 44(4), 1746-1759. [http://dx.doi.org/10.1093/nar/gkw006]. [PMID: 26792894].
[10]
Kwok, C.K.; Merrick, C.J. G-Quadruplexes: Prediction, characterization, and biological application. Trends Biotechnol., 2017, 35(10), 997-1013. [http://dx.doi.org/10.1016/j.tibtech.2017.06.012]. [PMID: 28755976].
[11]
Todd, A.K.; Johnston, M.; Neidle, S. Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res., 2005, 33(9), 2901-2907. [http://dx.doi.org/10.1093/nar/gki553]. [PMID: 15914666].
[12]
Garg, R.; Aggarwal, J.; Thakkar, B. Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants. Sci. Rep., 2016, 6(1), 28211. [http://dx.doi.org/10.1038/srep28211]. [PMID: 27324275].
[13]
Paeschke, K.; Capra, J.A.; Zakian, V.A. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell, 2011, 145(5), 678-691. [http://dx.doi.org/10.1016/j.cell.2011.04.015]. [PMID: 21620135].
[14]
Rawal, P.; Kummarasetti, V.B.; Ravindran, J.; Kumar, N.; Halder, K.; Sharma, R.; Mukerji, M.; Das, S.K.; Chowdhury, S. Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res., 2006, 16(5), 644-655. [http://dx.doi.org/10.1101/gr.4508806]. [PMID: 16651665].
[15]
Capra, J.A.; Paeschke, K.; Singh, M.; Zakian, V.A. G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. PLOS Comput. Biol., 2010, 6(7)e1000861 [http://dx.doi.org/10.1371/journal.pcbi.1000861]. [PMID: 20676380].
[16]
Biffi, G.; Tannahill, D.; McCafferty, J.; Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem., 2013, 5(3), 182-186. [http://dx.doi.org/10.1038/nchem.1548]. [PMID: 23422559].
[17]
Henderson, A.; Wu, Y.; Huang, Y.C.; Chavez, E.A.; Platt, J.; Johnson, F.B.; Brosh, R.M., Jr; Sen, D.; Lansdorp, P.M. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res., 2014, 42(2), 860-869. [http://dx.doi.org/10.1093/nar/gkt957]. [PMID: 24163102].
[18]
Wanrooij, P.H.; Uhler, J.P.; Simonsson, T.; Falkenberg, M.; Gustafsson, C.M. G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation. Proc. Natl. Acad. Sci. USA, 2010, 107(37), 16072-16077. [http://dx.doi.org/10.1073/pnas.1006026107]. [PMID: 20798345].
[19]
Agaronyan, K.; Morozov, Y.I.; Anikin, M.; Temiakov, D. Mitochondrial biology. Replication-transcription switch in human mitochondria. Science, 2015, 347(6221), 548-551. [http://dx.doi.org/10.1126/science.aaa0986]. [PMID: 25635099].
[20]
Dong, D.W.; Pereira, F.; Barrett, S.P.; Kolesar, J.E.; Cao, K.; Damas, J.; Yatsunyk, L.A.; Johnson, F.B.; Kaufman, B.A. Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints. BMC Genomics, 2014, 15(1), 677. [http://dx.doi.org/10.1186/1471-2164-15-677]. [PMID: 25124333].
[21]
Bharti, S.K.; Sommers, J.A.; Zhou, J.; Kaplan, D.L.; Spelbrink, J.N.; Mergny, J-L.; Brosh, R.M. Jr DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative Twinkle helicase. J. Biol. Chem., 2014, 289(43), 29975-29993. [http://dx.doi.org/10.1074/jbc.M114.567073]. [PMID: 25193669].
[22]
Oliveira, P.H.; da Silva, C.L.; Cabral, J.M. An appraisal of human mitochondrial DNA instability: New insights into the role of non-canonical DNA structures and sequence motifs. PLoS One, 2013, 8(3)e59907 [http://dx.doi.org/10.1371/journal.pone.0059907]. [PMID: 23555828].
[23]
Han, H.; Hurley, L.H.; Salazar, M. A DNA polymerase stop assay for G-quadruplex-interactive compounds. Nucleic Acids Res., 1999, 27(2), 537-542. [http://dx.doi.org/10.1093/nar/27.2.537]. [PMID: 9862977].
[24]
Fernando, H.; Rodriguez, R.; Balasubramanian, S. Europe PMC funders group selective recognition of a DNA G-quadruplex by an engineered antibody, 2009, 47(36), 9365-9371.
[25]
Chambers, V.S.; Marsico, G.; Boutell, J.M.; Di Antonio, M.; Smith, G.P.; Balasubramanian, S. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol., 2015, 33(8), 877-881. [http://dx.doi.org/10.1038/nbt.3295]. [PMID: 26192317].
[26]
Hänsel-Hertsch, R.; Beraldi, D.; Lensing, S.V.; Marsico, G.; Zyner, K.; Parry, A.; Di Antonio, M.; Pike, J.; Kimura, H.; Narita, M.; Tannahill, D.; Balasubramanian, S. G-quadruplex structures mark human regulatory chromatin. Nat. Genet., 2016, 48(10), 1267-1272. [http://dx.doi.org/10.1038/ng.3662]. [PMID: 27618450].
[27]
Liu, H.Y.; Zhao, Q.; Zhang, T.P.; Wu, Y.; Xiong, Y.X.; Wang, S.K.; Ge, Y.L.; He, J.H.; Lv, P.; Ou, T.M.; Tan, J.H.; Li, D.; Gu, L.Q.; Ren, J.; Zhao, Y.; Huang, Z.S. Conformation Selective antibody enables genome profiling and leads to discovery of parallel G-quadruplex in human telomeres. Cell Chem. Biol., 2016, 23(10), 1261-1270. [http://dx.doi.org/10.1016/j.chembiol.2016.08.013]. [PMID: 27693060].
[28]
Kim, N.W.; Piatyszek, M.A.; Prowse, K.R.; Harley, C.B.; West, M.D.; Ho, P.L.; Coviello, G.M.; Wright, W.E.; Weinrich, S.L.; Shay, J.W. Specific association of human telomerase activity with immortal cells and cancer. Science, 1994, 266(5193), 2011-2015. [http://dx.doi.org/10.1126/science.7605428]. [PMID: 7605428].
[29]
Henderson, E.; Hardin, C.C.; Walk, S.K.; Tinoco, I., Jr; Blackburn, E.H. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell, 1987, 51(6), 899-908. [http://dx.doi.org/10.1016/0092-8674(87)90577-0]. [PMID: 3690664].
[30]
Wolfe, A.L.; Singh, K.; Zhong, Y.; Drewe, P.; Rajasekhar, V.K.; Sanghvi, V.R.; Mavrakis, K.J.; Jiang, M.; Roderick, J.E.; Van Der Meulen, J. Rudimentary G-Quadruplex-Based Telomere Capping in Saccharomyces cerevisiae. Nucleic Acids Res., 2009, 18(4), 764-767.
[31]
Francisco, A.P.; Paulo, A. Oncogene expression modulation in cancer cell lines by DNA G-quadruplex-interactive small molecules. Curr. Med. Chem., 2017, 24(42), 4873-4904. [PMID: 27573064].
[32]
Vy Thi Le, T.; Han, S.; Chae, J.; Park, H-J. G-quadruplex binding ligands: from naturally occurring to rationally designed molecules. Curr. Pharm. Des., 2012, 18(14), 1948-1972. [http://dx.doi.org/10.2174/138161212799958431]. [PMID: 22376113].
[33]
Neidle, S. Human telomeric G-quadruplex: the current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS J., 2010, 277(5), 1118-1125. [http://dx.doi.org/10.1111/j.1742-4658.2009.07463.x]. [PMID: 19951354].
[34]
Riou, J.F.; Guittat, L.; Mailliet, P.; Laoui, A.; Renou, E.; Petitgenet, O.; Mégnin-Chanet, F.; Hélène, C.; Mergny, J.L. Cell senescence and telomere shortening induced by a new series of specific G-quadruplex DNA ligands. Proc. Natl. Acad. Sci. USA, 2002, 99(5), 2672-2677. [http://dx.doi.org/10.1073/pnas.052698099]. [PMID: 11854467].
[35]
Burger, A.M.; Dai, F.; Schultes, C.M.; Reszka, A.P.; Moore, M.J.; Double, J.A.; Neidle, S. The G-quadruplex-interactive molecule BRACO-19 inhibits tumor growth, consistent with telomere targeting and interference with telomerase function. Cancer Res., 2005, 65(4), 1489-1496. [http://dx.doi.org/10.1158/0008-5472.CAN-04-2910]. [PMID: 15735037].
[36]
Müller, S.; Sanders, D.A.; Di Antonio, M.; Matsis, S.; Riou, J-F.; Rodriguez, R.; Balasubramanian, S. Pyridostatin analogues promote telomere dysfunction and long-term growth inhibition in human cancer cells. Org. Biomol. Chem., 2012, 10(32), 6537-6546. [http://dx.doi.org/10.1039/c2ob25830g]. [PMID: 22790277].
[37]
Qi, H.; Lin, C-P.; Fu, X.; Wood, L.M.; Liu, A.A.; Tsai, Y.C.; Chen, Y.; Barbieri, C.M.; Pilch, D.S.; Liu, L.F. G-quadruplexes induce apoptosis in tumor cells. Cancer Res., 2006, 66(24), 11808-11816. [http://dx.doi.org/10.1158/0008-5472.CAN-06-1225]. [PMID: 17178877].
[38]
Moye, A.L.; Porter, K.C.; Cohen, S.B.; Phan, T.; Zyner, K.G.; Sasaki, N.; Lovrecz, G.O.; Beck, J.L.; Bryan, T.M. Telomeric G-quadruplexes are a substrate and site of localization for human telomerase. Nat. Commun., 2015, 6, 7643. [http://dx.doi.org/10.1038/ncomms8643]. [PMID: 26158869].
[39]
Oganesian, L.; Moon, I.K.; Bryan, T.M.; Jarstfer, M.B. Extension of G-quadruplex DNA by ciliate telomerase. EMBO J., 2006, 25(5), 1148-1159. [http://dx.doi.org/10.1038/sj.emboj.7601006]. [PMID: 16511573].
[40]
Huppert, J.L.; Balasubramanian, S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res., 2007, 35(2), 406-413. [http://dx.doi.org/10.1093/nar/gkl1057]. [PMID: 17169996].
[41]
Hershman, S.G.; Chen, Q.; Lee, J.Y.; Kozak, M.L.; Yue, P.; Wang, L-S.; Johnson, F.B. Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae. Nucleic Acids Res., 2008, 36(1), 144-156. [http://dx.doi.org/10.1093/nar/gkm986]. [PMID: 17999996].
[42]
Halder, R.; Riou, J-F.; Teulade-Fichou, M-P.; Frickey, T.; Hartig, J.S. Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. BMC Res. Notes, 2012, 5, 138. [http://dx.doi.org/10.1186/1756-0500-5-138]. [PMID: 22414013].
[43]
Tang, W.; Robles, A.I.; Beyer, R.P.; Gray, L.T.; Nguyen, G.H.; Oshima, J.; Maizels, N.; Harris, C.C.; Monnat, R.J., Jr The Werner syndrome RECQ helicase targets G4 DNA in human cells to modulate transcription. Hum. Mol. Genet., 2016, 25(10), 2060-2069. [http://dx.doi.org/10.1093/hmg/ddw079]. [PMID: 26984941].
[44]
Nguyen, G.H.; Tang, W.; Robles, A.I.; Beyer, R.P.; Gray, L.T.; Welsh, J.A.; Schetter, A.J.; Kumamoto, K.; Wang, X.W.; Hickson, I.D.; Maizels, N.; Monnat, R.J., Jr; Harris, C.C. Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs. Proc. Natl. Acad. Sci. USA, 2014, 111(27), 9905-9910. [http://dx.doi.org/10.1073/pnas.1404807111]. [PMID: 24958861].
[45]
Johnson, J.E.; Cao, K.; Ryvkin, P.; Wang, L.S.; Johnson, F.B. Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res., 2010, 38(4), 1114-1122. [http://dx.doi.org/10.1093/nar/gkp1103]. [PMID: 19966276].
[46]
Eddy, J.; Maizels, N. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res., 2006, 34(14), 3887-3896. [http://dx.doi.org/10.1093/nar/gkl529]. [PMID: 16914419].
[47]
Phan, A.T.; Modi, Y.S.; Patel, D.J. Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter. J. Am. Chem. Soc., 2004, 126(28), 8710-8716. [http://dx.doi.org/10.1021/ja048805k]. [PMID: 15250723].
[48]
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, 2002, 99(18), 11593-11598. [http://dx.doi.org/10.1073/pnas.182256799]. [PMID: 12195017].
[49]
Sun, D.; Liu, W-J.; Guo, K.; Rusche, J.J.; Ebbinghaus, S.; Gokhale, V.; Hurley, L.H. The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex-interactive agents. Mol. Cancer Ther., 2008, 7(4), 880-889. [http://dx.doi.org/10.1158/1535-7163.MCT-07-2119]. [PMID: 18413801].
[50]
Rankin, S.; Reszka, A.P.; Huppert, J.; Zloh, M.; Parkinson, G.N.; Todd, A.K.; Ladame, S.; Balasubramanian, S.; Neidle, S. Putative DNA quadruplex formation within the human c-kit oncogene. J. Am. Chem. Soc., 2005, 127(30), 10584-10589. [http://dx.doi.org/10.1021/ja050823u]. [PMID: 16045346].
[51]
Cogoi, S.; Xodo, L.E. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res., 2006, 34(9), 2536-2549. [http://dx.doi.org/10.1093/nar/gkl286]. [PMID: 16687659].
[52]
Palumbo, S.L.; Ebbinghaus, S.W.; Hurley, L.H. Formation of a unique end-to-end stacked pair of G-quadruplexes in the hTERT core promoter with implications for inhibition of telomerase by G-quadruplex-interactive ligands. J. Am. Chem. Soc., 2009, 131(31), 10878-10891. [http://dx.doi.org/10.1021/ja902281d]. [PMID: 19601575].
[53]
Dexheimer, T.S.; Sun, D.; Hurley, L.H. Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter. J. Am. Chem. Soc., 2006, 128(16), 5404-5415. [http://dx.doi.org/10.1021/ja0563861]. [PMID: 16620112].
[54]
Cogoi, S.; Rapozzi, V.; Cauci, S.; Xodo, L.E. Critical role of hnRNP A1 in activating KRAS transcription in pancreatic cancer cells: A molecular mechanism involving G4 DNA. Biochim. Biophys. Acta, Gen. Subj., 2017, 1861(5 Pt B), 1389-1398. [http://dx.doi.org/10.1016/j.bbagen.2016.11.031]. [PMID: 27888145].
[55]
Lopergolo, A.; Perrone, R.; Tortoreto, M.; Doria, F.; Beretta, G.L.; Zuco, V.; Freccero, M.; Borrello, M.G.; Lanzi, C.; Richter, S.N.; Zaffaroni, N.; Folini, M. Targeting of RET oncogene by naphthalene diimide-mediated gene promoter G-quadruplex stabilization exerts anti-tumor activity in oncogene-addicted human medullary thyroid cancer. Oncotarget, 2016, 7(31), 49649-49663. [http://dx.doi.org/10.18632/oncotarget.10105]. [PMID: 27351133].
[56]
Wu, P.; Ma, D.L.; Leung, C.H.; Yan, S.C.; Zhu, N.; Abagyan, R.; Che, C.M. Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression. Chemistry, 2009, 15(47), 13008-13021. [http://dx.doi.org/10.1002/chem.200901943]. [PMID: 19876976].
[57]
Murat, P.; Gormally, M. V; Sanders, D.; Di Antonio, M.; Balasubramanian, S. Light-mediated in cell downregulation of G-Quadruplex-containing genes using a photo-caged ligand (ESI). Chem. Commun. (Camb), 2013, 49(Scheme 1). , 8453-8455.
[58]
Halder, K.; Halder, R.; Chowdhury, S. Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals. Mol. Biosyst., 2009, 5(12), 1703-1712. [http://dx.doi.org/10.1039/b905132e]. [PMID: 19587895].
[59]
Song, J.; Perreault, J-P.; Topisirovic, I.; Richard, S. RNA G-quadruplexes and their potential regulatory roles in translation. Translation (Austin), 2016, 4(2)e1244031 [http://dx.doi.org/10.1080/21690731.2016.1244031]. [PMID: 28090421].
[60]
Guo, J. U.; Bartel, D. P. RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science (80-. ), 2016, 353(6306)
[61]
Besnard, E.; Babled, A.; Lapasset, L.; Milhavet, O.; Parrinello, H.; Dantec, C.; Marin, J-M.; Lemaitre, J-M. Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat. Struct. Mol. Biol., 2012, 19(8), 837-844. [http://dx.doi.org/10.1038/nsmb.2339]. [PMID: 22751019].
[62]
Bochman, M.L.; Paeschke, K.; Zakian, V.A. DNA secondary structures: Stability and function of G-quadruplex structures. Nat. Rev. Genet., 2012, 13(11), 770-780. [http://dx.doi.org/10.1038/nrg3296]. [PMID: 23032257].
[63]
Langley, A.R.; Gräf, S.; Smith, J.C.; Krude, T. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq). Nucleic Acids Res., 2016, 44(21), 10230-10247. [PMID: 27587586].
[64]
Cayrou, C.; Coulombe, P.; Vigneron, A.; Stanojcic, S.; Ganier, O.; Peiffer, I.; Rivals, E.; Puy, A.; Laurent-Chabalier, S.; Desprat, R.; Méchali, M. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res., 2011, 21(9), 1438-1449. [http://dx.doi.org/10.1101/gr.121830.111]. [PMID: 21750104].
[65]
Valton, A.L.; Hassan-Zadeh, V.; Lema, I.; Boggetto, N.; Alberti, P.; Saintomé, C.; Riou, J.F.; Prioleau, M.N. G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J., 2014, 33(7), 732-746. [http://dx.doi.org/10.1002/embj.201387506]. [PMID: 24521668].
[66]
Lopes, J.; Piazza, A.; Bermejo, R.; Kriegsman, B.; Colosio, A.; Teulade-Fichou, M-P.; Foiani, M.; Nicolas, A. G-quadruplex-induced instability during leading-strand replication. EMBO J., 2011, 30(19), 4033-4046. [http://dx.doi.org/10.1038/emboj.2011.316]. [PMID: 21873979].
[67]
Piazza, A.; Boulé, J-B.; Lopes, J.; Mingo, K.; Largy, E.; Teulade-Fichou, M-P.; Nicolas, A. Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae. Nucleic Acids Res., 2010, 38(13), 4337-4348. [http://dx.doi.org/10.1093/nar/gkq136]. [PMID: 20223771].
[68]
Rodriguez, R.; Miller, K.M.; Forment, J.V.; Bradshaw, C.R.; Nikan, M.; Britton, S.; Oelschlaegel, T.; Xhemalce, B.; Balasubramanian, S.; Jackson, S.P. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat. Chem. Biol., 2012, 8(3), 301-310. [http://dx.doi.org/10.1038/nchembio.780]. [PMID: 22306580].
[69]
De, S.; Michor, F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat. Struct. Mol. Biol., 2011, 18(8), 950-955. [http://dx.doi.org/10.1038/nsmb.2089]. [PMID: 21725294].
[70]
Zimmer, J.; Tacconi, E.M.; Folio, C.; Badie, S.; Porru, M.; Klare, K.; Tumiati, M.; Markkanen, E.; Halder, S.; Ryan, A.; Jackson, S.P.; Ramadan, K.; Kuznetsov, S.G.; Biroccio, A.; Sale, J.E.; Tarsounas, M. Targeting BRCA1 and BRCA2 deficiencies with G-quadruplex-interacting compounds. Mol. Cell, 2016, 61(3), 449-460. [http://dx.doi.org/10.1016/j.molcel.2015.12.004]. [PMID: 26748828].
[71]
van Wietmarschen, N.; Merzouk, S.; Halsema, N.; Spierings, D.C.; Guryev, V.; Lansdorp, P.M. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat. Commun., 2018, 9(1), 271. [http://dx.doi.org/10.1038/s41467-017-02760-1]. [PMID: 29348659].
[72]
Anderson, S.; Bankier, A.T.; Barrell, B.G.; de Bruijn, M.H.; Coulson, A.R.; Drouin, J.; Eperon, I.C.; Nierlich, D.P.; Roe, B.A.; Sanger, F.; Schreier, P.H.; Smith, A.J.; Staden, R.; Young, I.G. Sequence and organization of the human mitochondrial genome. Nature, 1981, 290(5806), 457-465. [http://dx.doi.org/10.1038/290457a0]. [PMID: 7219534].
[73]
Kang, E.; Wu, J.; Gutierrez, N.M.; Koski, A.; Tippner-Hedges, R.; Agaronyan, K.; Platero-Luengo, A.; Martinez-Redondo, P.; Ma, H.; Lee, Y.; Hayama, T.; Van Dyken, C.; Wang, X.; Luo, S.; Ahmed, R.; Li, Y.; Ji, D.; Kayali, R.; Cinnioglu, C.; Olson, S.; Jensen, J.; Battaglia, D.; Lee, D.; Wu, D.; Huang, T.; Wolf, D.P.; Temiakov, D.; Belmonte, J.C.; Amato, P.; Mitalipov, S. Mitochondrial replacement in human oocytes carrying pathogenic mitochondrial DNA mutations. Nature, 2016, 540(7632), 270-275. [http://dx.doi.org/10.1038/nature20592]. [PMID: 27919073].
[74]
Kukat, C.; Wurm, C.A.; Spåhr, H.; Falkenberg, M.; Larsson, N-G.; Jakobs, S. Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA. Proc. Natl. Acad. Sci. USA, 2011, 108(33), 13534-13539. [http://dx.doi.org/10.1073/pnas.1109263108]. [PMID: 21808029].
[75]
Alexeyev, M.; Shokolenko, I.; Wilson, G.; LeDoux, S. The maintenance of mitochondrial DNA integrity--critical analysis and update. Cold Spring Harb. Perspect. Biol., 2013, 5(5)a012641 [http://dx.doi.org/10.1101/cshperspect.a012641]. [PMID: 23637283].
[76]
Yakes, F.M.; Van Houten, B. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc. Natl. Acad. Sci. USA, 1997, 94(2), 514-519. [http://dx.doi.org/10.1073/pnas.94.2.514]. [PMID: 9012815].
[77]
Safdar, A.; Annis, S.; Kraytsberg, Y.; Laverack, C.; Saleem, A.; Popadin, K.; Woods, D.C.; Tilly, J.L.; Khrapko, K. Amelioration of premature aging in mtDNA mutator mouse by exercise: the interplay of oxidative stress, PGC-1α, p53, and DNA damage. A hypothesis. Curr. Opin. Genet. Dev., 2016, 38, 127-132. [http://dx.doi.org/10.1016/j.gde.2016.06.011]. [PMID: 27497229].
[78]
Valente, W.J.; Ericson, N.G.; Long, A.S.; White, P.A.; Marchetti, F.; Bielas, J.H. Mitochondrial DNA exhibits resistance to induced point and deletion mutations. Nucleic Acids Res., 2016, 44(18), 8513-8524. [http://dx.doi.org/10.1093/nar/gkw716]. [PMID: 27550180].
[79]
Szczepanowska, K.; Trifunovic, A. Origins of mtDNA mutations in ageing. Essays Biochem., 2017, 61(3), 325-337. [http://dx.doi.org/10.1042/EBC20160090]. [PMID: 28698307].
[80]
Kauppila, T.E.; Kauppila, J.H.; Larsson, N-G. Mammalian mitochondria and aging: An update. Cell Metab., 2017, 25(1), 57-71. [http://dx.doi.org/10.1016/j.cmet.2016.09.017]. [PMID: 28094012].
[81]
McKinney, E.A.; Oliveira, M.T. Replicating animal mitochondrial DNA. Genet. Mol. Biol., 2013, 36(3), 308. [3h1t5tp.. [http://dx.doi.org/10.1590/S1415-47572013000300002]. [PMID: 24130435].
[82]
Shadel, G.S.; Clayton, D.A. Mitochondrial DNA maintenance in vertebrates. Annu. Rev. Biochem., 1997, 66(1), 409-435. [http://dx.doi.org/10.1146/annurev.biochem.66.1.409]. [PMID: 9242913].
[83]
Eoff, R.L.; Raney, K.D. A catch and release program for single-stranded DNA. J. Biol. Chem., 2017, 292(31), 13085-13086. [http://dx.doi.org/10.1074/jbc.H117.791392]. [PMID: 28778884].
[84]
Yamada, T.; Akiyama, H.; McGeer, P.L. Complement-activated oligodendroglia: a new pathogenic entity identified by immunostaining with antibodies to human complement proteins C3d and C4d. Neurosci. Lett., 1990, 112(2-3), 161-166. [http://dx.doi.org/10.1016/0304-3940(90)90196-G]. [PMID: 2359515].
[85]
Reyes, A.; Gissi, C.; Pesole, G.; Saccone, C. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol., 1998, 15(8), 957-966. [http://dx.doi.org/10.1093/oxfordjournals.molbev.a026011]. [PMID: 9718723].
[86]
Kaasik, A.; Safiulina, D.; Zharkovsky, A.; Veksler, V. Regulation of mitochondrial matrix volume. Am. J. Physiol. Cell Physiol., 2007, 292(1), C157-C163. [http://dx.doi.org/10.1152/ajpcell.00272.2006]. [PMID: 16870828].
[87]
Clayton, D.A. Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol., 1992, 141, 217-232. [http://dx.doi.org/10.1016/S0074-7696(08)62067-7]. [PMID: 1452432].
[88]
Wanrooij, P.H.; Uhler, J.P.; Shi, Y.; Westerlund, F.; Falkenberg, M.; Gustafsson, C.M. A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop. Nucleic Acids Res., 2012, 40(20), 10334-10344. [http://dx.doi.org/10.1093/nar/gks802]. [PMID: 22965135].
[89]
Zheng, K.W.; Wu, R.Y.; He, Y.D.; Xiao, S.; Zhang, J.Y.; Liu, J.Q.; Hao, Y.H.; Tan, Z. A competitive formation of DNA:RNA hybrid G-quadruplex is responsible to the mitochondrial transcription termination at the DNA replication priming site. Nucleic Acids Res., 2014, 42(16), 10832-10844. [http://dx.doi.org/10.1093/nar/gku764]. [PMID: 25140009].
[90]
Lyonnais, S.; Tarrés-Solé, A.; Rubio-Cosials, A.; Cuppari, A.; Brito, R.; Jaumot, J.; Gargallo, R.; Vilaseca, M.; Silva, C.; Granzhan, A.; Teulade-Fichou, M.P.; Eritja, R.; Solà, M. The human mitochondrial transcription factor A is a versatile G-quadruplex binding protein. Sci. Rep., 2017, 7, 43992. [http://dx.doi.org/10.1038/srep43992]. [PMID: 28276514].
[91]
Agaronyan, K.; Morozov, Y.I.; Anikin, M.; Temiakov, D. Mitochondrial biology. Replication-transcription switch in human mitochondria. Science, 2015, 347(6221), 548-551. [http://dx.doi.org/10.1126/science.aaa0986]. [PMID: 25635099].
[92]
Boulé, J-B.; Zakian, V.A. Roles of Pif1-like helicases in the maintenance of genomic stability. Nucleic Acids Res., 2006, 34(15), 4147-4153. [http://dx.doi.org/10.1093/nar/gkl561]. [PMID: 16935874].
[93]
Futami, K.; Shimamoto, A.; Furuichi, Y. Mitochondrial and nuclear localization of human Pif1 helicase. Biol. Pharm. Bull., 2007, 30(9), 1685-1692. [http://dx.doi.org/10.1248/bpb.30.1685]. [PMID: 17827721].
[94]
Mendoza, O.; Bourdoncle, A.; Boulé, J.B.; Brosh, R.M., Jr; Mergny, J.L. G-quadruplexes and helicases. Nucleic Acids Res., 2016, 44(5), 1989-2006. [http://dx.doi.org/10.1093/nar/gkw079]. [PMID: 26883636].
[95]
Paeschke, K.; Bochman, M.L.; Garcia, P.D.; Cejka, P.; Friedman, K.L.; Kowalczykowski, S.C.; Zakian, V.A. Pif1 family helicases suppress genome instability at G-quadruplex motifs. Nature, 2013, 497(7450), 458-462. [http://dx.doi.org/10.1038/nature12149]. [PMID: 23657261].
[96]
Sabouri, N. The functions of the multi-tasking Pfh1Pif1 helicase. Curr. Genet., 2017, 63(4), 621-626. [http://dx.doi.org/10.1007/s00294-016-0675-2]. [PMID: 28054200].
[97]
O’Rourke, T.W.; Doudican, N.A.; Mackereth, M.D.; Doetsch, P.W.; Shadel, G.S. Mitochondrial dysfunction due to oxidative mitochondrial DNA damage is reduced through cooperative actions of diverse proteins. Mol. Cell. Biol., 2002, 22(12), 4086-4093. [http://dx.doi.org/10.1128/MCB.22.12.4086-4093.2002]. [PMID: 12024022].
[98]
Ribeyre, C.; Lopes, J.; Boulé, J.B.; Piazza, A.; Guédin, A.; Zakian, V.A.; Mergny, J.L.; Nicolas, A. The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo. PLoS Genet., 2009, 5(5)e1000475 [http://dx.doi.org/10.1371/journal.pgen.1000475]. [PMID: 19424434].
[99]
Paeschke, K.; Capra, J.A.; Zakian, V.A. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell, 2011, 145(5), 678-691. [http://dx.doi.org/10.1016/j.cell.2011.04.015]. [PMID: 21620135].
[100]
Snow, B.E.; Mateyak, M.; Paderova, J.; Wakeham, A.; Iorio, C.; Zakian, V.; Squire, J.; Harrington, L. Murine Pif1 interacts with telomerase and is dispensable for telomere function in vivo. Mol. Cell. Biol., 2007, 27(3), 1017-1026. [http://dx.doi.org/10.1128/MCB.01866-06]. [PMID: 17130244].
[101]
Bannwarth, S.; Berg-Alonso, L.; Augé, G.; Fragaki, K.; Kolesar, J.E.; Lespinasse, F.; Lacas-Gervais, S.; Burel-Vandenbos, F.; Villa, E.; Belmonte, F.; Michiels, J.F.; Ricci, J.E.; Gherardi, R.; Harrington, L.; Kaufman, B.A.; Paquis-Flucklinger, V. Inactivation of Pif1 helicase causes a mitochondrial myopathy in mice. Mitochondrion, 2016, 30, 126-137. [http://dx.doi.org/10.1016/j.mito.2016.02.005]. [PMID: 26923168].
[102]
Croteau, D.L.; Rossi, M.L.; Canugovi, C.; Tian, J.; Sykora, P.; Ramamoorthy, M.; Wang, Z.M.; Singh, D.K.; Akbari, M.; Kasiviswanathan, R.; Copeland, W.C.; Bohr, V.A. RECQL4 localizes to mitochondria and preserves mitochondrial DNA integrity. Aging Cell, 2012, 11(3), 456-466. [http://dx.doi.org/10.1111/j.1474-9726.2012.00803.x]. [PMID: 22296597].
[103]
Lyonnais, S.; Tarrés-Solé, A.; Rubio-Cosials, A.; Cuppari, A.; Brito, R.; Jaumot, J.; Gargallo, R.; Vilaseca, M.; Silva, C.; Granzhan, A.; Teulade-Fichou, M.P.; Eritja, R.; Solà, M. The human mitochondrial transcription factor A is a versatile G-quadruplex binding protein. Sci. Rep., 2017, 7, 43992. [http://dx.doi.org/10.1038/srep43992]. [PMID: 28276514].
[104]
Ohno, T.; Umeda, S.; Hamasaki, N.; Kang, D. Binding of human mitochondrial transcription factor A, an HMG box protein, to a four-way DNA junction. Biochem. Biophys. Res. Commun., 2000, 271(2), 492-498. [http://dx.doi.org/10.1006/bbrc.2000.2656]. [PMID: 10799324].
[105]
Antonicka, H.; Sasarman, F.; Nishimura, T.; Paupe, V.; Shoubridge, E.A. The mitochondrial RNA-binding protein GRSF1 localizes to RNA granules and is required for posttranscriptional mitochondrial gene expression. Cell Metab., 2013, 17(3), 386-398. [http://dx.doi.org/10.1016/j.cmet.2013.02.006]. [PMID: 23473033].
[106]
Emerman, A.B.; Zhang, Z-R.; Chakrabarti, O.; Hegde, R.S. LRPPRC and SLIRP Interact in a Ribonucleoprotein Complex That Regulates Posttranscriptional Gene Expression in Mitochondria. Mol. Biol. Cell, 2010, 21(24), 4325-4337. [http://dx.doi.org/10.1091/mbc.e10-09-0742]. [PMID: 20980618].
[107]
Williams, P.; Li, L.; Dong, X.; Wang, Y. Identification of SLIRP as a G quadruplex-binding protein. J. Am. Chem. Soc., 2017, 139(36), 12426-12429. [http://dx.doi.org/10.1021/jacs.7b07563]. [PMID: 28859475].
[108]
Huang, W-C.; Tseng, T-Y.; Chen, Y-T.; Chang, C-C.; Wang, Z-F.; Wang, C-L.; Hsu, T-N.; Li, P-T.; Chen, C-T.; Lin, J-J.; Lou, P.J.; Chang, T.C. Direct evidence of mitochondrial G-quadruplex DNA by using fluorescent anti-cancer agents. Nucleic Acids Res., 2015, 43(21), 10102-10113. [PMID: 26487635].
[109]
Li, C-P.; Huang, J-H.; Chang, A-C.; Hung, Y-M.; Lin, C-H.; Chao, Y.; Lee, S-D.; Whang-Peng, J.; Huang, T-S. A G-quadruplex ligand 3,3′-diethyloxadicarbocyanine iodide induces mitochondrion-mediated apoptosis but not decrease of telomerase activity in nasopharyngeal carcinoma NPC-TW01 cells. Pharm. Res., 2004, 21(1), 93-100. [http://dx.doi.org/10.1023/B:PHAM.0000012166.44521.1f]. [PMID: 14984262].
[110]
Zhuang, X-Y.; Yao, Y-G. Mitochondrial dysfunction and nuclear-mitochondrial shuttling of TERT are involved in cell proliferation arrest induced by G-quadruplex ligands. FEBS Lett., 2013, 587(11), 1656-1662. [http://dx.doi.org/10.1016/j.febslet.2013.04.010]. [PMID: 23603390].

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