GRSDB2 and GRS_UTRdb: Databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Kikin, Oleg ^b   Zappala, Zachary ^a   D'Antonio, Lawrence ^b   Bagga, Paramjeet S ^b  

^a Bergen County Academies   (United States)

^b RAMAPO COLLEGE OF NEW JERSEY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; COMPUTER PROGRAM; EUKARYOTE; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENE STRUCTURE; GENETIC TRANSCRIPTION; GRS UTR DATABASE; GRSDB2 DATABASE; HUMAN; INFORMATION SYSTEM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE DATABASE;

ALTERNATIVE SPLICING; ANIMALS; DATABASES, NUCLEIC ACID; G-QUADRUPLEXES; HUMANS; INTERNET; RATS; RNA PRECURSORS; RNA, MESSENGER; UNTRANSLATED REGIONS; USER-COMPUTER INTERFACE;

EUKARYOTA; MAMMALIA;

EID: 38549087401     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm982     Document Type: Article

References (41)

1. Gellert, M., Lipsett, M.N. and Davies, D.R. (1962) Helix formation by guanylic acid. Proc. Natl Acad. Sci. USA, 48, 2013-2018.
2. Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H.J. and Pluckthun, A. (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl Acad. Sci. USA, 98, 8572-8577.
3. Halder, K. and Chowdhury, S. (2005) Kinetic resolution of bimolecular hybridization versus intramolecular folding in nucleic acids by surface plasmon resonance: Application to G-quadruplex/duplex competition in human c-myc promoter. Nucleic Acids Res., 33, 4466-4474.
4. Simonsson,T. (2001) G-quadruplex DNA structures - variations on a theme. Biol. Chem., 382, 621-628.
5. Davis, J.T. (2004) G-quartets 40 years later: From 5′-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed. Engl., 43, 668-698.
6. Kelland, L.R. (2005) Overcoming the immortality of tumour cells by telomere and telomerase based cancer therapeutics - current status and future prospects. Eur. J. Cancer, 41, 971-979.
7. Burge, S., Parkinson, G.N., Hazel, P., Todd, A.K. and Neidle, S. (2006) Quadruplex DNA: Sequence, topology and structure. Nucleic Acids Res. 34, 5402-5415.
8. Maizels, N. (2006) Dynamic roles for G4 DNA in the biology of eukaryotic cells. Nat. Struct. Mol. Biol., 13, 1055-1059.
9. Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D. and Lipps, H.J. (2005) Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat. Struct. Mol. Biol., 12, 847-854.
10. Todd, A.K., Haider, S.M., Parkinson, G.N. and Neidle, S. (2007) Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter. Nucleic Acids Res, 35, 5799-5808.
11. Duquette, M.L., Handa, P., Vincent, J.A., Taylor, A.F. and Maizels, N. (2004) Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA. Genes Dev., 18, 1618-1629.
12. Wieland, M. and Hartig, J.S. (2007) RNA quadruplex-based modulation of gene expression. Chem. Biol., 14, 757-763.
13. Sacca, B., Lacroix, L. and Mergny, J.L. (2005) The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides. Nucleic Acids Res., 33, 1182-1192.
14. Kumari, S., Bugaut, A., Huppert, J.L. and Balasubramanian, S. (2007) An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol., 3, 218-221.
15. Bashkirov, V.I., Scherthan, H., Sotinger, J.A., Buerstedde, J.M. and Heyer, W.D. (1997) A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates. J. Cell Biol., 136, 761-773.
16. Nishimura, Y., Martin, C.L., Vazquez-Lopez, A., Spence, S.J., Alvarez-Retuerto, A.I., Sigman, M., Steindler, C., Pellegrini, S., Schanen, N.C. et al. (2007) Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways. Hum. Mol. Genet., 16, 1682-1698.
17. Bagga, P.S., Ford, L.P., Chen, F. and Wilusz, J. (1995) The G-rich auxiliary downstream element has distinct sequence and portion requirements and mediates efficient 3′ end pre-mRNA processing through a trans-acting factor. Nucleic Acids Res., 23, 1625-1631.
18. Bagga, P.S., Arhin, G.K. and Wilusz, J. (1998) DSEF-1 is a member of the hnRNP H family of RNA-binding proteins and simulates pre-mRNA cleavage and polyadenylation in vitro. Nucleic Acids Res., 26, 5343-5350.
19. Arhin, G.K., Boots, M., Bagga, P.S., Milcarek, C. and Witusz, J. (2002) Downstream sequence elements with different affinities for the hnRNP H/ H' protein influence the processing efficiency of mammalian polyadenylation signals. Nucleic Acids Res., 30, 1842-1850.
20. Dalziel, M., Nunes, N.M. and Furger, A. (2007) Two G-rich regulatory elements located adjacent to and 440 nucleotides downstream of the core poly(A) site of the intronless melanocortin receptor 1 gene are critical for efficient 3′ end processing. Mol Cell Biol., 27, 1568-1580.
21. 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.
22. Veraldi, K.L., Arhin, G.K., Martincic, K., Chung-Ganster, L.H., Wilusz, J. and Milcarek, C. (2001) hnRNP F influences binding of a 64-kilodalton subunit-of cleavage stimulation factor to mRNA precursors in mouse B cells. Mol. Cell. Biol., 21, 1228-1238.
23. Bruce, S.R., Dingle, R.W. and Peterson, M.L. (2003) B-cell and plasma-cell splicing differences: A potential role in regulated immunoglobulin RNA processing. RNA, 9, 1264-1273.
24. Garneau, D., Revil, T., Fisette, J.F. and Chabot, B. (2005) Heterogeneous nuclear ribonucleoprotein F/H proteins modulate the alternative splicing of the apoptotic mediator Bcl-x. J. Biol. Chem. 280, 22641-22650.
25. Zhang, Q.S., Manche, L., Xu, R.M. and Krainer, A.R. (2006) hnRNP A1 associates with telomere ends and stimulates telomerase activity. RNA 12, 1116-1128.
26. Han, K., Yeo, G., An, P., Burge, C.B. and Grabowski, P.J. (2005) A combinatorial code for splicing silencing: UAGG and GGGG motifs, PLoS Biol., 3, e158.
27. Wang, E., Dimova, N. and Cambi, F. (2007) PLP/DM20 ratio is regulated by haRNPH and F and a novel G-rich enhancer in oligodendrocytes. Nucleic Acids Res., 35, 4164-4178.
28. Tian, B., Hu, J., Zhang, H. and Lutz, C.S. (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33, 201-212.
29. Johnson, J.M., Castle, J., Garrett-Engele, P., Kan, Z., Loerch, P.M., Armour, C.D., Santos, R., Schadt, E.E., Stoughton, R. et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science, 302, 2141-2144.
30. Huppert, J.L. and Balasubramanian, S. (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res., 33, 2908-2916.
31. Todd, A.K., Johnston, M. and Neidle, S. (2005) Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res., 33 2901-2907.
32. Eddy, J. and Maizels, N. (2006) Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res., 34, 3887-3896.
33. Kostadinov, R., Malhotra, N., Viotti, M., Shine, R., D'Antonio, L. and Bagga, P. (2006) GRSDB: A database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. Nucleic Acids Res., 34, D119-D124.
34. Bonnal, S., Schaeffer, C., Creancier, L., Clamems, S., Moine, H., Prats, A.C. and Vagner, S. (2003) A single internal ribosome entry site containing a 13 quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons. J. Biol. Chem., 278, 39330-39336.
35. Oliver, A.W., Bogdarina, I., Schroeder, E., Taylor, I.A. and Kneale, G.G. (2000) Preferential building of fd gene 5 protein to tetraplex nucleic acid structures. J. Mol. Biol., 301, 575-584.
36. Mignone, F., Gissi, C., Liuni, S. and Pesole, G. (2002) Untranslated regions of mRNAs. Genome Biol., 3, reviews0004. 1-reviews0004.10.
37. Crnugelj, M., Sket, P. and Plavec, J. (2003) Small change in a G-rich sequence, a dramatic change in topology: New dimeric G-quadruplex folding motif with unique loop orientations. J. Am. Chem. Soc., 125, 7866-7871.
38. Hazel, P., Huppert, J., Balasubramanian, S. and Neidle, S. (2004) Loop-length-dependent folding of G-quadruplexes. J. Am. Chem. Soc. 126, 16405-16415.
39. Risitano, A. and Fox, K.R. (2004) Influence of loop size on the stability of intramolecular DNA qnadruplexes. Nucleic Acids Res., 32, 2598-2606.
40. Zarudnaya, M.I., Kolomiets, I.M., Potyahaylo, A.L. and Hovorun, D.M. (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higherorder structures. Nucleic Acids Res., 31, 1375-1386.
41. Kankia, B.I., Barany, G. and Musier-Forsyth, K. (2005) Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein. Nucleic Acids Res., 33, 4395-4403.