Abstract
Translational repression and degradation of transcripts by microRNAs (miRNAs) is mediated by a ribonucleoprotein complex called the miRNA-induced silencing complex (miRISC, or RISC). Advances in experimental determination of RISC structures have enabled detailed analysis and modeling of known miRNA targets, yet a full appreciation of the structural factors influencing target recognition remains a challenge, primarily because target recognition involves a combination of RNA–RNA and RNA–protein interactions that can vary greatly among different miRNA–target pairs. In this chapter, we review progress toward understanding the role of tertiary structure in miRNA target recognition using computational approaches to assemble RISC complexes at known targets and physics-based methods for computing target interactions. Using this framework to examine RISC structures and dynamics, we describe how the conformational flexibility of Argonautes plays an important role in accommodating the diversity of miRNA–target duplexes formed at canonical and noncanonical target sites. We then discuss applications of tertiary structure-based approaches to emerging topics, including the structural effects of SNPs in miRNA targets and cooperative interactions involving Argonaute–Argonaute complexes. We conclude by assessing the prospects for genome-scale modeling of RISC structures and modeling of higher-order Argonaute complexes associated with miRNA biogenesis, mRNA regulation, and other functions.
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Notes
- 1.
Broyden–Fletcher–Goldfarb–Shanno algorithm.
- 2.
Generalized Born Surface Area solvation approximation.
References
Fabian MR, Sonenberg N (2012) The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol 19(6):586–593. https://doi.org/10.1038/nsmb.2296
Ipsaro JJ, Joshua-Tor L (2015) From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat Struct Mol Biol 22(1):20–28. https://doi.org/10.1038/nsmb.2931
Elkayam E, Faehnle CR, Morales M, Sun J, Li H, Joshua-Tor L (2017) Multivalent recruitment of human Argonaute by GW182. Mol Cell 67(4):646–658e643. https://doi.org/10.1016/j.molcel.2017.07.007
Fabian MR, Cieplak MK, Frank F, Morita M, Green J, Srikumar T, Nagar B, Yamamoto T, Raught B, Duchaine TF, Sonenberg N (2011) miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Nat Struct Mol Biol 18(11):1211–1217. https://doi.org/10.1038/nsmb.2149
Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel DJ (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456(7224):921–926
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461(7265):754–761
Nakanishi K, Weinberg DE, Bartel DP, Patel DJ (2012) Structure of yeast Argonaute with guide RNA. Nature 486(7403):368–374
Schirle NT, MacRae IJ (2012) The crystal structure of human Argonaute2. Science 336(6084):1037–1040. https://doi.org/10.1126/science.1221551
Faehnle CR, Elkayam E, Haase AD, Hannon GJ, Joshua-Tor L (2013) The making of a slicer: activation of human Argonaute-1. Cell Rep 3(6):1901–1909. https://doi.org/10.1016/j.celrep.2013.05.033
Ming D, Wall ME, Sanbonmatsu KY (2007) Domain motions of Argonaute, the catalytic engine of RNA interference. BMC Bioinformatics 8:470. https://doi.org/10.1186/1471-2105-8-470
Gan HH, Gunsalus KC (2013) Tertiary structure-based analysis of microRNA-target interactions. RNA 19(4):539–551. https://doi.org/10.1261/rna.035691.112
Gan HH, Gunsalus KC (2015) Assembly and analysis of eukaryotic Argonaute-RNA complexes in microRNA-target recognition. Nucleic Acids Res 43(20):9613–9625. https://doi.org/10.1093/nar/gkv990
Leoni G, Tramontano A (2016) A structural view of microRNA-target recognition. Nucleic Acids Res 44(9):e82. https://doi.org/10.1093/nar/gkw043
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233
Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38(Suppl):S8–S13
Cao S, Chen SJ (2012) Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Res 40:4681–4690. https://doi.org/10.1093/nar/gks052
Parker JS, Parizotto EA, Wang M, Roe SM, Barford D (2009) Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol Cell 33(2):204–214
Kuhn CD, Joshua-Tor L (2013) Eukaryotic Argonautes come into focus. Trends Biochem Sci 38(5):263–271. https://doi.org/10.1016/j.tibs.2013.02.008
Parker JS (2010) How to slice: snapshots of Argonaute in action. Silence 1(1):3
Wang Y, Li Y, Ma Z, Yang W, Ai C (2010) Mechanism of microRNA-target interaction: molecular dynamics simulations and thermodynamics analysis. PLoS Comput Biol 6(7):e1000866
Iwasaki S, Kobayashi M, Yoda M, Sakaguchi Y, Katsuma S, Suzuki T, Tomari Y (2010) Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes. Mol Cell 39(2):292–299. https://doi.org/10.1016/j.molcel.2010.05.015
Jo MH, Shin S, Jung SR, Kim E, Song JJ, Hohng S (2015) Human Argonaute 2 has diverse reaction pathways on target RNAs. Mol Cell 59(1):117–124. https://doi.org/10.1016/j.molcel.2015.04.027
Flamand MN, Gan HH, Mayya VK, Gunsalus KC, Duchaine TF (2017) A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing. Nucleic Acids Res 45(12):7212–7225. https://doi.org/10.1093/nar/gkx340
Broderick JA, Salomon WE, Ryder SP, Aronin N, Zamore PD (2011) Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA 17(10):1858–1869. https://doi.org/10.1261/rna.2778911
Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW (2010) Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol 17(2):173–179
Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479–486
Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M, Gottwein E, Rajewsky N (2014) Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell 54(6):1042–1054. https://doi.org/10.1016/j.molcel.2014.03.049
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T (2010) Transcriptome-wide identification of RNA-binding protein and MicroRNA target sites by PAR-CLIP. Cell 141(1):129–141. https://doi.org/10.1016/j.cell.2010.03.009
Helwak A, Kudla G, Dudnakova T, Tollervey D (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153(3):654–665. https://doi.org/10.1016/j.cell.2013.03.043
Helwak A, Tollervey D (2014) Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nat Protoc 9(3):711–728. https://doi.org/10.1038/nprot.2014.043
Parisien M, Major F (2008) The MC-fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452(7183):51–55
Pappu RV, Hart RK, Ponder JW (1998) Analysis and application of potential energy smoothing and search methods for global optimization. J Phys Chem B 102(48):9725–9742
Tidor B, Karplus M (1994) The contribution of vibrational entropy to molecular association. The dimerization of insulin. J Mol Biol 238(3):405–414
Meister G (2013) Argonaute proteins: functional insights and emerging roles. Nat Rev Genet 14(7):447–459. https://doi.org/10.1038/nrg3462
Bahar I, Lezon TR, Yang LW, Eyal E (2010) Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys 39:23–42
Tama F, Valle M, Frank J, Brooks CL (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc Natl Acad Sci U S A 100(16):9319–9323
Suhre K, Sanejouand YH (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32(Web Server issue):W610–W614. https://doi.org/10.1093/nar/gkh368
Tama F, Wriggers W, Brooks CL (2002) Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J Mol Biol 321(2):297–305
Baker NA (2004) Poisson-Boltzmann methods for biomolecular electrostatics. Methods Enzymol 383:94–118
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39(10):1278–1284
Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3(3):e85
Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR (2015) A global reference for human genetic variation. Nature 526(7571):68–74. https://doi.org/10.1038/nature15393
Gong J, Liu C, Liu W, Wu Y, Ma Z, Chen H, Guo AY (2015) An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools. Database 2015:bav029. https://doi.org/10.1093/database/bav029
Ryan BM, Robles AI, Harris CC (2010) Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 10(6):389–402. https://doi.org/10.1038/nrc2867
Sethupathy P, Collins FS (2008) MicroRNA target site polymorphisms and human disease. Trends Genet 24(10):489–497. https://doi.org/10.1016/j.tig.2008.07.004
Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J (2014) Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites. PLoS One 9(1):e82699. https://doi.org/10.1371/journal.pone.0082699
Battle A, Brown CD, Engelhardt BE, Montgomery SB (2017) Genetic effects on gene expression across human tissues. Nature 550(7675):204–213. https://doi.org/10.1038/nature24277
Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31(13):3429–3431
Agarwal V, Bell GW, Nam JW, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4. https://doi.org/10.7554/eLife.05005
Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N (2006) A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 16(5):460–471
Friend K, Campbell ZT, Cooke A, Kroll-Conner P, Wickens MP, Kimble J (2012) A conserved PUF-Ago-eEF1A complex attenuates translation elongation. Nat Struct Mol Biol 19(2):176–183. https://doi.org/10.1038/nsmb.2214
Kimble J, Crittenden SL (2007) Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans. Annu Rev Cell Dev Biol 23:405–433. https://doi.org/10.1146/annurev.cellbio.23.090506.123326
Doxzen KW, Doudna JA (2017) DNA recognition by an RNA-guided bacterial Argonaute. PLoS One 12(5):e0177097. https://doi.org/10.1371/journal.pone.0177097
Miyoshi T, Ito K, Murakami R, Uchiumi T (2016) Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Nat Commun 7:11846. https://doi.org/10.1038/ncomms11846
Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJ, van der Oost J (2014) DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507(7491):258–261. https://doi.org/10.1038/nature12971
Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci U S A 111(2):652–657. https://doi.org/10.1073/pnas.1321032111
Toscano-Garibay JD, Aquino-Jarquin G (2014) Transcriptional regulation mechanism mediated by miRNA-DNA*DNA triplex structure stabilized by Argonaute. Biochim Biophys Acta 1839(11):1079–1083. https://doi.org/10.1016/j.bbagrm.2014.07.016
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Gan, H.H., Gunsalus, K.C. (2019). The Role of Tertiary Structure in MicroRNA Target Recognition. In: Laganà, A. (eds) MicroRNA Target Identification. Methods in Molecular Biology, vol 1970. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9207-2_4
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