MicroRNA buffering and altered variance of gene expression in response to Salmonella infection

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Bao, Hua ^a   Kommadath, Arun ^a   Plastow, Graham S ^a   Tuggle, Christopher K ^b   Guan, Le Luo ^a   Stothard, Paul ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; RNA BINDING PROTEIN;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NONHUMAN; SALMONELLOSIS; SWINE; ANIMAL; ANIMAL SALMONELLOSIS; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENETICS; METABOLISM; MICROBIOLOGY; PIG;

ANIMALS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; MICRORNAS; RNA, MESSENGER; RNA-BINDING PROTEINS; SALMONELLA INFECTIONS, ANIMAL; SUS SCROFA;

EID: 84899502410     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094352     Document Type: Article

References (43)

1. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9: 102-114.
2. Lai EC (2002) Micro RNAs are complementary to 39 UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30: 363-364.
3. Bao H, Kommadath A, Sun X, Meng Y, Arantes AS, et al. (2013) Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. BMC Genomics 14: 609.
4. Wu CI, Shen Y, Tang T (2009) Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res 19: 734-743.
5. Hornstein E, Shomron N (2006) Canalization of development by microRNAs. Nat Genet 38 Suppl: S20-24.
6. Bushati N, Cohen SM (2007) microRNA functions. Annu Rev Cell Dev Biol 23: 175-205.
7. Herranz H, Cohen SM (2010) MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems. Genes Dev 24: 1339-1344.
8. Xiao C, Calado DP, Galler G, Thai TH, Patterson HC, et al. (2007) MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell 131: 146-159. (Pubitemid 47498525)
9. Osella M, Bosia C, Cora D, Caselle M (2011) The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol 7: e1001101.
10. Mehta P, Goyal S, Wingreen NS (2008) A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol 4: 221.
11. Li X, Cassidy JJ, Reinke CA, Fischboeck S, Carthew RW (2009) A microRNA imparts robustness against environmental fluctuation during development. Cell 137: 273-282.
12. Karres JS, Hilgers V, Carrera I, Treisman J, Cohen SM (2007) The conserved microRNA miR-8 tunes atrophin levels to prevent neurodegeneration in Drosophila. Cell 131: 136-145. (Pubitemid 47498538)
13. Cui Q, Yu Z, Purisima EO, Wang E (2007) MicroRNA regulation and interspecific variation of gene expression. Trends Genet 23: 372-375. (Pubitemid 47088006)
14. Yang Z, Dong D, Zhang Z, Crabbe MJ, Wang L, et al. (2012) Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs. BMC Genomics 13 Suppl 7: S14.
15. Lu J, Clark AG (2012) Impact of microRNA regulation on variation in human gene expression. Genome Res 22: 1243-1254.
16. de Nadal E, Ammerer G, Posas F (2011) Controlling gene expression in response to stress. Nat Rev Genet 12: 833-845.
17. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
18. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31: 46-53.
19. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
20. Swain PS, Elowitz MB, Siggia ED (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 99: 12795-12800.
21. Komurov K, Ram PT (2010) Patterns of human gene expression variance show strong associations with signaling network hierarchy. BMC Syst Biol 4: 154.
22. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
23. Mar JC, Matigian NA, Mackay-Sim A, Mellick GD, Sue CM, et al. (2011) Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet 7: e1002207.
24. Kitano H (2004) Biological robustness. Nat Rev Genet 5: 826-837.
25. True JR, Haag ES (2001) Developmental system drift and flexibility in evolutionary trajectories. Evol Dev 3: 109-119. (Pubitemid 32406509)
26. Pelaez N, Carthew RW (2012) Biological robustness and the role of microRNAs: a network perspective. Curr Top Dev Biol 99: 237-255.
27. Cui Q, Yu Z, Purisima EO, Wang E (2006) Principles of microRNA regulation of a human cellular signaling network. Mol Syst Biol 2: 46.
28. Cui Q, Yu Z, Pan Y, Purisima EO, Wang E (2007) MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun 352: 733-738. (Pubitemid 44880316)
29. Mittal N, Roy N, Babu MM, Janga SC (2009) Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks. Proc Natl Acad Sci U S A 106: 20300-20305.
30. Lukong KE, Chang KW, Khandjian EW, Richard S (2008) RNA-binding proteins in human genetic disease. Trends Genet 24: 416-425.
31. Mittal N, Scherrer T, Gerber AP, Janga SC (2011) Interplay between posttranscriptional and posttranslational interactions of RNA-binding proteins. J Mol Biol 409: 466-479.
32. Ciafre SA, Galardi S (2013) microRNAs and RNA-binding proteins: a complex network of interactions and reciprocal regulations in cancer. RNA Biol 10: 935-942.
33. Yiakouvaki A, Dimitriou M, Karakasiliotis I, Eftychi C, Theocharis S, et al. (2012) Myeloid cell expression of the RNA-binding protein HuR protects mice from pathologic inflammation and colorectal carcinogenesis. J Clin Invest 122: 48-61.
34. Woloshen V, Huang S, Li X (2011) RNA-Binding Proteins in Plant Immunity. J Pathog 2011: 278697.
35. Yan L, Yang M, Guo H, Yang L, Wu J, et al. (2013) Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 20: 1131-1139.
36. Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, et al. (2014) From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing. Genome Res 24: 496-510.
37. Wu K, Miyada G, Martin J, Finkelstein D (2007) Globin reduction protocol: A method for processing whole blood RNA samples for improved array results. Affymetrix Technical Note. Available at: http://media.affymetrix.com:80/support/ technical/technotes/blood2-technote.pdf.
38. Friedlander MR, Mackowiak SD, Li N, Chen W, Rajewsky N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40: 37-52.
39. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
40. Zhang Y, Verbeek FJ (2010) Comparison and integration of target prediction algorithms for microRNA studies. J Integr Bioinform 7.
41. Li L, Liu F, Li W, Li Z, Pan J, et al. (2012) Differences in microRNAs and their expressions between foraging and dancing honey bees, Apis mellifera L. J Insect Physiol 58: 1438-1443.
42. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
43. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR (2011) RBPDB: a database of RNA-binding specificities. Nucleic Acids Res 39: D301-308.