Effects of local mRNA structure on posttranscriptional gene silencing

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 37, 2008, Pages 13787-13792

  Rudnick, Stephen I ^a   Swaminathan, Jyothishmathi ^a   Sumaroka, Marina ^a   Liebhaber, Stephen ^a   Gewirtz, Alan M ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Antisense; Oligodeoxynucleotide; siRNA

Indexed keywords

ALPHA CP 1 PROTEIN; ANTISENSE OLIGODEOXYNUCLEOTIDE; MESSENGER RNA; NUCLEOTIDE; RNA BINDING PROTEIN; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL LYSATE; CONTROLLED STUDY; DROSOPHILA; EMBRYO; HUMAN; HUMAN CELL; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; RNA STRUCTURE;

ANIMALS; BASE SEQUENCE; CELL LINE; DROSOPHILA MELANOGASTER; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES, ANTISENSE; RIBONUCLEASE H; RNA INTERFERENCE; RNA, MESSENGER; RNA-BINDING PROTEINS;

EID: 52949095730     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0805781105     Document Type: Article

References (39)

1. Elbashir SM, et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498.
2. Crooke ST (2004) Progress in antisense technology. Annu Rev Med 55:61-95.
3. de Fougerolles A, Vornlocher HP, Maraganore J, Lieberman J (2007) Interfering with disease: A progress report on siRNA-based therapeutics. Nat Rev Drug Discovery 6:443-453.
4. Gewirtz AM (2007) On future's doorstep: RNA interference and the pharmacopeia of tomorrow. J Clin Invest 117:3612-3614.
5. Lima WF, Monia BP, Ecker DJ, Freier SM (1992) Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31:12055-12061.
6. Mir KU, Southern EM (1999) Determining the influence of structure on hybridization using oligonucleotide arrays. Nat Biotechnol 17:788-792.
7. Brown KM, Chu CY, Rana TM (2005) Target accessibility dictates the potency of human RISC. Nat Struct Mol Biol 12:469-470.
8. Yoshinari K, Miyagishi M, Taira K (2004) Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Res 32:691-699.
9. Schubert S, Grunweller A, Erdmann VA, Kurreck J (2005) Local RNA target structure influences siRNA efficacy: Systematic analysis of intentionally designed binding regions. J Mol Biol 348:883-893.
10. Overhoff M, et al. (2005) Local RNA target structure influences siRNA efficacy: A systematic global analysis. J Mol Biol 348:871-881.
11. Stein CA (1999) Hybridization prediction gets to first base. Nat Biotechnol 17:751-752.
12. Braasch DA, et al. (2003) RNA interference in mammalian cells by chemically-modified RNA. Biochemistry 42:7967-7975.
13. Elmen J, et al. (2005) Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality. Nucleic Acids Res 33:439-447.
14. Schwarz DS, et al. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199-208.
15. Reynolds A, et al. (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22:326-330.
16. Tuschl T, et al. (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13:3191-3197.
17. Elbashir SM, et al. (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20:6877-6888.
18. Monia BP, et al. (1993) Evaluation of 2′-modified oligonucleotides containing 2′-deoxy gaps as antisense inhibitors of gene expression. J Biol Chem 268:14514-14522.
19. 2+-dependent endonuclease. Curr Biol 14:787-791.
20. Lima W, et al. (2007) Human RNase H1 discriminates between subtle variations in the structure of the heteroduplex substrate. Mol Pharmacol 71:83-91.
21. Kalota A, et al. (2006) 2′-deoxy-2′-fluoro-β-D- arabinonucleic acid (2′F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing. Nucleic Acids Res 34:451-461.
22. Dreyfuss G, Kim VN, Kataoka N (2002) Messenger-RNA-binding proteins and the messages they carry. Nat Rev Mol Cell Biol 3:195-205.
23. Thisted T, Lyakhov DL, Liebhaber SA (2001) Optimized RNA targets of two closely related triple KH domain proteins, heterogeneous nuclear ribonucleoprotein K and αCP-2KL, suggest distinct modes of RNA recognition. J Biol Chem 276:17484-17496.
24. Vickers TA, et al. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J Biol Chem 278:7108-7118.
25. Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130:101-112.
26. Song JJ, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305:1434-1437.
27. Patzel V, Sczakiel G (2000) In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells. Nucleic Acids Res 28:2462-2466.
28. Lima WF, et al. (2003) Human RNase H1 uses one tryptophan and two lysines to position the enzyme at the 3′-DNA/5′-RNA terminus of the heteroduplex substrate. J Biol Chem 278:49860-49867.
29. Yuan YR, et al. (2005) Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell 19:405-419.
30. Haley B, Zamore PD (2004) Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 11:599-606.
31. Ma JB, et al. (2005) Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434:666-670.
32. Cole CN, Scarcelli JJ (2006) Transport of messenger RNA from the nucleus to the cytoplasm. Curr Opin Cell Biol 18:299-306.
33. Weirich CS, et al. (2006) Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nat Cell Biol 8:668-676.
34. Gross T, et al. (2007) The DEAD-box RNA helicase Dbp5 functions in translation termination. Science 315:646-649.
35. Martinez J, et al. (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110:563-574.
36. Makeyev AV, Eastmond DL, Liebhaber SA (2002) Targeting a KH-domain protein with RNA decoys. RNA 8:1160-1173.
37. Haley B, Tang G, Zamore PD (2003) In vitro analysis of RNA interference in Drosophila melanogaster. Methods 30:330-336.
38. Rasband WS (1997-2007) http://rsb.info.nih.gov/ij (US National Institutes of Health, Bethesda, MD).
39. Chkheidze AN, et al. (1999) Assembly of the α-globin mRNA stability complex reflects binary interaction between the pyrimidine-rich 3′ untranslated region determinant and poly(C)-binding protein αCP. Mol Cell Biol 19:4572-4581.