Quantifying the strength of miRNA-target interactions

Methods

Volumn 85, Issue , 2015, Pages 90-99

  Breda, Jeremie ^a   Rzepiela, Andrzej J ^a   Gumienny, Rafal ^a   Van Nimwegen, Erik ^a   Zavolan, Mihaela ^a  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

CLASH; CLIP; MiRNA; MiRNA target prediction; MIRZA; Non canonical miRNA binding

Indexed keywords

ARGONAUTE PROTEIN; MESSENGER RNA; MICRORNA;

ARTICLE; GENE EXPRESSION; GENETIC TRANSFECTION; MICHAELIS CONSTANT; PREDICTION; PRIORITY JOURNAL; RNA BINDING; RNA SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; GENE TARGETING; HUMAN; METABOLISM; PHYSIOLOGY; PROCEDURES; PROTEIN SECONDARY STRUCTURE;

BINDING SITES; GENE TARGETING; HUMANS; MICRORNAS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY;

EID: 84939776670     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.04.012     Document Type: Article

References (44)

1. Huntzinger E., Izaurralde E. Nat. Rev. Genet. 2011, 12:99-110.
2. Lewis B.P., Burge C.B., Bartel D.P. Cell 2005, 120:15-20.
3. Eichhorn S.W., Guo H., McGeary S.E., Rodriguez-Mias R.A., Shin C., Baek D., et al. Mol. Cell 2014, 56:104-115.
4. Levine E., Zhang Z., Kuhlman T., Hwa T. PLoS Biol. 2007, 5:e229.
5. Mukherji S., Ebert M.S., Zheng G.X.Y., Tsang J.S., Sharp P.A., van Oudenaarden A. Nat. Genet. 2011, 43:854-859.
6. Buchler N.E., Louis M. J. Mol. Biol. 2008, 384:1106-1119.
7. Hausser J., Zavolan M. Nat. Rev. Genet. 2014, 15:599-612.
8. Khan A.A., Betel D., Miller M.L., Sander C., Leslie C.S., Marks D.S. Nat. Biotechnol. 2009, 27:549-555.
9. Bosson A.D., Zamudio J.R., Sharp P.A. Mol. Cell 2014, 56:347-359.
10. Figliuzzi M., Marinari E., De Martino A. Biophys. J. 2013, 104:1203-1213.
11. Bosia C., Pagnani A., Zecchina R. PLoS One 2013, 8:e66609.
12. Bissels U., Wild S., Tomiuk S., Holste A., Hafner M., Tuschl T., et al. RNA 2009, 15:2375-2384.
13. Chang J., Nicolas E., Marks D., Sander C., Lerro A., Buendia M.A., et al. RNA Biol. 2004, 1:106-113.
14. Wang D., Zhang Z., O'Loughlin E., Lee T., Houel S., O'Carroll D., et al. Genes Dev. 2012, 26:693-704.
15. Grün D., Kester L., van Oudenaarden A. Nat. Methods 2014, 11:637-640.
16. Gumienny R., Zavolan M. Nucleic Acids Res. 2015.
17. Chi S.W., Zang J.B., Mele A., Darnell R.B. Nature 2009, 460:479-486.
18. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., et al. Cell 2010, 141:129-141.
19. Khorshid M., Hausser J., Zavolan M., van Nimwegen E. Nat. Methods 2013, 10:253-255.
20. Helwak A., Kudla G., Dudnakova T., Tollervey D. Cell 2013, 153:654-665.
21. Grosswendt S., Filipchyk A., Manzano M., Klironomos F., Schilling M., Herzog M., et al. Mol. Cell 2014, 54:1042-1054.
22. Elkayam E., Kuhn C.-D., Tocilj A., Haase A.D., Greene E.M., Hannon G.J., et al. Cell 2012, 150:100-110.
23. Xia T., SantaLucia J., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., et al. Biochemistry 1998, 37:14719-14735.
24. Kishore S., Jaskiewicz L., Burger L., Hausser J., Khorshid M., Zavolan M. Nat. Methods 2011, 8:559-564.
25. Wang X. Bioinformatics 2014, 30:1377-1383.
26. Wee L.M., Flores-Jasso C.F., Salomon W.E., Zamore P.D. Cell 2012, 151:1055-1067.
27. Reuter J.S., Mathews D.H. BMC Bioinformatics 2010, 11:129.
28. Hausser J., Landthaler M., Jaskiewicz L., Gaidatzis D., Zavolan M. Genome Res. 2009, 19:2009-2020.
29. Vasudevan S., Tong Y., Steitz J.A. Science 2007, 318:1931-1934.
30. Jackson A.L., Burchard J., Schelter J., Chau B.N., Cleary M., Lim L., et al. RNA 2006, 12:1179-1187.
31. Dahiya N., Sherman-Baust C.A., Wang T.-L., Davidson B., Shih I.-M., Zhang Y., et al. PLoS One 2008, 3:e2436.
32. Frankel L.B., Wen J., Lees M., Høyer-Hansen M., Farkas T., Krogh A., et al. EMBO J. 2011, 30:4628-4641.
33. Gennarino V.A., Sardiello M., Avellino R., Meola N., Maselli V., Anand S., et al. Genome Res. 2008, 19:481-490.
34. Hudson R.S., Yi M., Esposito D., Glynn S.A., Starks A.M., Yang Y., et al. Oncogene 2012, 32:4139-4147.
35. Leivonen S.-K., Mäkelä R., Ostling P., Kohonen P., Haapa-Paananen S., Kleivi K., et al. Oncogene 2009, 28:3926-3936.
36. Linsley P.S., Schelter J., Burchard J., Kibukawa M., Martin M.M., Bartz S.R., et al. Mol. Cell. Biol. 2007, 27:2240-2252.
37. Selbach M., Schwanhäusser B., Thierfelder N., Fang Z., Khanin R., Rajewsky N. Nature 2008, 455:58-63.
38. Olive V., Sabio E., Bennett M.J., De Jong C.S., Biton A., McGann J.C., et al. Elife 2013, 2:e00822.
39. Poliseno L., Salmena L., Zhang J., Carver B., Haveman W.J., Pandolfi P.P. Nature 2010, 465:1033-1038.
40. Denzler R., Agarwal V., Stefano J., Bartel D.P., Stoffel M. Mol. Cell 2014, 54:766-776.
41. Nyayanit D., Gadgil C.J. RNA 2015.
42. Nam J.-W., Rissland O.S., Koppstein D., Abreu-Goodger C., Jan C.H., Agarwal V., et al. Mol. Cell 2014, 53:1031-1043.
43. Kim Y.-K., Heo I., Kim V.N. Cell 2010, 143:703-709.
44. Ha M., Kim V.N. Nat. Rev. Mol. Cell Biol. 2014, 15:509-524.