Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Lekprasert, Parawee ^a   Mayhew, Michael ^a   Ohler, Uwe ^a,b  

^a DUKE UNIVERSITY   (United States)

^b DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE PROTEIN; MESSENGER RNA; MICRORNA; INITIATION FACTOR 2; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; ENERGY; GENE EXPRESSION; GENE TARGETING; GENETIC CONSERVATION; GENETIC REGULATION; GENOME ANALYSIS; PREDICTION; PROTEIN EXPRESSION; PROTEIN INTERACTION; RNA ANALYSIS; THERMODYNAMICS; ALGORITHM; BIOLOGY; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; METABOLISM; METHODOLOGY;

MAMMALIA;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DOWN-REGULATION; EUKARYOTIC INITIATION FACTOR-2; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MICRORNAS; RNA, VIRAL; THERMODYNAMICS;

EID: 79958165626     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020622     Document Type: Article

References (44)

1. Flynt AS, Lai EC, (2008) Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet 9: 831-842.
2. Jones-Rhoades MW, Bartel DP, Bartel B, (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
3. Filipowicz W, Bhattacharyya SN, Sonenberg N, (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9: 102-114.
4. Chi SW, Zang JB, Mele A, Darnell RB, (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
5. Easow G, Teleman AA, Cohen SM, (2007) Isolation of microRNA targets by miRNP immunopurification. RNA 13: 1198-1204.
6. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
7. 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.
8. Hammell M, Long D, Zhang L, Lee A, Carmack CS, et al. (2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods 5: 813-819.
9. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
10. Ritchie W, Flamant S, Rasko JE, (2009) Predicting microRNA targets and functions: traps for the unwary. Nat Methods 6: 397-398.
11. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
12. Lewis BP, Burge CB, Bartel DP, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
13. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, et al. (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10: 295.
14. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
15. Nielsen CB, Shomron N, Sandberg R, Hornstein E, Kitzman J, et al. (2007) Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13: 1894-1910.
16. Ha I, Wightman B, Ruvkun G, (1996) A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev 10: 3041-3050.
17. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
18. Wightman B, Ha I, Ruvkun G, (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
19. Shin C, Nam JW, Farh KK, Chiang HR, Shkumatava A, et al. Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell 38: 789-802.
20. Ghosh Z, Mallick B, Chakrabarti J, (2009) Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res 37: 1035-1048.
21. Gottwein E, Cullen BR, (2008) Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe 3: 375-387.
22. Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, et al. (2007) A viral microRNA functions as an orthologue of cellular miR-155. Nature 450: 1096-1099.
23. Skalsky RL, Samols MA, Plaisance KB, Boss IW, Riva A, et al. (2007) Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol 81: 12836-12845.
24. Zhao Y, Samal E, Srivastava D, (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220.
25. Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, et al. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26: 578-583.
26. Long D, Lee R, Williams P, Chan CY, Ambros V, et al. (2007) Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14: 287-294.
27. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA targets. PLoS Biol 2: e363.
28. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB, (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
29. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R, (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517.
30. Stark A, Brennecke J, Russell RB, Cohen SM, (2003) Identification of Drosophila MicroRNA targets. PLoS Biol 1: E60.
31. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, et al. (2008) The impact of microRNAs on protein output. Nature 455: 64-71.
32. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
33. Bernhart SH, Tafer H, Muckstein U, Flamm C, Stadler PF, et al. (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol 1: 3.
34. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster, (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte fur Chemie 125: 22.
35. Bernhart SH, Hofacker IL, Stadler PF, (2006) Local RNA base pairing probabilities in large sequences. Bioinformatics 22: 614-615.
36. Bompfunewerer AF, Backofen R, Bernhart SH, Hertel J, Hofacker IL, et al. (2008) Variations on RNA folding and alignment: lessons from Benasque. J Math Biol 56: 129-144.
37. Sethupathy P, Corda B, Hatzigeorgiou AG, (2006) TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA 12: 192-197.
38. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, et al. (2009) The UCSC genome browser database: update 2010. Nucleic Acids Res.
39. Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, et al. (2007) Ensembl 2007. Nucleic Acids Res 35: D610-617.
40. Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M., Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs. PLoS One 5: e11710.
41. Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, et al. Evidence-ranked motif identification. Genome Biol 11: R19.
42. Chen K, Maaskola J, Siegal ML, Rajewsky N, (2009) Reexamining microRNA site accessibility in Drosophila: a population genomics study. PLoS One 4: e5681.
43. Guo H, Ingolia NT, Weissman JS, Bartel DP., Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
44. Betel D, Koppal A, Agius P, Sander C, Leslie C., Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11: R90.