The folding of 5′-UTR human G-quadruplexes possessing a long central loop

RNA

Volumn 20, Issue 7, 2014, Pages 1129-1141

  Jodoin, Rachel ^a   Bauer, Lubos ^a   Garant, Jean Michel ^a   Laaref, Abdelhamid Mahdi ^a   Phaneuf, Francis ^a   Perreault, Jean Pierre ^a  

^a UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

5 uTR; G quadruplex; In line probing; RNA structure; Translation regulation

Indexed keywords

APC PROTEIN; GUANINE; GUANINE QUADRUPLEX; MESSENGER RNA; PROTEIN; PROTEIN BAG1; PROTEIN CBX1; PROTEIN CTGLF6; PROTEIN HIRA; PROTEIN LRRC37A3; PROTEIN MDS1; PROTEIN TOM1L2; TRANSCRIPTOME; UNCLASSIFIED DRUG; BCL2 ASSOCIATED ATHANOGENE 1 PROTEIN; BCL2-ASSOCIATED ATHANOGENE 1 PROTEIN; CELL CYCLE PROTEIN; CHAPERONE; DNA BINDING PROTEIN; HIRA PROTEIN, HUMAN; MECOM PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

5' UNTRANSLATED REGION; ARTICLE; AUTORADIOGRAPHY; BIOLOGICAL ACTIVITY; HUMAN; IN VITRO STUDY; LUCIFERASE ASSAY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; QUANTITATIVE ANALYSIS; RNA CLEAVAGE; RNA FOLDING; RNA LONG CENTRAL LOOP; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSCRIPTION; 5′-UTR; CHEMISTRY; CONFORMATION; G-QUADRUPLEX; GENETICS; IN-LINE PROBING; METABOLISM; MOLECULAR GENETICS; PROTEIN SYNTHESIS; PROTO ONCOGENE; RNA PROCESSING; TRANSLATION REGULATION;

5′-UTR; G-QUADRUPLEX; IN-LINE PROBING; RNA STRUCTURE; TRANSLATION REGULATION;

5' UNTRANSLATED REGIONS; BASE SEQUENCE; CELL CYCLE PROTEINS; DNA-BINDING PROTEINS; G-QUADRUPLEXES; HISTONE CHAPERONES; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; PROTO-ONCOGENES; RNA FOLDING; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; TRANSCRIPTION FACTORS;

EID: 84902651070     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.044578.114     Document Type: Article

References (42)

1. Beaudoin JD, Perreault JP. 2010. 5′-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res 38: 7022-7036.
2. Beaudoin JD, Perreault JP. 2013. Exploring mRNA 3′-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Res 41: 5898-5911.
3. Beaudoin JD, Jodoin R, Perreault JP. 2013a. In-line probing of RNA G-quadruplexes. Methods 64: 79-87.
4. Beaudoin JD, Jodoin R, Perreault JP. 2013b. New scoring system to identify RNA G-quadruplex folding. Nucleic Acids Res 42: 1209-1223.
5. Bian Y, Tan C, Wang J, Sheng Y, Zhang J, Wang W. 2014. Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex. PLoS Comput Biol 10: e1003562.
6. Biffi G, Di Antonio M, Tannahill D, Balasubramanian S. 2013. Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells. Nat Chem 6: 75-80.
7. Bugaut A, Balasubramanian S. 2012. 5′-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res 40: 4727-4741.
8. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. 2006. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34: 5402-5415.
9. Collie GW, Parkinson GN. 2011. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 40: 5867-5892.
10. Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. 2005. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11: 344-354.
11. Eddy J, Maizels N. 2006. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res 34: 3887-3896.
12. Gellert M, Lipsett MN, Davies DR. 1962. Helix formation by guanylic acid. Proc Natl Acad Sci 48: 2013-2018.
13. Guedin A, Alberti P, Mergny JL. 2009. Stability of intramolecular quadruplexes: sequence effects in the central loop. Nucleic Acids Res 37: 5559-5567.
14. Guedin A, Gros J, Alberti P, Mergny JL. 2010. How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res 38: 7858-7868.
15. Halder K, Hartig JS. 2011. RNA quadruplexes. Met Ions Life Sci 9: 125-139.
16. Hardin CC, Perry AG, White K. 2000. Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids. Biopolymers 56: 147-194.
17. Hazel P, Huppert J, Balasubramanian S, Neidle S. 2004. Loop-length-dependent folding of G-quadruplexes. J Am Chem Soc 126: 16405-16415.
18. Huppert JL, Balasubramanian S. 2005. Prevalence of quadruplexes in the human genome. Nucleic Acids Res 33: 2908-2916.
19. Huppert JL, Bugaut A, Kumari S, Balasubramanian S. 2008. G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res 36: 6260-6268.
20. Jacobs GH, Chen A, Stevens SG, Stockwell PA, Black MA, Tate WP, Brown CM. 2009. Transterm: database to aid the analysis of regulatory sequences in mRNAs. Nucleic Acids Res 37: D72-D76.
21. Joachimi A, Benz A, Hartig JS. 2009. A comparison of DNA and RNA quadruplex structures and stabilities. Bioorg Med Chem 17: 6811-6815.
22. Karsisiotis AI, O'Kane C, Webba da Silva M. 2013. DNA quadruplex folding formalism-a tutorial on quadruplex topologies. Methods 64: 28-35.
23. Koirala D, Ghimire C, Bohrer C, Sannohe Y, Sugiyama H, Mao H. 2013. Long-loop G-quadruplexes are misfolded population minorities with fast transition kinetics in human telomeric sequences. J Am Chem Soc 135: 2235-2241.
24. Kwok CK, Sherlock ME, Bevilacqua PC. 2013. Effect of loop sequence and loop length on the intrinsic fluorescence of G-quadruplexes. Biochemistry 52: 3019-3021.
25. Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. 2008. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nat Protoc 3: 1395-1401.
26. Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. 2011. ViennaRNA Package 2.0. Algorithms Mol Biol 6: 26.
27. Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R. 2001. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 29: 4724-4735.
28. Marcel V, Tran PL, Sagne C, Martel-Planche G, Vaslin L, Teulade-Fichou MP, Hall J, Mergny JL, Hainaut P, Van Dyck E. 2011. G-quadruplex structures in TP53 intron 3: role in alternative splicing and in production of p53 mRNA isoforms. Carcinogenesis 32: 271-278.
29. McLuckie KI, Di Antonio M, Zecchini H, Xian J, Caldas C, Krippendorff BF, Tannahill D, Lowe C, Balasubramanian S. 2013. G-quadruplex DNA as a molecular target for induced synthetic lethality in cancer cells. J Am Chem Soc 135: 9640-9643.
30. Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G. 2005. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 33: D141-D146.
31. Millevoi S, Moine H, Vagner S. 2012. G-quadruplexes in RNA biology. Wiley Interdiscip Rev RNA 3: 495-507.
32. Mukundan VT, Phan AT. 2013. Bulges in G-quadruplexes: broadening the definition of G-quadruplex-forming sequences. J Am Chem Soc 135: 5017-5028.
33. Olsen CM, Lee HT, Marky LA. 2009. Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops. J Phys Chem B 113: 2587-2595.
34. Pandey S, Agarwala P, Maiti S. 2013. Effect of loops and G-quartets on the stability of RNA G-quadruplexes. J Phys Chem B 117: 6896-6905.
35. Patel DJ, Phan AT, Kuryavyi V. 2007. Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res 35: 7429-7455.
36. Rachwal PA, Findlow IS, Werner JM, Brown T, Fox KR. 2007. Intramolecular DNA quadruplexes with different arrangements of short and long loops. Nucleic Acids Res 35: 4214-4222.
37. Risitano A, Fox KR. 2004. Influence of loop size on the stability of intramolecular DNA quadruplexes. Nucleic Acids Res 32: 2598-2606.
38. Sacca B, Lacroix L, Mergny JL. 2005. The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides. Nucleic Acids Res 33: 1182-1192.
39. Shafer RH, Smirnov I. 2000. Biological aspects of DNA/RNA quadruplexes. Biopolymers 56: 209-227.
40. Viglasky V, Bauer L, Tluckova K. 2010. Structural features of intra- and intermolecular G-quadruplexes derived from telomeric repeats. Biochemistry 49: 2110-2120.
41. Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. 2011. Kinetic and thermodynamic control of G-quadruplex folding. Angew Chem Int Ed Engl 50: 8046-8050.
42. Zhang AY, Bugaut A, Balasubramanian S. 2011. A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology. Biochemistry 50: 7251-7258.