Transcriptional override: A regulatory network model of indirect responses to modulations in microRNA expression

BMC Systems Biology

Volumn 8, Issue 1, 2014, Pages

  Hill, Christopher G ^a   Matyunina, Lilya V ^a   Walker, DeEtte ^a   Benigno, Benedict B ^b   McDonald, John F ^a,b  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b Ovarian Cancer Institute   (United States)

Author keywords

Cancer systems biology; Feed forward loops; Gene regulation; miRNAs; Ovarian cancer

Indexed keywords

MICRORNA; TRANSCRIPTOME;

ARTICLE; BIOLOGICAL MODEL; FEEDBACK SYSTEM; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETICS; SYSTEMS BIOLOGY;

FEEDBACK, PHYSIOLOGICAL; GENE REGULATORY NETWORKS; MICRORNAS; MODELS, GENETIC; SYSTEMS BIOLOGY; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84899133739     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-36     Document Type: Article

References (35)

1. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233. 10.1016/j.cell.2009.01.002, 3794896, 19167326.
2. Matkovich SJ, Hu Y, Dorn GW. Regulation of cardiac MicroRNAs by cardiac MicroRNAs. Circ Res 2013, 113:62-71. 10.1161/CIRCRESAHA.113.300975, 23625950.
3. Shahab SW, Matyunina LV, Mezencev R, Walker LD, Bowen NJ, Benigno BB, McDonald JF. Evidence for the complexity of MicroRNA-mediated regulation in ovarian cancer: a systems approach. PLoS One 2011, 6:e22508. 10.1371/journal.pone.0022508, 3141058, 21811625.
4. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433:769-773. 10.1038/nature03315, 15685193.
5. Witkos TM, Koscianska E, Krzyzosiak WJ. Practical aspects of microRNA target prediction. Curr Mol Med 2011, 11:93-109. 10.2174/156652411794859250, 3182075, 21342132.
6. Tsang J, Zhu J, van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops Are recurrent network motifs in mammals. Mol Cell 2007, 26:753-767. 10.1016/j.molcel.2007.05.018, 2072999, 17560377.
7. 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 2010, 11:R90. 10.1186/gb-2010-11-8-r90, 2945792, 20799968.
8. Friedman RC, Farh KKH, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19:92-105. 2612969, 18955434.
9. Liu H, Yue D, Chen Y, Gao SJ, Huang Y. Improving performance of mammalian microRNA target prediction. BMC Bioinforma 2010, 11:476.
10. Jia D, Hasso SM, Chan J, Filingeri D, D'Amore PA, Rice L, Pampo C, Siemann DW, Zurakowski D, Rodig SJ, Moses MA. Transcriptional repression of VEGF by ZNF24: mechanistic studies and vascular consequences in vivo. Blood 2013, 121:707-715. 10.1182/blood-2012-05-433045, 3557646, 23212515.
11. Bonavida B, Baritaki S. The novel role of Yin Yang 1 in the regulation of epithelial to mesenchymal transition in cancer via the dysregulated NF-kappaB/Snail/YY1/RKIP/PTEN Circuitry. Crit Rev Oncog 2011, 16:211-226. 10.1615/CritRevOncog.v16.i3-4.50, 22248055.
12. Ariyoshi M, Schwabe JW. A conserved structural motif reveals the essential transcriptional repression function of Spen proteins and their role in developmental signaling. Genes Dev 2003, 17:1909-1920. 10.1101/gad.266203, 196244, 12897056.
13. Kitamuro T, Takahashi K, Ogawa K, Udono-Fujimori R, Takeda K, Furuyama K, Nakayama M, Sun J, Fujita H, Hida W, Hattori T, Shirato K, Igarashi K, Shibahara S. Bach1 functions as a hypoxia-inducible repressor for the heme oxygenase-1 gene in human cells. J Biol Chem 2003, 278:9125-9133. 10.1074/jbc.M209939200, 12511571.
14. 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. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
15. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34:D108-D110. 10.1093/nar/gkj143, 1347505, 16381825.
16. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. Human MicroRNA targets. PLoS Biol 2004, 2:e363. 10.1371/journal.pbio.0020363, 521178, 15502875.
17. Remenyi A, Scholer HR, Wilmanns M. Combinatorial control of gene expression. Nat Struct Mol Biol 2004, 11:812-815. 10.1038/nsmb820, 15332082.
18. Mansson R, Tsapogas P, Akerlund M, Lagergren A, Gisler R, Sigvardsson M. Pearson correlation analysis of microarray data allows for the identification of genetic targets for early B-cell factor. J Biol Chem 2004, 279:17905-17913. 10.1074/jbc.M400589200, 14960572.
19. Allocco DJ, Kohane IS, Butte AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinforma 2004, 5:18.
20. Di Leva G, Croce CM. miRNA profiling of cancer. Curr Opin Genet Dev 2013, 23:3-11. 10.1016/j.gde.2013.01.004, 3632255, 23465882.
21. Tijsen AJ, Pinto YM, Creemers EE. Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases. Am J Physiol Heart Circ Physiol 2012, 303:H1085-H1095. 10.1152/ajpheart.00191.2012, 22942181.
22. Shahab SW, Matyunina LV, Hill CG, Wang L, Mezencev R, Walker LD, McDonald JF. The effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated. BMC Med Genomics 2012, 5:33. 10.1186/1755-8794-5-33, 3481362, 22853714.
23. Gurtan AM, Sharp PA. The role of miRNAs in regulating gene expression networks. J Mol Biol 2013, 425:3582-3600. 10.1016/j.jmb.2013.03.007, 23500488.
24. Ritchie W, Rasko JE, Flamant S. MicroRNA target prediction and validation. Adv Exp Med Biol 2013, 774:39-53. 10.1007/978-94-007-5590-1_3, 23377967.
25. Vera J, Lai X, Schmitz U, Wolkenhauer O. MicroRNA-regulated networks: the perfect storm for classical molecular biology, the ideal scenario for systems biology. Adv Exp Med Biol 2013, 774:55-76. 10.1007/978-94-007-5590-1_4, 23377968.
26. Li Y, Goldenberg A, Wong KC, Zhang Z. A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics 2014, 30:621-628. 10.1093/bioinformatics/btt599, 24135265.
27. Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity. Mol Syst Biol 2010, 2010(6):1-7.
28. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 2009, 27:549-555. 2782465, 19465925.
29. Larsson E, Sander C, Marks D. mRNA turnover rate limits siRNA and microRNA efficacy. Mol Syst Biol 2010, 6:433-441. 3010119, 21081925.
30. Vidal M, Cusick ME, Barabasi AL. Interactome networks and human disease. Cell 2011, 144:986-998. 10.1016/j.cell.2011.02.016, 3102045, 21414488.
31. Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J. Cancer: a systems biology disease. Biosystems 2006, 83:81-90. 10.1016/j.biosystems.2005.05.014, 16426740.
32. Bowen NJ, Walker LD, Matyunina LV, Logani S, Totten KA, Benigno BB, McDonald JF. Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells. BMC Med Genomics 2009, 2:71-84. 10.1186/1755-8794-2-71, 2806370, 20040092.
33. Eijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Muller M, Evelo CT. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. Nucleic Acids Res 2013, 41:W71-W76. 10.1093/nar/gkt293, 3692049, 23620278.
34. Affymetrix Affymetrix® expression console™ software. http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=131414#1_1., Affymetrix.
35. Wolfram Research I Mathematica. Book Mathematica 2010, City: Wolfram Research, Inc, vol. Version 80, 80, Wolfram Research I.