siRNA Has Greatly Elevated Mismatch Tolerance at 3′-UTR Sites

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Wei, Na ^a   Zhang, Lei ^a   Huang, Huang ^a   Chen, Yue ^b   Zheng, Jie ^a   Zhou, Xiao ^a   Yi, Fan ^a   Du, Quan ^a,b   Liang, Zicai ^a  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY HEALTH SCIENCE CENTER   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE 1 PROTEIN; ARGONAUTE 3 PROTEIN; ARGONAUTE 4 PROTEIN; ARGONAUTE PROTEIN; MESSENGER RNA; RNA 18S; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; AMINO ACID SEQUENCE; ARTICLE; CELL STRAIN HEK293; CONTROLLED STUDY; DOWN REGULATION; EMBRYO; GENE SILENCING; GENETIC CODE; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA DEGRADATION; RNA INTERFERENCE; RNA SEQUENCE; TRANSLATION REGULATION; WESTERN BLOTTING;

3' UNTRANSLATED REGIONS; ARGONAUTE PROTEINS; BASE PAIR MISMATCH; BINDING SITES; HUMANS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 84869044165     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049309     Document Type: Article

References (38)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
2. Hannon GJ, (2002) RNA interference. Nature 418: 244-251.
3. Mello CC, Conte D Jr, (2004) Revealing the world of RNA interference. Nature 431: 338-342.
4. Hutvagner G, Zamore PD, (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056-2060.
5. Meister G, Tuschl T, (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431: 343-349.
6. Carthew RW, Sontheimer EJ, (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
7. Djuranovic S, Nahvi A, Green R, (2011) A parsimonious model for gene regulation by miRNAs. Science 331: 550-553.
8. Sasaki T, Shiohama A, Minoshima S, Shimizu N, (2003) Identification of eight members of the Argonaute family in the human genome. Genomics 82: 323-330.
9. Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, et al. (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Molecular Cell 15: 185-197.
10. Ma JB, Ye K, Patel DJ, (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429: 318-322.
11. Landthaler M, Gaidatzis D, Rothballer A, Chen PY, Soll SJ, et al. (2008) Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA 14: 2580-2596.
12. Yoda M, Kawamata T, Paroo Z, Ye X, Iwasaki S, et al. (2010) ATP-dependent human RISC assembly pathways. Nature structural & molecular biology 17: 17-23.
13. Forstemann K, Horwich MD, Wee L, Tomari Y, Zamore PD, (2007) Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130: 287-297.
14. Tomari Y, Du T, Zamore PD, (2007) Sorting of Drosophila small silencing RNAs. Cell 130: 299-308.
15. Steiner FA, Hoogstrate SW, Okihara KL, Thijssen KL, Ketting RF, et al. (2007) Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nature structural & molecular biology 14: 927-933.
16. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, et al. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
17. 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.
18. Pillai RS, Artus CG, Filipowicz W, (2004) Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. RNA 10: 1518-1525.
19. Wu L, Fan J, Belasco JG, (2008) Importance of translation and nonnucleolytic ago proteins for on-target RNA interference. Curr Biol 18: 1327-1332.
20. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, et al. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21: 635-637.
21. Lin X, Ruan X, Anderson MG, McDowell JA, Kroeger PE, et al. (2005) siRNA-mediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Research 33: 4527-4535.
22. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, et al. (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 12: 1179-1187.
23. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, et al. (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3: 199-204.
24. Du Q, Thonberg H, Wang J, Wahlestedt C, Liang Z, (2005) A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites. Nucleic Acids Res 33: 1671-1677.
25. Dahlgren C, Zhang HY, Du Q, Grahn M, Norstedt G, et al. (2008) Analysis of siRNA specificity on targets with double-nucleotide mismatches. Nucleic Acids Res 36: e53.
26. Huang H, Qiao R, Zhao D, Zhang T, Li Y, et al. (2009) Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs. Nucleic Acids Res 37: 7560-7569.
27. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, et al. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.
28. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nature Genetics 39: 1278-1284.
29. Gu S, Rossi JJ, (2005) Uncoupling of RNAi from active translation in mammalian cells. RNA 11: 38-44.
30. Martin SE, Caplen NJ, (2006) Mismatched siRNAs downregulate mRNAs as a function of target site location. FEBS letters 580: 3694-3698.
31. Wang J, Pitarque M, Ingelman-Sundberg M, (2006) 3′-UTR polymorphism in the human CYP2A6 gene affects mRNA stability and enzyme expression. Biochem Biophys Res Commun 340: 491-497.
32. Gusella M, Padrini R, (2007) G>C SNP of thymidylate synthase with respect to colorectal cancer. Pharmacogenomics 8: 985-996.
33. Hikami K, Kawasaki A, Ito I, Koga M, Ito S, et al. (2011) Association of a functional polymorphism in the 3′-untranslated region of SPI1 with systemic lupus erythematosus. Arthritis & rheumatism 63: 755-763.
34. Schmitter D, Filkowski J, Sewer A, Pillai RS, Oakeley EJ, et al. (2006) Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Research 34: 4801-4815.
35. Aleman LM, Doench J, Sharp PA, (2007) Comparison of siRNA-induced off-target RNA and protein effects. RNA 13: 385-395.
36. Gu S, Jin L, Zhang F, Sarnow P, Kay MA, (2009) Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16: 144-150.
37. Du Q, Thonberg H, Zhang HY, Wahlestedt C, Liang Z, (2004) Validating siRNA using a reporter made from synthetic DNA oligonucleotides. Biochem Biophys Res Commun 325: 243-249.
38. Mathews DH, Sabina J, Zuker M, Turner DH, (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology 288: 911-940.