Quantitative analysis of competition in posttranscriptional regulation reveals a novel signature in target expression variation

Biophysical Journal

Volumn 104, Issue 4, 2013, Pages 951-958

  Klironomos, Filippos D ^a   Berg, Johannes ^a,b  

^a UNIVERSITY OF COLOGNE   (Germany)

^b Systems Biology of Ageing Sybacol   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE PROTEIN; MICRORNA; SMALL INTERFERING RNA;

ARTICLE; BIOLOGICAL MODEL; METABOLISM; RNA INTERFERENCE;

ARGONAUTE PROTEINS; MICRORNAS; MODELS, GENETIC; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 84874151559     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.01.013     Document Type: Article

References (32)

1. V.N. Kim, J. Han, and M.C. Siomi Biogenesis of small RNAs in animals Nat. Rev. Mol. Cell Biol. 10 2009 126 139
2. M.W. Jones-Rhoades, D.P. Bartel, and B. Bartel MicroRNAS and their regulatory roles in plants Annu. Rev. Plant Biol. 57 2006 19 53
3. H. Guo, and N.T. Ingolia D.P. Bartel Mammalian microRNAs predominantly act to decrease target mRNA levels Nature 466 2010 835 840
4. G. Hutvágner, and P.D. Zamore A microRNA in a multiple-turnover RNAi enzyme complex Science 297 2002 2056 2060
5. B. Haley, and P.D. Zamore Kinetic analysis of the RNAi enzyme complex Nat. Struct. Mol. Biol. 11 2004 599 606
6. L. Wu, J. Fan, and J.G. Belasco MicroRNAs direct rapid deadenylation of mRNA Proc. Natl. Acad. Sci. USA 103 2006 4034 4039
7. A. Baccarini, and H. Chauhan B.D. Brown Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells Curr. Biol. 21 2011 369 376
8. E. Levine, and Z. Zhang T. Hwa Quantitative characteristics of gene regulation by small RNA PLoS Biol. 5 2007 e229
9. Y. Shimoni, and G. Friedlander H. Margalit Regulation of gene expression by small non-coding RNAs: a quantitative view Mol. Syst. Biol. 3 2007 138
10. Y. Hao, L. Xu, and H. Shi Theoretical analysis of catalytic-sRNA-mediated gene silencing J. Mol. Biol. 406 2011 195 204
11. A. Loinger, and Y. Shemla O. Biham Competition between small RNAs: a quantitative view Biophys. J. 102 2012 1712 1721
12. E. Koller, and S. Propp N.M. Dean Competition for RISC binding predicts in vitro potency of siRNA Nucleic Acids Res. 34 2006 4467 4476
13. D. Castanotto, and K. Sakurai J.J. Rossi Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC Nucleic Acids Res. 35 2007 5154 5164
14. A.A. Khan, and D. Betel D.S. Marks Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs Nat. Biotechnol. 27 2009 549 555
15. Z.S. Kai, and A.E. Pasquinelli MicroRNA assassins: factors that regulate the disappearance of miRNAs Nat. Struct. Mol. Biol. 17 2010 5 10
16. M.S. Ebert, and P.A. Sharp Emerging roles for natural microRNA sponges Curr. Biol. 20 2010 R858 R861
17. R. Hussein, and H.N. Lim Disruption of small RNA signaling caused by competition for Hfq Proc. Natl. Acad. Sci. USA 108 2011 1110 1115
18. A. Arvey, and E. Larsson D.S. Marks Target mRNA abundance dilutes microRNA and siRNA activity Mol. Syst. Biol. 6 2010 363
19. A.E. Pasquinelli MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship Nat. Rev. Genet. 13 2012 271 282
20. S. Mukherji, and M.S. Ebert A. van Oudenaarden MicroRNAs can generate thresholds in target gene expression Nat. Genet. 43 2011 854 859
21. M. Thattai, and A. van Oudenaarden Intrinsic noise in gene regulatory networks Proc. Natl. Acad. Sci. USA 98 2001 8614 8619
22. J. Paulsson Models of stochastic gene expression Phys. Life Rev. 2 2005 157 175
23. D. Gillespie Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 1977 2340 2361
24. N.G. van Kampen Stochastic Processes in Physics and Chemistry 2007 North Holland Amsterdam
25. G. Cuccato, and A. Polynikis D. di Bernardo Modeling RNA interference in mammalian cells BMC Syst. Biol. 5 2011 19
26. L.P. Lim, and N.C. Lau J.M. Johnson Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs Nature 433 2005 769 773
27. D. Baek, and J. Villén D.P. Bartel The impact of microRNAs on protein output Nature 455 2008 64 71
28. M. Selbach, and B. Schwanhäusser N. Rajewsky Widespread changes in protein synthesis induced by microRNAs Nature 455 2008 58 63
29. D. Wang, and Z. Zhang R. Yi Quantitative functions of Argonaute proteins in mammalian development Genes Dev. 26 2012 693 704
30. A. Esquela-Kerscher, and F.J. Slack Oncomirs - microRNAs with a role in cancer Nat. Rev. Cancer 6 2006 259 269
31. J. van der Oost, and S.J. Brouns RNAi: prokaryotes get in on the act Cell 139 2009 863 865
32. M. Overgaard, and J. Johansen P. Valentin-Hansen Switching off small RNA regulation with trap-mRNA Mol. Microbiol. 73 2009 790 800