Small RNA biology is systems biology

BMB Reports

Volumn 44, Issue 1, 2011, Pages 11-21

  Jost, Daniel ^a   Nowojewski, Andrzej ^a   Levine, Erel ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Mathematical modeling; Post transcriptional regulation; Small regulatory RNAs; Systems biology

Indexed keywords

MICRORNA; SMALL INTERFERING RNA; SMALL UNTRANSLATED RNA;

ANIMAL; BACTERIUM; GENETICS; METABOLISM; OXIDATIVE STRESS; REVIEW; SYSTEMS BIOLOGY;

ANIMALS; BACTERIA; MICRORNAS; OXIDATIVE STRESS; RNA, SMALL INTERFERING; RNA, SMALL UNTRANSLATED; SYSTEMS BIOLOGY;

ANIMALIA;

EID: 79751480724     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.5483/BMBRep.2011.44.1.11     Document Type: Review

References (110)

1. Jacob, F. and Monod, J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356.
2. Lee, R. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 175, 843-854.
3. Wightman, B., Ha, I. and Ruvkun, G. (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855-862.
4. Argaman, L., Hershberg, R., Vogel, J., Bejerano, G., Wagner, E. H., Margalit, H. and Altuvia, S. (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology. 11, 941-950.
5. Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G. and Gottesman, S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes & Development 15, 1637-1651.
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.
7. Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E. and Mello, C. C. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
8. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R. and Ruvkun, G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901-906.
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 of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86-89.
10. Ghildiyal, M. and Zamore, P. D. (2009) Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10, 94-108.
11. Bartel, D. P. (2009) MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233.
12. Alvarez-Garcia, I. and Miska, E. A. (2005) MicroRNA functions in animal development and human disease. Development 132, 4653-4662.
13. Hagen, J. W. and Lai, E. C. (2008) microRNA control of cell-cell signaling during development and disease. Cell Cycle 7, 2327-2332.
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 regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2, 219-229.
15. Khurana, J. S. and Theurkauf, W. E. (2008) piRNA function in 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's role in germline differentiation (September 15, 2008), Stem Book, 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 of microRNA dysregulation in cancer. Nat. Rev. Genet 10, 704-714.
18. Leung, A. K. L. and Sharp, P. A. (2010) MicroRNA functions in stress responses. Mol. Cell 40, 205-215.
19. Aravin, A. A., Hannon, G. J. and Brennecke, J. (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761-764.
20. Lee, Y., Jeon, K., Lee, J., Kim, S. and Kim, V. N. (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663-4670.
21. Lee, Y., Kim, M., Han, J., Yeom, K., Lee, S., Baek, S. H. and Kim, V. N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051-4060.
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 RNA pathway in Drosophila. Nature 453, 798-802.
23. Okamura, K., Chung, W., Ruby, J. G., Guo, H., Bartel, D. P. and Lai, E. C. (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453, 803-806.
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 to Argonaute(thinsp)2 in somatic cells. Nature 453, 793-797.
25. Okamura, K., Balla, S., Martin, R., Liu, N. and Lai, E. C. (2008) Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat. Struct. Mol. Biol. 15, 581-590.
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 expression in mouse oocytes. Nature 453, 534-538.
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. and Sasaki, H. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539-543.
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 and RNaseD. Cell 99, 133-141.
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 Transposon Silencing in C. elegans. Cell 99, 123-132.
30. Chung, W., Okamura, K., Martin, R. and Lai, E. C. (2008) Endogenous RNA Interference Provides a Somatic Defense against Drosophila Transposons. Current Biology 18, 795-802.
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 derived from transposons and mRNAs in Drosophila somatic cells. Science 320, 1077-1081.
32. Hammond, S. M., Bernstein, E., Beach, D. and Hannon, G. J. (2000) An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells. Nature 404, 293-296.
33. Zamore, P. D., Tuschl, T., Sharp, P. A. and Bartel, D. P. (2000) RNAi: Double-Stranded RNA Directs the ATPDependent Cleavage of mRNA at 21 to 23 Nucleotide Intervals. Cell 101, 25-33.
34. Pak, J. and Fire, A. (2007) Distinct populations of primary and secondary effectors during RNAi in C. elegans. Science 315, 241-244.
35. Sijen, T., Steiner, F. A., Thijssen, K. L. and Plasterk, R. H. A. (2007) Secondary siRNAs result from unprimed RNA synthesis and form a distinct class. Science 2007, 315, 244-247.
36. Sijen, T., Fleenor, J., Simmer, F., Thijssen, K. L., Parrish, S., Timmons, L., Plasterk, R. H. and Fire, A. (2001) On the Role of RNA Amplification in dsRNA-Triggered Gene Silencing. Cell 107, 465-476.
37. Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R. and Hannon, G. J. (2007) Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila. Cell 128, 1089-1103.
38. Hunter, C. P., Winston, W. M., Molodowitch, C., Feinberg, E. H., Shih, J., Sutherlin, M., Wright, A. J. and Fitzgerald, M. C. (2006) Systemic RNAi in Caenorhabditis elegans. Cold Spring Harb. Symp. Quant. Biol. 71, 95-100.
39. Gottesman, S. (2005) Micros for microbes: non-coding regulatory RNAs in bacteria. Trends in Genetics 21, 399-404.
40. Aiba, H. (2007) Mechanism of RNA silencing by Hfq-binding small RNAs. Current Opinion in Microbiology 10, 134-139.
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 response to stress. Cold Spring Harb. Symp. Quant. Biol. 71, 1-11.
42. Geissmann, T., Possedko, M., Huntzinger, E., Fechter, P., Ehresmann, C. and Romby, P. (2006) Regulatory RNAs as mediators of virulence gene expression in bacteria. Handb Exp. Pharmacol. 173, 9-43.
43. Murphy, E. R. and Payne, S. M. (2007) RyhB, an iron-responsive small RNA molecule, regulates Shigella dysenteriae virulence. Infect. Immun. 75, 3470-3477.
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 of Salmonella typhimurium show host-induced expression and role in virulence. Nucleic. Acids. Res. 36, 1913-1927.
45. Schiano, C. A., Bellows, L. E. and Lathem, W. W. (2010) The small RNA chaperone Hfq is required for the virulence of Yersinia pseudotuberculosis. Infect. Immun. 78, 2034-2044.
46. Chabelskaya, S., Gaillot, O. and Felden, B. (2010) A Staphylococcus aureus small RNA is required for bacterial virulence and regulates the expression of an immune-evasion molecule. PLoS Pathog. 6, e1000927.
47. Podkaminski, D. and Vogel, J. (2010) Small RNAs promote mRNA stability to activate the synthesis of virulence factors. Mol. Microbiol. 78, 1327-1331.
48. Hammond, S. M., Bernstein, E., Beach, D. and Hannon, G. J. (2000) An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells. Nature 404, 293-296.
49. Hutvágner, G. and Zamore, P. D. (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056-2060.
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 catalytic engine of mammalian RNAi. Science 305, 1437-1441.
51. Haley, B. and Zamore, P. D. (2004) Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol. 11, 599-606.
52. Arvey, A., Larsson, E., Sander, C., Leslie, C. S. and Marks, D. S. (2010) Target mRNA abundance dilutes microRNA and siRNA activity. Mol. Syst. Biol. 6, 363.
53. Massé, E., Escorcia, F. E. and Gottesman, S. (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev. 17, 2374-2383.
54. Figueroa-Bossi, N., Valentini, M., Malleret, L. and Bossi, L. (2009) Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes & Development 23, 2004-2015.
55. Levine, E., Zhang, Z., Kuhlman, T. and Hwa, T. (2007) Quantitative characteristics of gene regulation by small RNA. PLoS Biol. 5, e229.
56. Mitarai, N., Andersson, A. M., Krishna, S., Semsey, S. and Sneppen, K. (2007) Efficient degradation and expression prioritization with small RNAs. Phys. Biol. 4, 164-171.
57. Shimoni, Y., Friedlander, G., Hetzroni, G., Niv, G., Altuvia, S., Biham, O. and Margalit, H. (2007) Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol. 3, 138.
58. Mehta, P., Goyal, S. and Wingreen, N. S. (2008) A quantitative comparison of sRNA-based and protein-based gene 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 regulation by small RNA. In submission.
60. Lease, R. A. and Belfort, M. (2000) A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc. Natl. Acad. Sci. U.S.A. 97, 9919-9924.
61. Fang, F. C. and Rimsky, S. (2008) New insights into transcriptional regulation by H-NS. Current Opinion in Microbiology. 11, 113-120.
62. Amit, R., Oppenheim, A. B. and Stavans, J. (2003) Increased Bending Rigidity of Single DNA Molecules by H-NS, a Temperature and Osmolarity Sensor. Biophysical Journal 84, 2467-2473.
63. Dorman, C. J. (2007) H-NS, the genome sentinel. Nat. Rev. Micro. 5, 157-161.
64. Majdalani, N., Cunning, C., Sledjeski, D., Elliott, T. and Gottesman, S. (1998) DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc. Natl. Acad. Sci. U.S.A. 95, 12462-12467.
65. Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R. and Storz, G. (1998) The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J. 17, 6061-6068.
66. Basineni, S. R., Madhugiri, R., Kolmsee, T., Hengge, R. and Klug, G. (2009) The influence of Hfq and ribonucleases on the stability of the small non-coding RNA OxyS and its target rpoS in E. coli is growth phase dependent. RNA Biol. 6, 584-594.
67. Repoila, F., Majdalani, N. and Gottesman, S. (2003) Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol. Microbiol 48, 855-861.
68. Madhugiri, R., Basineni, S. R. and Klug, G. (2010) Turnover of the small non-coding RNA RprA in E. coli is influenced by osmolarity. Mol. Genet. Genomics. 284, 307-318.
69. Repoila, F. and Gottesman, S. (2001) Signal Transduction Cascade for Regulation of RpoS: Temperature Regulation of DsrA. J. Bacteriol. 183, 4012-4023.
70. Repoila, F. and Gottesman, S. (2003) Temperature Sensing by the dsrA Promoter. J. Bacteriol. 185, 6609-6614.
71. Lenz, D., Mok, K., Lilley, B., Kulkarni, R., Wingreen, N. and Bassler, B. (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69-82.
72. Tu, K. C. and Bassler, B. L. (2007) Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev. 21, 221-233.
73. Svenningsen, S. L., Tu, K. C. and Bassler, B. L. (2009) Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing. EMBO J. 28, 429-439.
74. Long, T., Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L. and Wingreen, N. S. (2009) Quantifying the integration of quorum-sensing signals with single-cell resolution. PLoS Biol. 7, e68.
75. Thomas, M., Lieberman, J. and Lal, A. (2010) Desperately seeking microRNA targets. Nat. Struct. Mol. Biol. 17, 1169-1174.
76. Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P. and Bartel, D. P. (2008) The impact of microRNAs on protein output. Nature 455, 64-71.
77. Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z., Khanin, R. and Rajewsky, N. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63.
78. Stark, A., Brennecke, J., Bushati, N., Russell, R. B. and Cohen, S. M. (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 123, 1133-1146.
79. Jan, C. H., Friedman, R. C., Ruby, J. G. and Bartel, D. P. (2010) Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature doi:10.1038/nature09616.
80. Overgaard, M., Johansen, J., Møller-Jensen, J. and Valentin-Hansen, P. (2009) Switching off small RNA regulation with trap-mRNA. Mol. Microbiol. 73, 790-800.
81. Plumbridge, J. and Pellegrini, O. (2004) Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP. Mol. Microbiol. 52, 437-449.
82. Nowojewski, A. and Levine, E. Manuscript in preparation.
83. Massé, E. and Gottesman, S. (2002) A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 99, 4620-4625.
84. Mey, A. R., Craig, S. A. and Payne, S. M. (2005) Characterization of Vibrio cholerae RyhB: the RyhB regulon and role of RyhB in biofilm formation. Infect. Immun. 73, 5706-5719.
85. Massé, E., Vanderpool, C. K. and Gottesman, S. (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J. Bacteriol. 187, 6962-6971.
86. Jacques, J., Jang, S., Prévost, K., Desnoyers, G., Desmarais, M., Imlay, J. and Massé, E. (2006) RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli. Mol. Microbiol. 62, 1181-1190.
87. Wyckoff, E. E., Mey, A. R. and Payne, S. M. (2007) Iron acquisition in Vibrio cholerae. Biometals 20, 405-416.
88. Prévost, K., Salvail, H., Desnoyers, G., Jacques, J., Phaneuf, E. and Massé, E. (2007) The small RNA RyhB activates the translation of shiA mRNA encoding a permease of shikimate, a compound involved in siderophore synthesis. Mol. Microbiol. 64, 1260-1273.
89. Vecerek, B., Moll, I. and Bläsi, U. (2007) Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding. EMBO J. 26, 965-975.
90. Semsey, S., Andersson, A. M. C., Krishna, S., Jensen, M. H., Massé, E. and Sneppen, K. (2006) Genetic regulation of fluxes: iron homeostasis of Escherichia coli. Nucleic. Acids. Res. 34, 4960-4967.
91. Andrews, S. C., Robinson, A. K. and Rodríguez-Quiñones, F. (2003) Bacterial iron homeostasis. FEMS Microbiol. Rev. 27, 215-237.
92. Ambros, V. (1989) A hierarchy of regulatory genes controls a larva-to-adult developmental switch in C. elegans. Cell 57, 49-57.
93. Slack, F. J., Basson, M., Liu, Z., Ambros, V., Horvitz, H. R. and Ruvkun, G. (2000) The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5, 659-669.
94. Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T., Hannon, G. J. and Plasterk, R. H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Development 15, 2654-2659.
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 RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing. Cell 106, 23-34.
96. Lee, Y. S., Nakahara, K., Pham, J. W., Kim, K., He, Z., Sontheimer, E. J. and Carthew, R. W. (2004) Distinct Roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA Silencing Pathways. Cell 117, 69-81.
97. Tolia, N. H. and Joshua-Tor, L. (2007) Slicer and the Argonautes. Nat. Chem. Biol. 3, 36-43.
98. Jackson, A. L. and Linsley, P. S. (2010) Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat. Rev. Drug Discov. 9, 57-67.
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 regulation by RNAi. Nat. Biotechnol 21, 635-637.
100. Yi, R., Doehle, B. P., Qin, Y., Macara, I. G. and Cullen, B. R. (2005) Overexpression of Exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA 11, 220-226.
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 of cellular microRNA/short hairpin RNA pathways. Nature 441, 537-541.
102. Khan, A. A., Betel, D., Miller, M. L., Sander, C., Leslie, C. S. and Marks, D. S. (2009) Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat. Biotech. 27, 549-555.
103. Larsson, E., Sander, C. and Marks, D. (2010) mRNA turnover rate 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 noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet. 4, e1000163.
105. Jousselin, A., Metzinger, L. and Felden, B. (2009) On the facultative requirement of the bacterial RNA chaperone, Hfq. Trends. Microbiol. 17, 399-405.
106. Le Derout, J., Boni, I. V., Régnier, P. and Hajnsdorf, E. (2010) Hfq affects mRNA levels independently of degradation. BMC Mol. Biol. 11, 17.
107. Valentin-Hansen, P., Eriksen, M. and Udesen, C. (2004) The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol. Microbiol. 51, 1525-1533.
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-molecule sensitivity in single cells. Science 329, 533-538.
109. Hussein, R. and Lim, H. N. (2010) Disruption of small RNA 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.