Interactions between distant ceRNAs in regulatory networks

Biophysical Journal

Volumn 106, Issue 10, 2014, Pages 2254-2266

  Nitzan, Mor ^a,b   Steiman Shimony, Avital ^b   Altuvia, Yael ^b   Biham, Ofer ^a   Margalit, Hanah ^b  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; RNA;

BIOLOGICAL MODEL; GENE REGULATORY NETWORK; GENETICS; HEK293 CELL LINE; HUMAN;

GENE REGULATORY NETWORKS; HEK293 CELLS; HUMANS; MICRORNAS; MODELS, GENETIC; RNA; RNA, MESSENGER;

EID: 84901273489     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.03.040     Document Type: Article

References (50)

1. D.P. Bartel MicroRNAs: target recognition and regulatory functions Cell 136 2009 215 233
2. J.M. Franco-Zorrilla, and A. Valli J. Paz-Ares Target mimicry provides a new mechanism for regulation of microRNA activity Nat. Genet. 39 2007 1033 1037
3. M.S. Ebert, J.R. Neilson, and P.A. Sharp MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells Nat. Methods 4 2007 721 726
4. L. Poliseno, and L. Salmena P.P. Pandolfi A coding-independent function of gene and pseudogene mRNAs regulates tumour biology Nature 465 2010 1033 1038
5. S. Memczak, and M. Jens N. Rajewsky Circular RNAs are a large class of animal RNAs with regulatory potency Nature 495 2013 333 338
6. Y. Wang, and Z. Xu H. Liu Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal Dev. Cell 25 2013 69 80
7. T.B. Hansen, and T.I. Jensen J. Kjems Natural RNA circles function as efficient microRNA sponges Nature 495 2013 384 388
8. M. Cesana, and D. Cacchiarelli I. Bozzoni A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA Cell 147 2011 358 369
9. D. Cazalla, T. Yario, and J.A. Steitz Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA Science 328 2010 1563 1566
10. Y. Tay, and L. Kats P.P. Pandolfi Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs Cell 147 2011 344 357
11. U. Ala, and F.A. Karreth P.P. Pandolfi Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments Proc. Natl. Acad. Sci. USA 110 2013 7154 7159
12. S. Ling, and Y. Birnbaum Y. Ye MicroRNA-dependent cross-talk between VEGF and HIF1α in the diabetic retina Cell. Signal. 25 2013 2840 2847
13. Y. Tay, J. Rinn, and P.P. Pandolfi The multilayered complexity of ceRNA crosstalk and competition Nature 505 2014 344 352
14. L. Salmena, and L. Poliseno P.P. Pandolfi A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146 2011 353 358
15. P. Sumazin, and X. Yang A. Califano An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma Cell 147 2011 370 381
16. M. Figliuzzi, E. Marinari, and A. De Martino MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory Biophys. J. 104 2013 1203 1213
17. C. Bosia, A. Pagnani, and R. Zecchina Modelling competing endogenous RNA networks PLoS ONE 8 2013 e66609
18. L. Poliseno, and A. Haimovic I. Osman Deletion of PTENP1 pseudogene in human melanoma J. Invest. Dermatol. 131 2011 2497 2500
19. F.A. Karreth, and Y. Tay P.P. Pandolfi In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma Cell 147 2011 382 395
20. A.L. Barabási, and Z.N. Oltvai Network biology: understanding the cell's functional organization Nat. Rev. Genet. 5 2004 101 113
21. R. Milo, and S. Shen-Orr U. Alon Network motifs: simple building blocks of complex networks Science 298 2002 824 827
22. S.S. Shen-Orr, and R. Milo U. Alon Network motifs in the transcriptional regulation network of Escherichia coli Nat. Genet. 31 2002 64 68
23. E. Yeger-Lotem, and S. Sattath H. Margalit Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction Proc. Natl. Acad. Sci. USA 101 2004 5934 5939
24. R. Albert Scale-free networks in cell biology J. Cell Sci. 118 2005 4947 4957
25. A. Helwak, and G. Kudla D. Tollervey Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding Cell 153 2013 654 665
26. E. Yeger-Lotem, and H. Margalit Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation Nucleic Acids Res. 31 2003 6053 6061
27. N.M. Luscombe, and M.M. Babu M. Gerstein Genomic analysis of regulatory network dynamics reveals large topological changes Nature 431 2004 308 312
28. P. Shannon, and A. Markiel T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504
29. Y. Assenov, and F. Ramírez M. Albrecht Computing topological parameters of biological networks Bioinformatics 24 2008 282 284
30. A. Hagberg, D.A. Schult, and P.J. Swart Exploring network structure, dynamics, and function using NetworkX Proc. 7th Python Sci. Conf. Pasadena, CA 2008 11 15
31. Q.K. Telesford, K.E. Joyce, S. Hayasaka, J.H. Burdette, and P.J. Laurienti The ubiquity of small-world networks Brain Connect. 1 2011 367 375
32. M. Uhlen, and P. Oksvold F. Ponten Towards a knowledge-based Human Protein Atlas Nat. Biotechnol. 28 2010 1248 1250
33. B. Barzel, and O. Biham Quantifying the connectivity of a network: the network correlation function method Phys. Rev. E 80 2009 046104
34. A. Loinger, and Y. Shemla O. Biham Competition between small RNAs: a quantitative view Biophys. J. 102 2012 1712 1721
35. 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
36. A. Arvey, and E. Larsson D.S. Marks Target mRNA abundance dilutes microRNA and siRNA activity Mol. Syst. Biol. 6 2010 363
37. S. Mukherji, and M.S. Ebert A. van Oudenaarden MicroRNAs can generate thresholds in target gene expression Nat. Genet. 43 2011 854 859
38. 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
39. A. Alimonti, and A. Carracedo P.P. Pandolfi Subtle variations in Pten dose determine cancer susceptibility Nat. Genet. 42 2010 454 458
40. M.S. Ebert, and P.A. Sharp Roles for microRNAs in conferring robustness to biological processes Cell 149 2012 515 524
41. A.S. Flynt, and E.C. Lai Biological principles of microRNA-mediated regulation: shared themes amid diversity Nat. Rev. Genet. 9 2008 831 842
42. H. Seitz Redefining microRNA targets Curr. Biol. 19 2009 870 873
43. D. Jost, A. Nowojewski, and E. Levine Regulating the many to benefit the few: role of weak small RNA targets Biophys. J. 104 2013 1773 1782
44. E. Levine, and Z. Zhang T. Hwa Quantitative characteristics of gene regulation by small RNA PLoS Biol. 5 2007 e229
45. E. Levine, and T. Hwa Small RNAs establish gene expression thresholds Curr. Opin. Microbiol. 11 2008 574 579
46. J. Elf, and J. Paulsson M. Ehrenberg Near-critical phenomena in intracellular metabolite pools Biophys. J. 84 2003 154 170
47. N.E. Buchler, and M. Louis Molecular titration and ultrasensitivity in regulatory networks J. Mol. Biol. 384 2008 1106 1119
48. 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
49. N. Figueroa-Bossi, and M. Valentini L. Bossi Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target Genes Dev. 23 2009 2004 2015
50. M. Overgaard, and J. Johansen P. Valentin-Hansen Switching off small RNA regulation with trap-mRNA Mol. Microbiol. 73 2009 790 800