Portal de Periódicos da CAPES

Roles for MicroRNAs in Conferring Robustness to Biological Processes

2012; Cell Press; Volume: 149; Issue: 3 Linguagem: Inglês

10.1016/j.cell.2012.04.005

1097-4172

Margaret S. Ebert, Phillip A. Sharp,

RNA Research and Splicing

Biological systems use a variety of mechanisms to maintain their functions in the face of environmental and genetic perturbations. Increasing evidence suggests that, among their roles as posttranscriptional repressors of gene expression, microRNAs (miRNAs) help to confer robustness to biological processes by reinforcing transcriptional programs and attenuating aberrant transcripts, and they may in some network contexts help suppress random fluctuations in transcript copy number. These activities have important consequences for normal development and physiology, disease, and evolution. Here, we will discuss examples and principles of miRNAs that contribute to robustness in animal systems. Biological systems use a variety of mechanisms to maintain their functions in the face of environmental and genetic perturbations. Increasing evidence suggests that, among their roles as posttranscriptional repressors of gene expression, microRNAs (miRNAs) help to confer robustness to biological processes by reinforcing transcriptional programs and attenuating aberrant transcripts, and they may in some network contexts help suppress random fluctuations in transcript copy number. These activities have important consequences for normal development and physiology, disease, and evolution. Here, we will discuss examples and principles of miRNAs that contribute to robustness in animal systems. MicroRNAs (miRNAs) are hairpin-derived RNAs ∼20–24 nucleotides (nt) long, which posttranscriptionally repress the expression of target genes usually by binding to the 3′ UTR of messenger RNA (mRNA). As a class, miRNAs constitute about 1%–2% of genes in worms, flies, and mammals (Bartel, 2009Bartel D.P. MicroRNAs: target recognition and regulatory functions.Cell. 2009; 136: 215-233Abstract Full Text Full Text PDF PubMed Scopus (15858) Google Scholar). Their regulatory potential is vast: more than 60% of protein-coding genes are computationally predicted as targets based on conserved base-pairing between the 3′ UTR and the 5′ region of the miRNA, which is called the seed (Friedman et al., 2009Friedman R.C. Farh K.K. Burge C.B. Bartel D.P. Most mammalian mRNAs are conserved targets of microRNAs.Genome Res. 2009; 19: 92-105Crossref PubMed Scopus (6362) Google Scholar). Although many miRNAs and their target binding sites are deeply conserved, which suggests important function, a typical miRNA-target interaction produces only subtle reduction ( 10-fold repression by a moderately expressed endogenous miRNA for a target expressed at low mRNA level (Mukherji et al., 2011Mukherji S. Ebert M.S. Zheng G.X. Tsang J.S. Sharp P.A. van Oudenaarden A. MicroRNAs can generate thresholds in target gene expression.Nat. Genet. 2011; 43: 854-859Crossref PubMed Scopus (487) Google Scholar). Nevertheless, a small change in the level of protein can sometimes have a large physiological effect, such as when a positive feedback loop amplifies the change. Iliopoulos et al., 2009Iliopoulos D. Hirsch H.A. Struhl K. An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation.Cell. 2009; 139: 693-706Abstract Full Text Full Text PDF PubMed Scopus (1156) Google Scholar recently described a network of feedback loops that flips a switch in cancer. Transient activation of Src or other triggers of NF-κB induce stable transformation of a mammary epithelial cell line. NF-κB transcriptionally activates IL6 and inhibits let-7 family members by activating Lin-28B, which prompts destruction of let-7 precursor RNAs (Figure 3). The ensuing drop in let-7 level derepresses IL6, a direct let-7 target, and IL6 is further activated by derepression of the let-7 target Ras. IL6 feeds back in both an autocrine and paracrine fashion to activate NF-κB, which further inhibits let-7, and it signals through STAT3 to promote cell growth and motility. In normal tissue, a transient inflammatory cue could signal through this pathway to induce cell growth to repair damage, and the miRNA holds the positive feedbacks in check. In cancer, in which let-7 is typically downregulated (Kumar et al., 2008Kumar M.S. Erkeland S.J. Pester R.E. Chen C.Y. Ebert M.S. Sharp P.A. Jacks T. Suppression of non-small cell lung tumor development by the let-7 microRNA family.Proc. Natl. Acad. Sci. USA. 2008; 105: 3903-3908Crossref PubMed Scopus (761) Google Scholar, Dong et al., 2010Dong Q. Meng P. Wang T. Qin W. Qin W. Wang F. Yuan J. Chen Z. Yang A. Wang H. MicroRNA let-7a inhibits proliferation of human prostate cancer cells in vitro and in vivo by targeting E2F2 and CCND2.PLoS ONE. 2010; 5: e10147Crossref PubMed Scopus (208) Google Scholar), the positive feedbacks would go unchecked, and continuous, self-reinforcing proliferation would result. In human tumors, the positive feedback loop could be made even stronger by the presence of oncogenic mutations such as v-Src or Ras-V12 (Iliopoulos et al., 2009Iliopoulos D. Hirsch H.A. Struhl K. An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation.Cell. 2009; 139: 693-706Abstract Full Text Full Text PDF PubMed Scopus (1156) Google Scholar). Another mechanism by which a miRNA can increase its impact is by targeting a set of genes that are in a shared pathway or protein complex. Linsley et al., 2007Linsley P.S. Schelter J. Burchard J. Kibukawa M. Martin M.M. Bartz S.R. Johnson J.M. Cummins J.M. Raymond C.K. Dai H. et al.Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression.Mol. Cell. Biol. 2007; 27: 2240-2252Crossref PubMed Scopus (465) Google Scholar provided the first experimental demonstration of this principle, showing coordinate regulation of the G0/G1-to-S cell-cycle transition by the miR-16 family (Linsley et al., 2007Linsley P.S. Schelter J. Burchard J. Kibukawa M. Martin M.M. Bartz S.R. Johnson J.M. Cummins J.M. Raymond C.K. Dai H. et al.Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression.Mol. Cell. Biol. 2007; 27: 2240-2252Crossref PubMed Scopus (465) Google Scholar). A statistical analysis of target predictions crossed against functional annotations found such coordinated repression to be prevalent in mammalian genomes (Tsang et al., 2010Tsang J.S. Ebert M.S. van Oudenaarden A. Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures.Mol. Cell. 2010; 38: 140-153Abstract Full Text Full Text PDF PubMed Scopus (187) Google Scholar). By reducing the concentration of several components in a signaling cascade, a miRNA could create significant reductions in signal output over time. On the other hand, by repressing negative regulators in a pathway, a miRNA could increase signal output. In T lymphocytes, miR-181 plays this role by regulating multiple phosphatases downstream of the T cell receptor, and its dynamic expression at different stages of maturation tunes the sensitivity of the pathway to different levels of antigen (Li et al., 2007Li Q.J. Chau J. Ebert P.J. Sylvester G. Min H. Liu G. Braich R. Manoharan M. Soutschek J. Skare P. et al.miR-181a is an intrinsic modulator of T cell sensitivity and selection.Cell. 2007; 129: 147-161Abstract Full Text Full Text PDF PubMed Scopus (989) Google Scholar). Concentrating effects within functional modules is a common feature of robust systems (Kitano, 2004Kitano H. Biological robustness.Nat. Rev. Genet. 2004; 5: 826-837Crossref PubMed Scopus (1746) Google Scholar). In spite of the large numbers of target genes predicted to be affected by miRNA loss of function, gene knockout experiments for individual miRNAs have yielded many disappointing results. In worms, most individual miRNA mutants show no gross phenotype (Miska et al., 2007Miska E.A. Alvarez-Saavedra E. Abbott A.L. Lau N.C. Hellman A.B. McGonagle S.M. Bartel D.P. Ambros V.R. Horvitz H.R. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability.PLoS Genet. 2007; 3: e215Crossref PubMed Scopus (365) Google Scholar); the same is true for several of the mouse knockouts generated to date, including miR-21, miR-210, miR-214, miR-206, and miR-143 (E. Olson, personal communication). A partial explanation for these results resides in the functional redundancy of many miRNAs that share their seed sequence with others. For example, the let-7 family members miR-48, miR-84, and miR-241 operate redundantly to control the L2-to-L3 larval transition in C. elegans (Abbott et al., 2005Abbott A.L. Alvarez-Saavedra E. Miska E.A. Lau N.C. Bartel D.P. Horvitz H.R. Ambros V. The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans.Dev. Cell. 2005; 9: 403-414Abstract Full Text Full Text PDF PubMed Scopus (380) Google Scholar). Additionally, many miRNAs of different seed families work together to cotarget a given gene or set of genes, providing overlapping functions. To generate an observable impairment in the animal, it might be necessary to delete all members of a seed family and also nonseed family members that have a high degree of cotargeting. It is also possible that a mutant phenotype would only arise upon acute miRNA deletion if, during development, miRNA loss can be compensated at the level of gene expression or by one cell type populating a niche to assist an impaired or underpopulated cell type within an organ or system such as the immune system. Use of conditional knockouts or hypomorphs could possibly reveal physiological phenotypes of miRNAs that are not observed with germline nulls because of early lethality or compensation processes. Along these lines, Smibert et al., 2011Smibert P. Bejarano F. Wang D. Garaulet D.L. Yang J.S. Martin R. Bortolamiol-Becet D. Robine N. Hiesinger P.R. Lai E.C. A Drosophila genetic screen yields allelic series of core microRNA biogenesis factors and reveals post-developmental roles for microRNAs.RNA. 2011; 17: 1997-2010Crossref PubMed Scopus (24) Google Scholar found synaptic transmission defects in photoreceptor neurons of flies with hypomorphic alleles of miRNA core biogenesis genes pasha, drosha, and dcr-1. Even once an organ has developed, miRNAs may be required for maintenance: Dicer loss in the mouse thymic epithelium or the highly structured retina leads to progressive degeneration of tissue architecture (Papadopoulou et al., 2012Papadopoulou A.S. Dooley J. Linterman M.A. Pierson W. Ucar O. Kyewski B. Zuklys S. Hollander G.A. Matthys P. Gray D.H. et al.The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor.Nat. Immunol. 2012; 13: 181-187Crossref Scopus (138) Google Scholar, Damiani et al., 2008Damiani D. Alexander J.J. O'Rourke J.R. McManus M. Jadhav A.P. Cepko C.L. Hauswirth W.W. Harfe B.D. Strettoi E. Dicer inactivation leads to progressive functional and structural degeneration of the mouse retina.J. Neurosci. 2008; 28: 4878-4887Crossref PubMed Scopus (186) Google Scholar). However, there are several contrary examples in which deletion of Dicer and loss of all miRNAs in mature tissue do not appear to generate a phenotype. Deletion of Dicer in the mouse olfactory system had no apparent phenotype over periods of several months (Choi et al., 2008Choi P.S. Zakhary L. Choi W.Y. Caron S. Alvarez-Saavedra E. Miska E.A. McManus M. Harfe B. Giraldez A.J. Horvitz H.R. et al.Members of the miRNA-200 family regulate olfactory neurogenesis.Neuron. 2008; 57: 41-55Abstract Full Text Full Text PDF PubMed Scopus (221) Google Scholar), whereas the same deletion in developing olfactory tissue led to severe neurogenesis defects. Finally, a miRNA phenotype may appear only upon the application of certain internal or external stresses. The most well-characterized example of this mechanism is in the Drosophila eye, in which miR-7 plays a role in the determination of sensory organs (Li and Carthew, 2005Li X. Carthew R.W. A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye.Cell. 2005; 123: 1267-1277Abstract Full Text Full Text PDF PubMed Scopus (286) Google Scholar). Loss of miR-7 had little observable impact on the development of the sensory organs under normal, uniform conditions, and expression of the proneural transcription factor Atonal was also detected at wild-type level (Li et al., 2009Li X. Cassidy J.J. Reinke C.A. Fischboeck S. Carthew R.W. A microRNA imparts robustness against environmental fluctuation during development.Cell. 2009; 137: 273-282Abstract Full Text Full Text PDF PubMed Scopus (362) Google Scholar). But when an environmental perturbation was added during larval development (i.e., fluctuating the temperature between 31°C and 18°C roughly every 90 min), the miR-7 mutant eyes showed abnormally low Atonal expression and abnormally high, irregular expression of the antineural transcription factor Yan. Sensory organ precursor (SOP) defects also appeared: some groups of antennal SOPs failed to develop or developed with abnormal patterning; their cells showed low Atonal levels. The ability of miR-7 to confer developmental robustness against temperature perturbations likely depends on its placement in a network of feedback and feedforward loops with Atonal and Yan (Li et al., 2009Li X. Cassidy J.J. Reinke C.A. Fischboeck S. Carthew R.W. A microRNA imparts robustness against environmental fluctuation during development.Cell. 2009; 137: 273-282Abstract Full Text Full Text PDF PubMed Scopus (362) Google Scholar, Herranz and Cohen, 2010Herranz H. Cohen S.M. MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems.Genes Dev. 2010; 24: 1339-1344Crossref PubMed Scopus (306) Google Scholar). In mice, deletion of the heart muscle-specific miRNA miR-208 has little phenotype under normal conditions but results in a failure to induce cardiac remodeling upon stress (van Rooij et al., 2007van Rooij E. Sutherland L.B. Qi X. Richardson J.A. Hill J. Olson E.N. Control of stress-dependent cardiac growth and gene expression by a microRNA.Science. 2007; 316: 575-579Crossref PubMed Scopus (1389) Google Scholar). When the mice were treated to induce pressure overload or hypothyroidism, miR-208 activity was required in the cardiomyocytes to upregulate βMHC by targeting the thyroid receptor signaling pathway. The embryonic stem cell-specific miR-290-295 cluster is not required for cell viability until DNA damage stress, upon which it promotes cell survival (Zheng et al., 2011Zheng G.X. Ravi A. Calabrese J.M. Medeiros L.A. Kirak O. Dennis L.M. Jaenisch R. Burge C.B. Sharp P.A. A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells.PLoS Genet. 2011; 7: e1002054Crossref PubMed Scopus (81) Google Scholar). In worms sensitized by mutations in a variety of regulatory pathways, 25 of 31 deleted miRNAs revealed a mutant phenotype (Brenner et al., 2010Brenner J.L. Jasiewicz K.L. Fahley A.F. Kemp B.J.