G4RNA: An RNA G-quadruplex database

Database

Volumn 2015, Issue , 2015, Pages

  Garant, Jean Michel ^a   Luce, Mikael J ^a   Scott, Michelle S ^a   Perreault, Jean Pierre ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE QUADRUPLEX; RNA;

GENETICS; NUCLEIC ACID DATABASE; NUCLEOTIDE MOTIF;

DATABASES, NUCLEIC ACID; G-QUADRUPLEXES; NUCLEOTIDE MOTIFS; RNA;

EID: 85051605046     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bav059     Document Type: Article

References (21)

1. Gellert, M., Lipsett, M.N., and Davies, D.R. (1962) Helix formation by guanylic acid. Proc. Natl Acad. Sci. U. S. A., 48, 2013-2018.
2. Guédin, A., Gros, J., Alberti, P., et al. (2010) How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res., 38, 7858-7868.
3. Pandey, S., Agarwala, P., and Maiti, S. (2013) Effect of loops and G-Quartets on the stability of RNA G-Quadruplexes. J. Phys. Chem. B, 117, 6896-6905.
4. Beaudoin, J.D., Jodoin, R., and Perreault, J.P. (2014) New scoring system to identify RNA G-quadruplex folding. Nucleic Acids Res., 42, 1209-1223.
5. Kumari, S., Bugaut, A., Huppert, J.L., et al. (2007) An RNA Gquadruplex in the 5'UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol., 3, 218-221.
6. Huppert, J.L., Bugaut, A., Kumari, S., et al. (2008) G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res., 36, 6260-6268.
7. Beaudoin, J.D. and Perreault, J.P. (2010) 5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res., 38, 7022-7036.
8. Beaudoin, J.D. and Perreault, J.P. (2013) Exploring mRNA 3'- UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Res., 41, 5898-5911.
9. Wolfe, A.L., Singh, K., Zhong, Y., et al. (2014) RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature, 513, 65-70.
10. Perrone, R., Butovskaya, E., Daelemans, D., et al. (2014) Anti-HIV-1 activity of the G-quadruplex ligand BRACO-19. J. Antimicrob. Chemother., 69, 3248-3258.
11. Zhang, Y., Gaetano, C.M., Williams, K.R., et al. (2014) FMRP interacts with G-quadruplex structures in the 3'-UTR of its dendritic target Shank1 mRNA. RNA Biology, 11, 1364-1374.
12. Brázda, V., Hároníková, L., Liao, J.C., et al. (2014) DNA and RNA quadruplex-binding proteins. Int. J. Mol. Sci., 15, 17493-17517.
13. Huang, H., Suslov, N.B., Li, N.S., et al. (2014) A G-quadruplex containing RNA activates fluorescence in a GFP-like fluorophore. Nat. Chem. Biol., 10, 686-691.
14. Rouleau, S.G., Beaudoin, J.D., Bisaillon, M., et al. (2015) Small antisense oligonucleotides against G-quadruplexes: specific mRNA translational switches. Nucleic Acid Res., 43, 595-606.
15. Huppert, J.L. and Balasubramanian, S. (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res., 33, 2908-2916.
16. Mukundan, V.T. and Phan, A.T. (2013) Bulges in GQuadruplexes: broadening the definition of G-Quadruplexforming sequences. J. Am. Chem. Soc., 135, 5017-5028.
17. Jodoin, R., Bauer, L., Garant, J.M., et al. (2014) The folding of 5'-UTR human G-quadruplexes possessing a long central loop. RNA, 20, 1129-1141.
18. Lorenz, R., Bernhart, S.H., Qin, J., et al. (2013) 2D meets 4G: GQuadruplexes in RNA secondary structure prediction. IEEE ACM Trans. Comput. Biol. Bioinforma., 10, 832-844.
19. Kikin, O., D'Antonio, L., and Bagga, P.S. (2006) QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res., 34, W676-W682.
20. Kikin, O., Zappala, Z., D'Antonio, L., et al. (2008) GRSDB2 and GRS-UTRdb: databases of Quadruplex forming G-rich sequences in pre-mRNAs and mRNAs. Nucleic Acids Res., 36, D141-D148.
21. Howe, D., Costanzo, M., Fey, P., et al. (2008) Big data: the future of biocuration. Nature, 455, 47-50.