DNA G-quadruplexes: functional significance in plant and farm animal science

References

• Wells RD. Non-B DNA conformations, mutagenesis and disease. Trends Biochem Sci. 2007;32(6):271–278.
   PubMed Web of Science ®Google Scholar
• Gellert M, Lipsett MN, Davies DR. Helix formation by guanylic acid. Proc Natl Acad Sci USA. 1962;48(12):2013–2018.
   PubMed Web of Science ®Google Scholar
• Lipps HJ, Gruissem W, Prescott DM. Higher order DNA structure in macronuclear chromatin of the hypotrichous ciliate Oxytricha nova. Proc Natl Acad Sci USA. 1982;79(8):2495–2499.
   PubMed Web of Science ®Google Scholar
• Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 2006;34(19):5402–5415.
   PubMed Web of Science ®Google Scholar
• Huppert JL, Bugaut A, Kumari S, Balasubramanian S. G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 2008;36(19):6260–6268.
   PubMed Web of Science ®Google Scholar
• Mukundan VT, Phan AT. Bulges in G-quadruplexes: broadening the definition of G-quadruplex-forming sequences. J Am Chem Soc. 2013;135(13):5017–5028.
   PubMed Web of Science ®Google Scholar
• Cammas A, Millevoi S. RNA G-quadruplexes: emerging mechanisms in disease. Nucleic Acids Res. 2017;45(4):1584–1595.
   PubMed Web of Science ®Google Scholar
• Malgowska M, Czajczynska K, Gudanis D, Tworak A, Gdaniec Z. Overview of the RNA G-quadruplex structures. Acta Biochim Pol. 2016;63(4):609–621.
   PubMed Web of Science ®Google Scholar
• Huppert JL, Balasubramanian S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 2005;33(9):2908–2916.
   PubMed Web of Science ®Google Scholar
• Wong HM, Stegle O, Rodgers S, Huppert JL. A toolbox for predicting G-quadruplex formation and stability. J Nucleic Acids. 2010;2010:1–6.
   Google Scholar
• Vorlíčková M, Kejnovská I, Sagi J, et al. Circular dichroism and guanine quadruplexes. Methods. 2012;57(1):64–75.
   PubMed Web of Science ®Google Scholar
• Adrian M, Heddi B, Phan AT. NMR spectroscopy of G-quadruplexes. Methods. 2012;57(1):11–24.
   PubMed Web of Science ®Google Scholar
• Mergny JL, Lacroix L. UV melting of G-quadruplexes. Curr Protoc Nucleic Acid Chem. 2009;37:1–15.
   Google Scholar
• Han H, Hurley LH, Salazar M. A DNA polymerase stop assay for G-quadruplex-interactive compounds. Nucleic Acids Res. 1999;27(2):537–542.
   PubMed Web of Science ®Google Scholar
• Biffi G, Tannahill D, McCafferty J, Balasubramanian S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nature Chem. 2013;5(3):182–186.
   PubMed Web of Science ®Google Scholar
• Henderson A, Wu Y, Huang YC, et al. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res. 2014;42(2):860–869.
   PubMed Web of Science ®Google Scholar
• Ma DL, Zhang Z, Wang M, Lu L, Zhong HJ, Leung CH. Recent developments in G-quadruplex Probes. Chem Biol. 2015;22(7):812–828.
   PubMedGoogle Scholar
• Lam EYN, Beraldi D, Tannahill D, Balasubramanian S. G-quadruplex structures are stable and detectable in human genomic DNA. Nat Commun. 2013;4(1):1796–1798.
   PubMedGoogle Scholar
• Fernando H, Rodriguez R, Balasubramanian S. Europe PMC funders group selective recognition of a DNA G-quadruplex by an engineered antibody. Biochemistry. 2008;47(36):9365–9371.
   PubMed Web of Science ®Google Scholar
• Hänsel-Hertsch R, Beraldi D, Lensing SV, et al. G-quadruplex structures mark human regulatory chromatin. Nat Genet. 2016;48(10):1267–1272.
   PubMed Web of Science ®Google Scholar
• Rodriguez R, Miller KM, Forment JV, et al. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat Chem Biol. 2012;8(3):301–310.
   PubMed Web of Science ®Google Scholar
• Marsico G, Chambers VS, Sahakyan AB, et al. Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 2019;47:3862–3874.
   PubMed Web of Science ®Google Scholar
• Zeng W, Wu F, Liu C, et al. Small-molecule-based human genome G4 profiling reveals potential gene regulation activity. Chem Commun. 2019;55(16):2269–2272.
   PubMed Web of Science ®Google Scholar
• Yoshida W, Saikyo H, Nakabayashi K, et al. Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand. Sci Rep. 2018;8(1):1–8.
   PubMedGoogle Scholar
• Weldon C, Eperon IC, Dominguez C. Do we know whether potential G-quadruplexes actually form in long functional RNA molecules? Biochem Soc Trans. 2016;44(6):1761–1768.
   PubMedGoogle Scholar
• Wanrooij PH, Uhler JP, Simonsson T, Falkenberg M, Gustafsson CM. G-quadruplex structures in RNA stimulate mitochondrial transcription termination and primer formation. Proc Natl Acad Sci USA. 2010;107(37):16072–16077.
   PubMed Web of Science ®Google Scholar
• Sahakyan AB, Murat P, Mayer C, Balasubramanian S. G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition. Nat Struct Mol Biol. 2017;24(3):243–247.
   PubMed Web of Science ®Google Scholar
• Simonsson T, Pecinka P, Kubista M. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 1998;26(5):1167–1172.
   PubMed Web of Science ®Google Scholar
• Verma A, Halder K, Halder R, et al. Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species. J Med Chem. 2008;51(18):5641–5649.
   PubMed Web of Science ®Google Scholar
• Cayrou C, Coulombe P, Puy A, et al. New insights into replication origin characteristics in metazoans. Cell Cycle. 2012;11(4):658–667.
   PubMed Web of Science ®Google Scholar
• Besnard E, Babled A, Lapasset L, et al. 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.
   PubMed Web of Science ®Google Scholar
• Prioleau MN. G-quadruplexes and DNA replication origins. Adv Exp Med Biol. 2017;1042:273–286.
   PubMed Web of Science ®Google Scholar
• Paeschke K, Simonsson T, Postberg J, Rhodes D, Lipps HJ. Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat Struct Mol Biol. 2005;12(10):847–854.
   PubMed Web of Science ®Google Scholar
• Harkness RW, Mittermaier AK. G-quadruplex dynamics. Biochim Biophys Acta - Proteins Proteomics. 2017;1865(11):1544–1554.
   PubMed Web of Science ®Google Scholar
• Lattmann S, Giri B, Vaughn JP, Akman SA, Nagamine Y. Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU. Nucleic Acids Res. 2010;38(18):6219–6233.
   PubMed Web of Science ®Google Scholar
• Ito K, Go S, Komiyama M, Xu Y. Inhibition of translation by small RNA-stabilized mRNA structures in human cells. J Am Chem Soc. 2011;133(47):19153–19159.
   PubMed Web of Science ®Google Scholar
• Bonnal S, Schaeffer C, Créancier L, 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. 2003;278(41):39330–39336.
   PubMed Web of Science ®Google Scholar
• Kostadinov R. GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. Nucleic Acids Res. 2006;34(90001):D119–24.
   PubMedGoogle Scholar
• Subramanian M, Rage F, Tabet R, Flatter E, Mandel JL, Moine H. G-quadruplex RNA structure as a signal for neurite mRNA targeting. EMBO Rep. 2011;12(7):697–704.
   PubMed Web of Science ®Google Scholar
• Biffi G, Tannahill D, Balasubramanian S. An intramolecular G-quadruplex structure is required for TERRA RNA binding to the telomeric protein TRF2. J Am Chem Soc. 2012;134(29):11974–11976.
   PubMed Web of Science ®Google Scholar
• Takahama K, Takada A, Tada S, et al. Regulation of telomere length by G-quadruplex telomere DNA- and TERRA-binding protein TLS/FUS. Chem Biol. 2013;20(3):341–350.
   PubMedGoogle Scholar
• Mullen MA, Olson KJ, Dallaire P, Major F, Assmann SM, Bevilacqua PC. RNA G-quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Res. 2010;38(22):8149–8163.
   PubMed Web of Science ®Google Scholar
• Takahashi H, Nakagawa A, Kojima S, et al. Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods. J Biosci Bioeng. 2012;114(5):570–575.
   PubMed Web of Science ®Google Scholar
• Andorf CM, Kopylov M, Dobbs D, et al. G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation. J Genet Genomics. 2014;41(12):627–647.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zhao M, Zhang Q, Zhu GF, Li FF, Du LF. Genomic distribution and possible functional roles of putative G-quadruplex motifs in two subspecies of Oryza sativa. Comput Biol Chem. 2015;56:122–130.
   PubMed Web of Science ®Google Scholar
• Yang M, Wu Y, Jin S, et al. Flower bud transcriptome analysis of Sapium sebiferum (Linn.) Roxb. and primary investigation of drought induced flowering: pathway construction and G-Quadruplex prediction based on transcriptome. PLoS One. 2015;10(3):1–20.
   Web of Science ®Google Scholar
• 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):31–35.
   Google Scholar
• Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC. A stable RNA G-quadruplex within the 5′-UTR of Arabidopsis thaliana ATR mRNA inhibits translation. Biochem J. 2015;467(1):91–102.
   PubMedGoogle Scholar
• Cho H, Cho HS, Nam H, et al. Translational control of phloem development by RNA G-quadruplex-JULGI determines plant sink strength. Nat Plants. 2018;4(6):376–390.
   PubMed Web of Science ®Google Scholar
• Ge F, Wang Y, Li H, et al. Plant-GQ: an integrative database of G-quadruplex in plant. J Comput Biol. 2019;26(0):1–7.
   PubMedGoogle Scholar
• Armas P, Calcaterra NB. G-quadruplex in animal development: contribution to gene expression and genomic heterogeneity. Mech Dev. 2018;154:64–72.
   PubMed Web of Science ®Google Scholar
• Du Z, Kong P, Gao Y, Li N. Enrichment of G4 DNA motif in transcriptional regulatory region of chicken genome. Biochem Biophys Res Commun. 2007;354(4):1067–1070.
   PubMed Web of Science ®Google Scholar
• Sarkies P, Reams C, Simpson LJ, Sale JE. Epigenetic instability due to defective replication of structured DNA. Mol Cell. 2010;40(5):703–713.
   PubMed Web of Science ®Google Scholar
• Sarkies P, Murat P, Phillips LG, Patel KJ, Balasubramanian S, Sale JE. FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA. Nucleic Acids Res. 2012;40(4):1485–1498.
   PubMed Web of Science ®Google Scholar
• Papadopoulou C, Guilbaud G, Schiavone D, Sale JE. Nucleotide pool depletion induces G-quadruplex-dependent perturbation of gene expression. Cell Rep. 2015;13(11):2491–2503.
   PubMed Web of Science ®Google Scholar
• Winding P, Berchtold MW. The chicken B cell line DT40: a novel tool for gene disruption experiments. J Immunol Methods. 2001;249(1–2):1–16.
   PubMed Web of Science ®Google Scholar
• Jackowiak P, Hojka-Osinska A, Gasiorek K, et al. Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro. Int J Biochem Cell Biol. 2017;92:148–154.
   PubMed Web of Science ®Google Scholar
• Derecka K, Balkwill GD, Garner TP, Hodgman C, Flint APF, Searle MS. Occurrence of a quadruplex motif in a unique insert within exon C of the bovine estrogen receptor α gene (ESR1). Biochemistry. 2010;49(35):7625–7633.
   PubMed Web of Science ®Google Scholar
• Olsthoorn R. G-quadruplexes within prion mRNA: the missing link in prion disease? Nucleic Acids Res. 2014;42(14):9327–9333.
   PubMed Web of Science ®Google Scholar
• Cavaliere P, Pagano B, Granata V, et al. Cross-talk between prion protein and quadruplex-forming nucleic acids: a dynamic complex formation. Nucleic Acids Res. 2013;41(1):327–339.
   PubMed Web of Science ®Google Scholar
• Murakami K, Nishikawa F, Noda K, Yokoyama T, Nishikawa S. Anti-bovine prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its beta isoform with high affinity. Prion. 2008;2(2):73–80.
   PubMed Web of Science ®Google Scholar
• González C, Salces-Ortiz J, Calvo JH, Serrano MM. In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene. Cell Stress Chaperones. 2016;21(3):415–427.
   PubMed Web of Science ®Google Scholar
• Wang Q, Han G, Ye J, et al. Characterization of the polycystic kidney disease 2 gene promoter. Genomics. 2014;104(6):512–519.
   PubMed Web of Science ®Google Scholar
• Yurchenko AA, Deniskova TE, Yudin NS, et al. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics. 2019;20(S3):1–19.
   PubMedGoogle Scholar
• Kalaldeh MA, van de Werf JHJ, Gondro C. Identification of loci associated with parasite resistance in australian sheep. Proc Assoc Advmt Breed Genet. 2015;21:69–72.
   Google Scholar
• Jing H, Zhou Y, Fang L, et al. DExD/H-Box helicase 36 signaling via myeloid differentiation primary response gene 88 contributes to NF-κB activation to type 2 porcine reproductive and respiratory syndrome virus infection. Front Immunol. 2017;8:1–11.
   PubMed Web of Science ®Google Scholar
• Yafe A, Shklover J, Weisman-Shomer P, Bengal E, Fry M. Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin. Nucleic Acids Res. 2008;36(12):3916–3925.
   PubMed Web of Science ®Google Scholar
• Yuan Z, Li J, Li J, et al. Investigation on BRCA1 SNPs and its effects on mastitis in Chinese commercial cattle. Gene. 2012;505(1):190–194.
   PubMed Web of Science ®Google Scholar
• Brázda V, Hároníková L, Liao JCC, Fridrichová H, Jagelská EB. Strong preference of BRCA1 protein to topologically constrained non-B DNA structures. BMC Mol Biol. 2016;17(1):1–9.
   PubMedGoogle Scholar
• Cer RZ, Donohue DE, Mudunuri US, et al. Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. Nucleic Acids Res. 2013;41(D1):94–100.
   Web of Science ®Google Scholar
• Dhapola P, Chowdhury S. QuadBase2: web server for multiplexed guanine quadruplex mining and visualization. Nucleic Acids Res. 2016;44(W1):W277–W283.
   PubMed Web of Science ®Google Scholar
• Nakken S, Rognes T, Hovig E. The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts. Nucleic Acids Res. 2009;37(17):5749–5756.
   PubMed Web of Science ®Google Scholar
• Baral A, Kumar P, Halder R, et al. Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals. Nucleic Acids Res. 2012;40(9):3800–3811.
   PubMed Web of Science ®Google Scholar