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생화학분자생물학회 (Korean Society for Biochemistry and Molecular Biology)
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Small RNA biology is systems biology

  • Jost, Daniel (Department of Physics, FAS Center for Systems Biology, Harvard University) ;
  • Nowojewski, Andrzej (Department of Physics, FAS Center for Systems Biology, Harvard University) ;
  • Levine, Erel (Department of Physics, FAS Center for Systems Biology, Harvard University)
  • 투고 : 2011.01.12
  • 발행 : 2011.01.31
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초록

During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.

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참고문헌

  1. Jacob, F. and Monod, J. (1961) Genetic regulatory mechanismsin the synthesis of proteins. J. Mol. Biol. 3,318-356. https://doi.org/10.1016/S0022-2836(61)80072-7
  2. Lee, R. (1993) The C. elegans heterochronic gene lin-4encodes small RNAs with antisense complementarity tolin-14. Cell 175, 843-854.
  3. Wightman, B., Ha, I. and Ruvkun, G. (1993) Posttranscriptionalregulation of the heterochronic gene lin-14 bylin-4 mediates temporal pattern formation in C. elegans.Cell 75, 855-862. https://doi.org/10.1016/0092-8674(93)90530-4
  4. Argaman, L., Hershberg, R., Vogel, J., Bejerano, G.,Wagner, E. H., Margalit, H. and Altuvia, S. (2001) Novelsmall RNA-encoding genes in the intergenic regions ofEscherichia coli. Current Biology. 11, 941-950. https://doi.org/10.1016/S0960-9822(01)00270-6
  5. Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G.and Gottesman, S. (2001) Identification of novel smallRNAs using comparative genomics and microarrays.Genes & Development 15, 1637-1651. https://doi.org/10.1101/gad.901001
  6. Rivas, E., Klein, R. J., Jones, T. A. and Eddy, S. R. (2001)Computational identification of noncoding RNAs in E.coli by comparative genomics. Current Biology 11,1369-1373. https://doi.org/10.1016/S0960-9822(01)00401-8
  7. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A.,Driver, S. E. and Mello, C. C. (1998) Potent and specificgenetic interference by double-stranded RNA in Caenorhabditiselegans. Nature 391, 806-811. https://doi.org/10.1038/35888
  8. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E.,Bettinger, J. C., Rougvie, A. E., Horvitz, H. R. andRuvkun, G. (2000) The 21-nucleotide let-7 RNA regulatesdevelopmental timing in Caenorhabditis elegans.Nature 403, 901-906. https://doi.org/10.1038/35002607
  9. Pasquinelli, A. E., Reinhart, B. J., Slack, F., Martindale,M. Q., Kuroda, M. I., Maller, B., Hayward, D. C., Ball, E.E., Degnan, B., Müller, P., Spring, J., Srinivasan, A.,Fishman, M., Finnerty, J., Corbo, J., Levine, M., Leahy,P., Davidson, E. and Ruvkun, G. (2000) Conservation ofthe sequence and temporal expression of let-7 heterochronicregulatory RNA. Nature 408, 86-89. https://doi.org/10.1038/35040556
  10. Ghildiyal, M. and Zamore, P. D. (2009) Small silencingRNAs: an expanding universe. Nat. Rev. Genet. 10, 94-108. https://doi.org/10.1038/nrg2504
  11. Bartel, D. P. (2009) MicroRNAs: target recognition andregulatory functions. Cell 136, 215-233. https://doi.org/10.1016/j.cell.2009.01.002
  12. Alvarez-Garcia, I. and Miska, E. A. (2005) MicroRNAfunctions in animal development and human disease.Development 132, 4653-4662. https://doi.org/10.1242/dev.02073
  13. Hagen, J. W. and Lai, E. C. (2008) microRNA control ofcell-cell signaling during development and disease. CellCycle 7, 2327-2332. https://doi.org/10.4161/cc.6447
  14. Ivey, K. N., Muth, A., Arnold, J., King, F. W., Yeh, R.,Fish, J. E., Hsiao, E. C., Schwartz, R. J., Conklin, B. R.,Bernstein, H. S. and Srivastava, D. (2008) MicroRNA regulationof cell lineages in mouse and human embryonicstem cells. Cell Stem Cell 2, 219-229. https://doi.org/10.1016/j.stem.2008.01.016
  15. Khurana, J. S. and Theurkauf, W. E. (2008) piRNA functionin germline development (July 30, 2008), StemBook,ed. The Stem Cell Research Community, StemBook, doi/10.3824/stembook.1.12.1, http://www.stembook.org.
  16. Reynolds, S. and Ruohola-Baker, H. (2008) microRNA’srole in germline differentiation (September 15, 2008), StemBook, ed. The Stem Cell Research Community, StemBook,doi/ 10.3824/stembook.1.17.1, http://www.stembook.org.
  17. Croce, C. M. (2009) Causes and consequences ofmicroRNA dysregulation in cancer. Nat. Rev. Genet 10,704-714. https://doi.org/10.1038/nrg2634
  18. Leung, A. K. L. and Sharp, P. A. (2010) MicroRNA functionsin stress responses. Mol. Cell 40, 205-215. https://doi.org/10.1016/j.molcel.2010.09.027
  19. Aravin, A. A., Hannon, G. J. and Brennecke, J. (2007)The Piwi-piRNA pathway provides an adaptive defensein the transposon arms race. Science 318, 761-764. https://doi.org/10.1126/science.1146484
  20. Lee, Y., Jeon, K., Lee, J., Kim, S. and Kim, V. N. (2002)MicroRNA maturation: stepwise processing and subcellularlocalization. EMBO J. 21, 4663-4670. https://doi.org/10.1093/emboj/cdf476
  21. Lee, Y., Kim, M., Han, J., Yeom, K., Lee, S., Baek, S. H.and Kim, V. N. (2004) MicroRNA genes are transcribedby RNA polymerase II. EMBO J. 23, 4051-4060. https://doi.org/10.1038/sj.emboj.7600385
  22. Czech, B., Malone, C. D., Zhou, R., Stark, A., Schlingeheyde,C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel,J. A., Sachidanandam, R., Hannon, G. J. and Brennecke,J. (2008) An endogenous small interfering RNApathway in Drosophila. Nature 453, 798-802. https://doi.org/10.1038/nature07007
  23. Okamura, K., Chung, W., Ruby, J. G., Guo, H., Bartel,D. P. and Lai, E. C. (2008) The Drosophila hairpin RNApathway generates endogenous short interfering RNAs.Nature 453, 803-806. https://doi.org/10.1038/nature07015
  24. Kawamura, Y., Saito, K., Kin, T., Ono, Y., Asai, K.,Sunohara, T., Okada, T. N., Siomi, M. C. and Siomi, H.(2008) Drosophila endogenous small RNAs bind toArgonaute(thinsp)2 in somatic cells. Nature 453, 793-797. https://doi.org/10.1038/nature06938
  25. Okamura, K., Balla, S., Martin, R., Liu, N. and Lai, E. C.(2008) Two distinct mechanisms generate endogenoussiRNAs from bidirectional transcription in Drosophilamelanogaster. Nat. Struct. Mol. Biol. 15, 581-590. https://doi.org/10.1038/nsmb.1438
  26. Tam, O. H., Aravin, A. A., Stein, P., Girard, A., Murchison,E. P., Cheloufi, S., Hodges, E., Anger, M., Sachidanandam,R., Schultz, R. M. and Hannon, G. J. (2008) Pseudogene-derived small interfering RNAs regulate gene expressionin mouse oocytes. Nature 453, 534-538. https://doi.org/10.1038/nature06904
  27. Watanabe, T., Totoki, Y., Toyoda, A., Kaneda, M., Kuramochi-Miyagawa, S., Obata, Y., Chiba, H., Kohara, Y.,Kono, T., Nakano, T., Surani, M. A., Sakaki, Y. andSasaki, H. (2008) Endogenous siRNAs from naturallyformed dsRNAs regulate transcripts in mouse oocytes.Nature 453, 539-543. https://doi.org/10.1038/nature06908
  28. Ketting, R. F., Haverkamp, T. H. A., van Luenen, H. G.A. M. and Plasterk, R. H. A. (1999) mut-7 of C. elegans,Required for Transposon Silencing and RNA Interference,Is a Homolog of Werner Syndrome Helicase andRNaseD. Cell 99, 133-141. https://doi.org/10.1016/S0092-8674(00)81645-1
  29. Tabara, H., Sarkissian, M., Kelly, W. G., Fleenor, J.,Grishok, A., Timmons, L., Fire, A. and Mello, C. C. (1999)The rde-1 Gene, RNA Interference, and TransposonSilencing in C. elegans. Cell 99, 123-132. https://doi.org/10.1016/S0092-8674(00)81644-X
  30. Chung, W., Okamura, K., Martin, R. and Lai, E. C.(2008) Endogenous RNA Interference Provides a SomaticDefense against Drosophila Transposons. Current Biology18, 795-802. https://doi.org/10.1016/j.cub.2008.05.006
  31. Ghildiyal, M., Seitz, H., Horwich, M. D., Li, C., Du, T.,Lee, S., Xu, J., Kittler, E. L. W., Zapp, M. L., Weng, Z.and Zamore, P. D. (2008) Endogenous siRNAs derivedfrom transposons and mRNAs in Drosophila somaticcells. Science 320, 1077-1081. https://doi.org/10.1126/science.1157396
  32. Hammond, S. M., Bernstein, E., Beach, D. and Hannon,G. J. (2000) An RNA-directed nuclease mediates posttranscriptionalgene silencing in Drosophila cells. Nature404, 293-296. https://doi.org/10.1038/35005107
  33. Zamore, P. D., Tuschl, T., Sharp, P. A. and Bartel, D. P.(2000) RNAi: Double-Stranded RNA Directs the ATPDependentCleavage of mRNA at 21 to 23 NucleotideIntervals. Cell 101, 25-33. https://doi.org/10.1016/S0092-8674(00)80620-0
  34. Pak, J. and Fire, A. (2007) Distinct populations of primaryand secondary effectors during RNAi in C. elegans.Science 315, 241-244. https://doi.org/10.1126/science.1132839
  35. Sijen, T., Steiner, F. A., Thijssen, K. L. and Plasterk, R. H.A. (2007) Secondary siRNAs result from unprimed RNAsynthesis and form a distinct class. Science 2007, 315,244-247. https://doi.org/10.1126/science.1136699
  36. Sijen, T., Fleenor, J., Simmer, F., Thijssen, K. L., Parrish,S., Timmons, L., Plasterk, R. H. and Fire, A. (2001) Onthe Role of RNA Amplification in dsRNA-Triggered GeneSilencing. Cell 107, 465-476. https://doi.org/10.1016/S0092-8674(01)00576-1
  37. Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis,M., Sachidanandam, R. and Hannon, G. J. (2007) DiscreteSmall RNA-Generating Loci as Master Regulators ofTransposon Activity in Drosophila. Cell 128, 1089-1103. https://doi.org/10.1016/j.cell.2007.01.043
  38. Hunter, C. P., Winston, W. M., Molodowitch, C.,Feinberg, E. H., Shih, J., Sutherlin, M., Wright, A. J. andFitzgerald, M. C. (2006) Systemic RNAi in Caenorhabditiselegans. Cold Spring Harb. Symp. Quant. Biol. 71, 95-100. https://doi.org/10.1101/sqb.2006.71.060
  39. Gottesman, S. (2005) Micros for microbes: non-codingregulatory RNAs in bacteria. Trends in Genetics 21,399-404. https://doi.org/10.1016/j.tig.2005.05.008
  40. Aiba, H. (2007) Mechanism of RNA silencing byHfq-binding small RNAs. Current Opinion in Microbiology10, 134-139. https://doi.org/10.1016/j.mib.2007.03.010
  41. Gottesman, S., McCullen, C. A., Guillier, M., Vanderpool,C. K., Majdalani, N., Benhammou, J., Thompson,K. M., FitzGerald, P. C., Sowa, N. A. and FitzGerald, D.J. (2006) Small RNA regulators and the bacterial responseto stress. Cold Spring Harb. Symp. Quant. Biol.71, 1-11. https://doi.org/10.1101/sqb.2006.71.016
  42. Geissmann, T., Possedko, M., Huntzinger, E., Fechter,P., Ehresmann, C. and Romby, P. (2006) Regulatory RNAsas mediators of virulence gene expression in bacteria.Handb Exp. Pharmacol. 173, 9-43. https://doi.org/10.1007/3-540-27262-3_2
  43. Murphy, E. R. and Payne, S. M. (2007) RyhB, an iron-responsivesmall RNA molecule, regulates Shigella dysenteriaevirulence. Infect. Immun. 75, 3470-3477. https://doi.org/10.1128/IAI.00112-07
  44. Padalon-Brauch, G., Hershberg, R., Elgrably-Weiss, M.,Baruch, K., Rosenshine, I., Margalit, H. and Altuvia, S.(2008) Small RNAs encoded within genetic islands ofSalmonella typhimurium show host-induced expressionand role in virulence. Nucleic. Acids. Res. 36, 1913-1927. https://doi.org/10.1093/nar/gkn050
  45. Schiano, C. A., Bellows, L. E. and Lathem, W. W. (2010)The small RNA chaperone Hfq is required for the virulenceof Yersinia pseudotuberculosis. Infect. Immun. 78,2034-2044. https://doi.org/10.1128/IAI.01046-09
  46. Chabelskaya, S., Gaillot, O. and Felden, B. (2010) AStaphylococcus aureus small RNA is required for bacterialvirulence and regulates the expression of an immune-evasion molecule. PLoS Pathog. 6, e1000927. https://doi.org/10.1371/journal.ppat.1000927
  47. Podkaminski, D. and Vogel, J. (2010) Small RNAs promotemRNA stability to activate the synthesis of virulencefactors. Mol. Microbiol. 78, 1327-1331. https://doi.org/10.1111/j.1365-2958.2010.07428.x
  48. Hammond, S. M., Bernstein, E., Beach, D. and Hannon,G. J. (2000) An RNA-directed nuclease mediates post-transcriptionalgene silencing in Drosophila cells. Nature404, 293-296. https://doi.org/10.1038/35005107
  49. Hutvagner, G. and Zamore, P. D. (2002) A microRNA ina multiple-turnover RNAi enzyme complex. Science 297,2056-2060. https://doi.org/10.1126/science.1073827
  50. Liu, J., Carmell, M. A., Rivas, F. V., Marsden, C. G,Thomson, J. M., Song, J., Hammond, S. M., Joshua-Tor,L. and Hannon, G. J. (2004) Argonaute2 is the catalyticengine of mammalian RNAi. Science 305, 1437-1441. https://doi.org/10.1126/science.1102513
  51. Haley, B. and Zamore, P. D. (2004) Kinetic analysis ofthe RNAi enzyme complex. Nat. Struct. Mol. Biol. 11,599-606. https://doi.org/10.1038/nsmb780
  52. Arvey, A., Larsson, E., Sander, C., Leslie, C. S. andMarks, D. S. (2010) Target mRNA abundance dilutesmicroRNA and siRNA activity. Mol. Syst. Biol. 6, 363.
  53. Masse, E., Escorcia, F. E. and Gottesman, S. (2003)Coupled degradation of a small regulatory RNA and itsmRNA targets in Escherichia coli. Genes Dev. 17, 2374-2383. https://doi.org/10.1101/gad.1127103
  54. Figueroa-Bossi, N., Valentini, M., Malleret, L. and Bossi,L. (2009) Caught at its own game: regulatory small RNAinactivated by an inducible transcript mimicking itstarget. Genes & Development 23, 2004 -2015. https://doi.org/10.1101/gad.541609
  55. Levine, E., Zhang, Z., Kuhlman, T. and Hwa, T. (2007)Quantitative characteristics of gene regulation by smallRNA. PLoS Biol. 5, e229. https://doi.org/10.1371/journal.pbio.0050229
  56. Mitarai, N., Andersson, A. M., Krishna, S., Semsey, S.and Sneppen, K. (2007) Efficient degradation and expressionprioritization with small RNAs. Phys. Biol. 4,164-171. https://doi.org/10.1088/1478-3975/4/3/003
  57. Shimoni, Y., Friedlander, G., Hetzroni, G., Niv, G.,Altuvia, S., Biham, O. and Margalit, H. (2007) Regulationof gene expression by small non-coding RNAs: a quantitativeview. Mol. Syst. Biol. 3, 138.
  58. Mehta, P., Goyal, S. and Wingreen, N. S. (2008) A quantitativecomparison of sRNA-based and protein-basedgene regulation. Mol. Syst. Biol. 4, 221.
  59. Levine, E., Huang, M., Huang, Y., Kuhlman, T., Zhang,Z. and Hwa, T. On noise and silence in gene regulationby small RNA. In submission.
  60. Lease, R. A. and Belfort, M. (2000) A trans-acting RNA asa control switch in Escherichia coli: DsrA modulatesfunction by forming alternative structures. Proc. Natl.Acad. Sci. U.S.A. 97, 9919-9924. https://doi.org/10.1073/pnas.170281497
  61. Fang, F. C. and Rimsky, S. (2008) New insights into transcriptionalregulation by H-NS. Current Opinion inMicrobiology. 11, 113-120. https://doi.org/10.1016/j.mib.2008.02.011
  62. Amit, R., Oppenheim, A. B. and Stavans, J. (2003)Increased Bending Rigidity of Single DNA Molecules byH-NS, a Temperature and Osmolarity Sensor. BiophysicalJournal 84, 2467-2473. https://doi.org/10.1016/S0006-3495(03)75051-6
  63. Dorman, C. J. (2007) H-NS, the genome sentinel. Nat.Rev. Micro. 5, 157-161. https://doi.org/10.1038/nrmicro1598
  64. Majdalani, N., Cunning, C., Sledjeski, D., Elliott, T. andGottesman, S. (1998) DsrA RNA regulates translation ofRpoS message by an anti-antisense mechanism, independentof its action as an antisilencer oftranscription. Proc. Natl. Acad. Sci. U.S.A. 95, 12462-12467. https://doi.org/10.1073/pnas.95.21.12462
  65. Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R. and Storz, G. (1998) The OxyS regulatoryRNA represses rpoS translation and binds the Hfq (HF-I)protein. EMBO J. 17, 6061-6068. https://doi.org/10.1093/emboj/17.20.6061
  66. Basineni, S. R., Madhugiri, R., Kolmsee, T., Hengge, R.and Klug, G. (2009) The influence of Hfq and ribonucleaseson the stability of the small non-coding RNAOxyS and its target rpoS in E. coli is growth phasedependent. RNA Biol. 6, 584-594. https://doi.org/10.4161/rna.6.5.10082
  67. Repoila, F., Majdalani, N. and Gottesman, S. (2003)Small non-coding RNAs, co-ordinators of adaptationprocesses in Escherichia coli: the RpoS paradigm. Mol.Microbiol 48, 855-861. https://doi.org/10.1046/j.1365-2958.2003.03454.x
  68. Madhugiri, R., Basineni, S. R. and Klug, G. (2010) Turnoverof the small non-coding RNA RprA in E. coli is influencedby osmolarity. Mol. Genet. Genomics. 284,307-318. https://doi.org/10.1007/s00438-010-0568-x
  69. Repoila, F. and Gottesman, S. (2001) Signal TransductionCascade for Regulation of RpoS: TemperatureRegulation of DsrA. J. Bacteriol. 183, 4012-4023. https://doi.org/10.1128/JB.183.13.4012-4023.2001
  70. Repoila, F. and Gottesman, S. (2003) TemperatureSensing by the dsrA Promoter. J. Bacteriol. 185, 6609-6614. https://doi.org/10.1128/JB.185.22.6609-6614.2003
  71. Lenz, D., Mok, K., Lilley, B., Kulkarni, R., Wingreen, N.and Bassler, B. (2004) The small RNA chaperone Hfqand multiple small RNAs control quorum sensing inVibrio harveyi and Vibrio cholerae. Cell 118, 69-82. https://doi.org/10.1016/j.cell.2004.06.009
  72. Tu, K. C. and Bassler, B. L. (2007) Multiple small RNAsact additively to integrate sensory information and controlquorum sensing in Vibrio harveyi. Genes Dev. 21,221-233. https://doi.org/10.1101/gad.1502407
  73. Svenningsen, S. L., Tu, K. C. and Bassler, B. L. (2009)Gene dosage compensation calibrates four regulatoryRNAs to control Vibrio cholerae quorum sensing. EMBOJ. 28, 429-439. https://doi.org/10.1038/emboj.2008.300
  74. Long, T., Tu, K. C., Wang, Y., Mehta, P., Ong, N. P.,Bassler, B. L. and Wingreen, N. S. (2009) Quantifyingthe integration of quorum-sensing signals with single-cellresolution. PLoS Biol. 7, e68. https://doi.org/10.1371/journal.pbio.1000068
  75. Thomas, M., Lieberman, J. and Lal, A. (2010)Desperately seeking microRNA targets. Nat. Struct. Mol.Biol. 17, 1169-1174. https://doi.org/10.1038/nsmb.1921
  76. Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P.and Bartel, D. P. (2008) The impact of microRNAs onprotein output. Nature 455, 64-71. https://doi.org/10.1038/nature07242
  77. Selbach, M., Schwanhausser, B., Thierfelder, N., Fang,Z., Khanin, R. and Rajewsky, N. (2008) Widespreadchanges in protein synthesis induced by microRNAs.Nature 455, 58-63. https://doi.org/10.1038/nature07228
  78. Stark, A., Brennecke, J., Bushati, N., Russell, R. B. andCohen, S. M. (2005) Animal MicroRNAs confer robustnessto gene expression and have a significant impact on3'UTR evolution. Cell 123, 1133-1146. https://doi.org/10.1016/j.cell.2005.11.023
  79. Jan, C. H., Friedman, R. C., Ruby, J. G. and Bartel, D. P.(2010) Formation, regulation and evolution of Caenorhabditiselegans 3'UTRs. Nature doi:10.1038/nature09616.
  80. Overgaard, M., Johansen, J., Moller-Jensen, J. andValentin-Hansen, P. (2009) Switching off small RNA regulationwith trap-mRNA. Mol. Microbiol. 73, 790-800. https://doi.org/10.1111/j.1365-2958.2009.06807.x
  81. Plumbridge, J. and Pellegrini, O. (2004) Expression ofthe chitobiose operon of Escherichia coli is regulated bythree transcription factors: NagC, ChbR and CAP. Mol.Microbiol. 52, 437-449. https://doi.org/10.1111/j.1365-2958.2004.03986.x
  82. Nowojewski, A. and Levine, E. Manuscript in preparation.
  83. Masse, E. and Gottesman, S. (2002) A small RNA regulatesthe expression of genes involved in iron metabolismin Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 99,4620-4625. https://doi.org/10.1073/pnas.032066599
  84. Mey, A. R., Craig, S. A. and Payne, S. M. (2005) Characterizationof Vibrio cholerae RyhB: the RyhB regulonand role of RyhB in biofilm formation. Infect. Immun.73, 5706-5719. https://doi.org/10.1128/IAI.73.9.5706-5719.2005
  85. Masse, E., Vanderpool, C. K. and Gottesman, S. (2005)Effect of RyhB small RNA on global iron use inEscherichia coli. J. Bacteriol. 187, 6962-6971. https://doi.org/10.1128/JB.187.20.6962-6971.2005
  86. Jacques, J., Jang, S., Prevost, K., Desnoyers, G., Desmarais,M., Imlay, J. and Masse, E. (2006) RyhB small RNA modulatesthe free intracellular iron pool and is essential fornormal growth during iron limitation in Escherichia coli.Mol. Microbiol. 62, 1181-1190. https://doi.org/10.1111/j.1365-2958.2006.05439.x
  87. Wyckoff, E. E., Mey, A. R. and Payne, S. M. (2007) Ironacquisition in Vibrio cholerae. Biometals 20, 405-416. https://doi.org/10.1007/s10534-006-9073-4
  88. Prevost, K., Salvail, H., Desnoyers, G., Jacques, J.,Phaneuf, E. and Masse, E. (2007) The small RNA RyhBactivates the translation of shiA mRNA encoding a permeaseof shikimate, a compound involved in siderophoresynthesis. Mol. Microbiol. 64, 1260-1273. https://doi.org/10.1111/j.1365-2958.2007.05733.x
  89. Vecerek, B., Moll, I. and Blasi, U. (2007) Control of Fursynthesis by the non-coding RNA RyhB and iron-responsivedecoding. EMBO J. 26, 965-975. https://doi.org/10.1038/sj.emboj.7601553
  90. Semsey, S., Andersson, A. M. C., Krishna, S., Jensen, M.H., Masse, E. and Sneppen, K. (2006) Genetic regulationof fluxes: iron homeostasis of Escherichia coli. Nucleic.Acids. Res. 34, 4960-4967. https://doi.org/10.1093/nar/gkl627
  91. Andrews, S. C., Robinson, A. K. and Rodriguez-Quinones,F. (2003) Bacterial iron homeostasis. FEMS Microbiol.Rev. 27, 215-237. https://doi.org/10.1016/S0168-6445(03)00055-X
  92. Ambros, V. (1989) A hierarchy of regulatory genes controlsa larva-to-adult developmental switch in C. elegans.Cell 57, 49-57. https://doi.org/10.1016/0092-8674(89)90171-2
  93. Slack, F. J., Basson, M., Liu, Z., Ambros, V., Horvitz, H.R. and Ruvkun, G. (2000) The lin-41 RBCC gene acts inthe C. elegans heterochronic pathway between the let-7regulatory RNA and the LIN-29 transcription factor. Mol.Cell 5, 659-669. https://doi.org/10.1016/S1097-2765(00)80245-2
  94. Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T.,Hannon, G. J. and Plasterk, R. H. (2001) Dicer functionsin RNA interference and in synthesis of small RNA involvedin developmental timing in C. elegans. Genes &Development 15, 2654-2659. https://doi.org/10.1101/gad.927801
  95. Grishok, A., Pasquinelli, A. E., Conte, D., Li, N., Parrish,S., Ha, I., Baillie, D. L., Fire, A., Ruvkun, G. and Mello,C. C. (2001) Genes and Mechanisms Related to RNAInterference Regulate Expression of the Small TemporalRNAs that Control C. elegans Developmental Timing.Cell 106, 23-34. https://doi.org/10.1016/S0092-8674(01)00431-7
  96. Lee, Y. S., Nakahara, K., Pham, J. W., Kim, K., He, Z.,Sontheimer, E. J. and Carthew, R. W. (2004) DistinctRoles for Drosophila Dicer-1 and Dicer-2 in thesiRNA/miRNA Silencing Pathways. Cell 117, 69-81. https://doi.org/10.1016/S0092-8674(04)00261-2
  97. Tolia, N. H. and Joshua-Tor, L. (2007) Slicer and theArgonautes. Nat. Chem. Biol. 3, 36-43. https://doi.org/10.1038/nchembio848
  98. Jackson, A. L. and Linsley, P. S. (2010) Recognizing andavoiding siRNA off-target effects for target identificationand therapeutic application. Nat. Rev. Drug Discov. 9,57-67. https://doi.org/10.1038/nrd3010
  99. Jackson, A. L., Bartz, S. R., Schelter, J., Kobayashi, S. V.,Burchard, J., Mao, M., Li, B., Cavet, G. and Linsley, P. S.(2003) Expression profiling reveals off-target gene regulationby RNAi. Nat. Biotechnol 21, 635-637. https://doi.org/10.1038/nbt831
  100. Yi, R., Doehle, B. P., Qin, Y., Macara, I. G. and Cullen,B. R. (2005) Overexpression of Exportin 5 enhancesRNA interference mediated by short hairpin RNAs andmicroRNAs. RNA 11, 220-226. https://doi.org/10.1261/rna.7233305
  101. Grimm, D., Streetz, K. L., Jopling, C. L., Storm, T. A.,Pandey, K., Davis, C. R., Marion, P., Salazar, F. and Kay,M. A. (2006) Fatality in mice due to oversaturation ofcellular microRNA/short hairpin RNA pathways. Nature441, 537-541. https://doi.org/10.1038/nature04791
  102. Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie,C. S. and Marks, D. S. (2009) Transfection of small RNAsglobally perturbs gene regulation by endogenous microRNAs.Nat. Biotech. 27, 549-555. https://doi.org/10.1038/nbt.1543
  103. Larsson, E., Sander, C. and Marks, D. (2010) mRNA turnoverrate limits siRNA and microRNA efficacy. Mol. Syst.Biol. 6, 433.
  104. Sittka, A., Lucchini, S., Papenfort, K., Sharma, C. M.,Rolle, K., Binnewies, T. T., Hinton, J. C. D. and Vogel, J.(2008) Deep sequencing analysis of small noncodingRNA and mRNA targets of the global post-transcriptionalregulator, Hfq. PLoS Genet. 4, e1000163. https://doi.org/10.1371/journal.pgen.1000163
  105. Jousselin, A., Metzinger, L. and Felden, B. (2009) On thefacultative requirement of the bacterial RNA chaperone,Hfq. Trends. Microbiol. 17, 399-405. https://doi.org/10.1016/j.tim.2009.06.003
  106. Le Derout, J., Boni, I. V., Regnier, P. and Hajnsdorf, E.(2010) Hfq affects mRNA levels independently ofdegradation. BMC Mol. Biol. 11, 17. https://doi.org/10.1186/1471-2199-11-17
  107. Valentin-Hansen, P., Eriksen, M. and Udesen, C. (2004)The bacterial Sm-like protein Hfq: a key player in RNAtransactions. Mol. Microbiol. 51, 1525-1533. https://doi.org/10.1111/j.1365-2958.2003.03935.x
  108. Taniguchi, Y., Choi, P. J., Li, G., Chen, H., Babu, M.,Hearn, J., Emili, A. and Xie, X. S. (2010) Quantifying E.coli proteome and transcriptome with single-moleculesensitivity in single cells. Science 329, 533-538. https://doi.org/10.1126/science.1188308
  109. Hussein, R. and Lim, H. N. (2010) Disruption of smallRNA signaling caused by competition for Hfq. Proc.Natl. Acad. Sci. U.S.A. doi:10.1073/pnas.1010082108.
  110. Ebert, M. S. and Sharp, P. A. (2010) MicroRNA sponges:Progress and possibilities. RNA 16, 2043-2050. https://doi.org/10.1261/rna.2414110

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