MicroRNAs coordinately regulate protein complexes

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Sass, Steffen ^a   Dietmann, Sabine ^a,b   Burk, Ulrike ^c   Brabletz, Simone ^c   Lutter, Dominik ^a   Kowarsch, Andreas ^a   Mayer, Klaus F ^a   Brabletz, Thomas ^c   Ruepp, Andreas ^a   Theis, Fabian ^a   Wang, Yu ^a,d  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF FREIBURG   (Germany)

^d TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

ALCOHOL DEHYDROGENASE; C TERMINAL BINDING PROTEIN; C-TERMINAL BINDING PROTEIN; DNA BINDING PROTEIN; MICRORNA; MULTIPROTEIN COMPLEX;

ARTICLE; EPITHELIAL MESENCHYMAL TRANSITION; GENE EXPRESSION REGULATION; GENETICS; HUMAN; IMMUNOBLOTTING; METABOLISM; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; TUMOR CELL LINE;

ALCOHOL OXIDOREDUCTASES; CELL LINE, TUMOR; DNA-BINDING PROTEINS; EPITHELIAL-MESENCHYMAL TRANSITION; GENE EXPRESSION REGULATION; HUMANS; IMMUNOBLOTTING; MICRORNAS; MULTIPROTEIN COMPLEXES; PROTEIN INTERACTION MAPS;

EID: 80052028123     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-136     Document Type: Article

References (48)

1. Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ. "miRBase: tools for microRNA genomics,". Nucleic Acids Research 2008, 36:D154-158. 10.1093/nar/gkn221, 2238936, 17991681.
2. Bonci D, Coppola V, Musumeci M, Addario A, Giuffrida R, Memeo L, D'Urso L, Pagliuca A, Biffoni M, Labbaye C, Bartucci M, Muto G, Peschle C, De Maria R. "The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities,". Nature Medicine 2008, 14:1271-1277. 10.1038/nm.1880, 18931683.
3. Mendell JT. "miRiad roles for the miR-17-92 cluster in development and disease,". Cell 2008, 133:217-222. 10.1016/j.cell.2008.04.001, 2732113, 18423194.
4. Nakada C, Matsuura K, Tsukamoto Y, Tanigawa M, Yoshimoto T, Narimatsu T, Nguyen LT, Hijiya N, Uchida T, Sato F, Mimata H, Seto M, Moriyama M. "Genome-wide microRNA expression profiling in renal cell carcinoma: significant down-regulation of miR-141 and miR-200c,". The Journal of Pathology 2008, 216:418-427. 10.1002/path.2437, 18925646.
5. Ambros V. "The evolution of our thinking about microRNAs,". Nature Medicine 2008, 14:1036-1040. 10.1038/nm1008-1036, 18841144.
6. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. "Widespread changes in protein synthesis induced by microRNAs,". Nature 2008, 455:58-63. 10.1038/nature07228, 18668040.
7. Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. "The impact of microRNAs on protein output,". Nature 2008, 455:64-71. 10.1038/nature07242, 2745094, 18668037.
8. Flynt AS, Lai EC. "Biological principles of microRNA-mediated regulation: shared themes amid diversity,". Nature Reviews Genetics 2008, 9:831-842. 2729318, 18852696.
9. Liang H, Li W-H. "MicroRNA regulation of human protein protein interaction network,". RNA (New York, NY) 2007, 13:1402-1408.
10. Hsu C-W, Juan H-F, Huang H-C. "Characterization of microRNA-regulated protein-protein interaction network,". Proteomics 2008, 8:1975-1979. 10.1002/pmic.200701004, 18491312.
11. Yuan X, Liu C, Yang P, He S, Liao Q, Kang S, Zhao Y. "Clustered microRNAs' coordination in regulating protein-protein interaction network,". BMC Systems Biology 2009, 3:65. 10.1186/1752-0509-3-65, 2714305, 19558649.
12. Tsang JS, Ebert MS, van Oudenaarden A. "Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures,". Mol Cell 2010, 38:140-153. 10.1016/j.molcel.2010.03.007, 3110938, 20385095.
13. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp A-C, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP,". Cell 2010, 141:129-141. 10.1016/j.cell.2010.03.009, 2861495, 20371350.
14. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. "Fast and effective prediction of microRNA/target duplexes,". RNA (New York, NY) 2004, 10:1507-1517.
15. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium,". Nature Genetics 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
16. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. "KEGG for representation and analysis of molecular networks involving diseases and drugs,". Nucleic Acids Res 2010, 38:D355-360. 10.1093/nar/gkp896, 2808910, 19880382.
17. Falcon S, Gentleman R. "Using GOstats to test gene lists for GO term association,". Bioinformatics 2007, 23:257-258. 10.1093/bioinformatics/btl567, 17098774.
18. Brabletz T, Jung A, Hlubek F, Löhberg C, Meiler J, Suchy U, Kirchner T. "Negative regulation of CD4 expression in T cells by the transcriptional repressor ZEB,". International Immunology 1999, 11:1701-1708. 10.1093/intimm/11.10.1701, 10508188.
19. Pfaffl MW. "A new mathematical model for relative quantification in real-time RT-PCR,". Nucleic Acids Researchi 2001, 29:e45.
20. Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW. "CORUM: the comprehensive resource of mammalian protein complexes,". Nucleic Acids Research 2008, 36:D646-650. 2238909, 17965090.
21. Cui Q, Yu Z, Purisima EO, Wang E. "Principles of microRNA regulation of a human cellular signaling network,". Molecular Systems Biology 2006, 2:46. 1681519, 16969338.
22. Friggi-Grelin F, Lavenant-Staccini L, Therond P. "Control of antagonistic components of the hedgehog signaling pathway by microRNAs in Drosophila,". Genetics 2008, 179:429-439. 10.1534/genetics.107.083733, 2390621, 18493062.
23. Silver SJ, Hagen JW, Okamura K, Perrimon N, Lai EC. "Functional screening identifies miR-315 as a potent activator of Wingless signaling,". Proceedings of the National Academy of Sciences of the United States of America 2007, 104:18151-18156. 10.1073/pnas.0706673104, 2084312, 17989227.
24. Martello G, Zacchigna L, Inui M, Montagner M, Adorno M, Mamidi A, Morsut L, Soligo S, Tran U, Dupont S, Cordenonsi M, Wessely O, Piccolo S. "MicroRNA control of Nodal signalling,". Nature 2007, 449:183-188. 10.1038/nature06100, 17728715.
25. Li X, Carthew RW. "A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye,". Cell 2005, 123:1267-1277. 10.1016/j.cell.2005.10.040, 16377567.
26. Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG. "Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate,". Nature Genetics 2007, 39:259-263. 10.1038/ng1953, 17220889.
27. Neumüller RA, Betschinger J, Fischer A, Bushati N, Poernbacher I, Mechtler K, Cohen SM, Knoblich JA. "Mei-P26 regulates microRNAs and cell growth in the Drosophila ovarian stem cell lineage,". Nature 2008, 454:241-245. 10.1038/nature07014, 2988194, 18528333.
28. Carleton M, Cleary MA, Linsley PS. "MicroRNAs and cell cycle regulation,". Cell Cycle (Georgetown, Tex) 2007, 6:2127-2132.
29. Volinia S, Calin GA, Liu C-G, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, Lanza G, Scarpa A, Vecchione A, Negrini M, Harris CC, Croce CM. "A microRNA expression signature of human solid tumors defines cancer gene targets,". Proceedings of the National Academy of Sciences of the United States of America 2006, 103:2257-2261. 10.1073/pnas.0510565103, 1413718, 16461460.
30. Mahajan MC, Narlikar GJ, Boyapaty G, Kingston RE, Weissman SM. "Heterogeneous nuclear ribonucleoprotein C1/C2, MeCP1, and SWI/SNF form a chromatin remodeling complex at the beta-globin locus control region,". Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15012-15017. 10.1073/pnas.0507596102, 1257739, 16217013.
31. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. "A mammalian microRNA expression atlas based on small RNA library sequencing,". Cell 2007, 129:1401-1414. 10.1016/j.cell.2007.04.040, 2681231, 17604727.
32. Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y, Goodall GJ. "The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1,". Nature Cell Biology 2008, 10:593-601. 10.1038/ncb1722, 18376396.
33. Park S-M, Gaur AB, Lengyel E, Peter ME. "The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2,". Genes & Development 2008, 22:894-907. 10.1101/gad.1640608, 21874596.
34. Korpal M, Lee ES, Hu G, Kang Y. "The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2,". The Journal of Biological Chemistry 2008, 283:14910-14914. 10.1074/jbc.C800074200, 18411277.
35. Burk U, Schubert J, Wellner U, Schmalhofer O, Vincan E, Spaderna S, Brabletz T. "A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells,". EMBO Reports 2008, 9:582-589. 10.1038/embor.2008.74, 2396950, 18483486.
36. Postigo AA, Dean DC. "ZEB represses transcription through interaction with the corepressor CtBP,". Proceedings of the National Academy of Sciences of the United States of America 1999, 96:6683-6688. 10.1073/pnas.96.12.6683, 21975, 10359772.
37. Shi Y, Sawada J, Sui G, Affar EB, Whetstine JR, Lan F, Ogawa H, Luke MP-S, Nakatani Y, Shi Y. "Coordinated histone modifications mediated by a CtBP co-repressor complex,". Nature 2003, 422:735-738. 10.1038/nature01550, 12700765.
38. Bienz M. "beta-Catenin: a pivot between cell adhesion and Wnt signalling,". Current Biology CB 2005, 15:R64-67. 10.1016/j.cub.2004.12.058, 15668160.
39. Filipowicz W, Bhattacharyya SN, Sonenberg N. "Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?,". Nature Reviews Genetics 2008, 9:102-114.
40. Bushati N, Cohen SM. "microRNA functions,". Annual Review of Cell and Developmental Biology 2007, 23:175-205. 10.1146/annurev.cellbio.23.090506.123406, 17506695.
41. Axtell MJ, Snyder JA, Bartel DP. "Common functions for diverse small RNAs of land plants,". The Plant Cell 2007, 19:1750-1769. 10.1105/tpc.107.051706, 1955733, 17601824.
42. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. "High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes,". PloS One 2007, 2:e219. 10.1371/journal.pone.0000219, 1790633, 17299599.
43. Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew R, Wu C-I. "Adaptive evolution of newly emerged micro-RNA genes in Drosophila,". Molecular Biology and Evolution 2008, 25:929-938. 10.1093/molbev/msn040, 18296702.
44. Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu C-I. "The birth and death of microRNA genes in Drosophila,". Nature Genetics 2008, 40:351-355. 10.1038/ng.73, 18278047.
45. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. "A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana,". Genes & Development 2006, 20:3407-3425. 10.1101/gad.1476406, 21874596.
46. Glazov EA, McWilliam S, Barris WC, Dalrymple BP. "Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals,". Molecular Biology and Evolution 2008, 25:939-948. 10.1093/molbev/msn045, 18281269.
47. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. "Clustering and conservation patterns of human microRNAs,". Nucleic Acids Research 2005, 33:2697-2706. 10.1093/nar/gki567, 1110742, 15891114.
48. Keene JD. "RNA regulons: coordination of post-transcriptional events,". Nature Reviews Genetics 2007, 8:533-543. 10.1038/nrg2111, 17572691.