Structural Foundations of RNA Silencing by Argonaute

Journal of Molecular Biology - Tập 429 Số 17 - Trang 2619-2639 - 2017
Jessica Sheu‐Gruttadauria1, Ian J. MacRae1
1Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA

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Tài liệu tham khảo

Hammond, 2000, An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells, Nature, 404, 293, 10.1038/35005107

Rivas, 2005, Purified Argonaute2 and an siRNA form recombinant human RISC, Nat. Struct. Mol. Biol., 12, 340, 10.1038/nsmb918

Liu, 2004, Argonaute2 is the catalytic engine of mammalian RNAi, Science, 305, 1437, 10.1126/science.1102513

Meister, 2004, Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs, Mol. Cell, 15, 185, 10.1016/j.molcel.2004.07.007

Martinez, 2002, Single-stranded antisense siRNAs guide target RNA cleavage in RNAi, Cell, 110, 563, 10.1016/S0092-8674(02)00908-X

Salomon, 2015, Single-molecule imaging reveals that Argonaute reshapes the binding properties of its nucleic acid guides, Cell, 162, 84, 10.1016/j.cell.2015.06.029

Chivukula, 2014, An essential mesenchymal function for miR-143/145 in intestinal epithelial regeneration, Cell, 157, 1104, 10.1016/j.cell.2014.03.055

Xin, 2013, Mending broken hearts: cardiac development as a basis for adult heart regeneration and repair, Nat. Rev. Mol. Cell Biol., 14, 529, 10.1038/nrm3619

Hasuwa, 2013, miR-200b and miR-429 function in mouse ovulation and are essential for female fertility, Science, 341, 71, 10.1126/science.1237999

Coolen, 2009, MicroRNAs in brain development and physiology, Curr. Opin. Neurobiol., 19, 461, 10.1016/j.conb.2009.09.006

Lee, 1993, The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14, Cell, 75, 843, 10.1016/0092-8674(93)90529-Y

Wightman, 1993, Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans, Cell, 75, 855, 10.1016/0092-8674(93)90530-4

Friedman, 2009, Most mammalian mRNAs are conserved targets of microRNAs, Genome Res., 19, 92, 10.1101/gr.082701.108

Kozomara, 2014, miRBase: annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res., 42, D68, 10.1093/nar/gkt1181

Agarwal, 2015, Predicting effective microRNA target sites in mammalian mRNAs, elife, 4, 10.7554/eLife.05005

Lujambio, 2012, The microcosmos of cancer, Nature, 482, 347, 10.1038/nature10888

Lee, 2002, MicroRNA maturation: stepwise processing and subcellular localization, EMBO J., 21, 4663, 10.1093/emboj/cdf476

Lee, 2004, MicroRNA genes are transcribed by RNA polymerase II, EMBO J., 23, 4051, 10.1038/sj.emboj.7600385

Cai, 2004, Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs, RNA, 10, 1957, 10.1261/rna.7135204

Lee, 2003, The nuclear RNase III Drosha initiates microRNA processing, Nature, 425, 415, 10.1038/nature01957

Han, 2006, Molecular basis for the recognition of primary microRNAs by the Drosha–DGCR8 complex, Cell, 125, 887, 10.1016/j.cell.2006.03.043

Denli, 2004, Processing of primary microRNAs by the Microprocessor complex, Nature, 432, 231, 10.1038/nature03049

Gregory, 2004, The Microprocessor complex mediates the genesis of microRNAs, Nature, 432, 235, 10.1038/nature03120

Landthaler, 2004, The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis, Curr. Biol, 14, 2162, 10.1016/j.cub.2004.11.001

Han, 2004, The Drosha–DGCR8 complex in primary microRNA processing, Genes Dev., 18, 3016, 10.1101/gad.1262504

Yi, 2003, Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs, Genes Dev., 17, 3011, 10.1101/gad.1158803

Lund, 2004, Nuclear export of microRNA precursors, Science, 303, 95, 10.1126/science.1090599

Bohnsack, 2004, Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs, RNA, 10, 185, 10.1261/rna.5167604

Gregory, 2005, Human RISC couples microRNA biogenesis and posttranscriptional gene silencing, Cell, 123, 631, 10.1016/j.cell.2005.10.022

Hutvagner, 2001, A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA, Science, 293, 834, 10.1126/science.1062961

Ketting, 2001, Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans, Genes Dev, 15, 2654, 10.1101/gad.927801

Matranga, 2005, Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes, Cell, 123, 607, 10.1016/j.cell.2005.08.044

Rand, 2005, Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation, Cell, 123, 621, 10.1016/j.cell.2005.10.020

Leuschner, 2006, Cleavage of the siRNA passenger strand during RISC assembly in human cells, EMBO Rep., 7, 314, 10.1038/sj.embor.7400637

Bernstein, 2001, Role for a bidentate ribonuclease in the initiation step of RNA interference, Nature, 409, 363, 10.1038/35053110

Fire, 1998, Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans, Nature, 391, 806, 10.1038/35888

Ding, 2007, Antiviral immunity directed by small RNAs, Cell, 130, 413, 10.1016/j.cell.2007.07.039

Chung, 2008, Endogenous RNA interference provides a somatic defense against Drosophila transposons, Curr. Biol., 18, 795, 10.1016/j.cub.2008.05.006

Czech, 2008, An endogenous small interfering RNA pathway in Drosophila, Nature, 453, 798, 10.1038/nature07007

Ghildiyal, 2008, Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells, Science (New York, N.Y.), 320, 1077, 10.1126/science.1157396

Kawamura, 2008, Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells, Nature, 453, 793, 10.1038/nature06938

Maillard, 2013, Antiviral RNA interference in mammalian cells, Science (New York, N.Y.), 342, 235, 10.1126/science.1241930

Cheloufi, 2010, A dicer-independent miRNA biogenesis pathway that requires ago catalysis, Nature, 465, 584, 10.1038/nature09092

Cifuentes, 2010, A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity, Science, 328, 1694, 10.1126/science.1190809

Elbashir, 2001, Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells, Nature, 411, 494, 10.1038/35078107

Czech, 2016, One loop to rule them all: the ping-pong cycle and piRNA-guided silencing, Trends Biochem. Sci., 41, 324, 10.1016/j.tibs.2015.12.008

Vagin, 2006, A distinct small RNA pathway silences selfish genetic elements in the germline, Science, 313, 320, 10.1126/science.1129333

Aravin, 2006, A novel class of small RNAs bind to MILI protein in mouse testes, Nature, 442, 203, 10.1038/nature04916

Girard, 2006, A germline-specific class of small RNAs binds mammalian Piwi proteins, Nature, 442, 199, 10.1038/nature04917

Lau, 2006, Characterization of the piRNA complex from rat testes, Science, 313, 363, 10.1126/science.1130164

Watanabe, 2011, Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus, Science, 332, 848, 10.1126/science.1203919

Brennecke, 2007, Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila, Cell, 128, 1089, 10.1016/j.cell.2007.01.043

Li, 2013, An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes, Mol. Cell, 50, 67, 10.1016/j.molcel.2013.02.016

Han, 2015, Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production, Science, 348, 817, 10.1126/science.aaa1264

Ipsaro, 2012, The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis, Nature, 491, 279, 10.1038/nature11502

Mohn, 2015, piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis, Science, 348, 812, 10.1126/science.aaa1039

Nishimasu, 2012, Structure and function of Zucchini endoribonuclease in piRNA biogenesis, Nature, 491, 284, 10.1038/nature11509

Izumi, 2016, Identification and functional analysis of the pre-piRNA 3′ trimmer in silkworms, Cell, 164, 962, 10.1016/j.cell.2016.01.008

Gunawardane, 2007, A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila, Science, 315, 1587, 10.1126/science.1140494

Rouget, 2010, Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo, Nature, 467, 1128, 10.1038/nature09465

Gou, 2014, Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis, Cell Res., 24, 680, 10.1038/cr.2014.41

Pratt, 2009, The RNA-induced silencing complex: a versatile gene-silencing machine, J. Biol. Chem., 284, 17897, 10.1074/jbc.R900012200

Wang, 2008, Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex, Nature, 456, 921, 10.1038/nature07666

Nakanishi, 2012, Structure of yeast Argonaute with guide RNA, Nature, 486, 368, 10.1038/nature11211

Schirle, 2012, The crystal structure of human Argonaute2, Science, 336, 1037, 10.1126/science.1221551

Song, 2004, Crystal structure of Argonaute and its implications for RISC slicer activity, Science, 305, 1434, 10.1126/science.1102514

Matsumoto, 2016, Crystal structure of silkworm PIWI-clade Argonaute Siwi bound to piRNA, Cell, 167, 484, 10.1016/j.cell.2016.09.002

Wang, 2008, Structure of the guide-strand-containing argonaute silencing complex, Nature, 456, 209, 10.1038/nature07315

Schirle, 2014, Structural basis for microRNA targeting, Science, 346, 608, 10.1126/science.1258040

Parker, 2005, Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex, Nature, 434, 663, 10.1038/nature03462

Ma, 2005, Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein, Nature, 434, 666, 10.1038/nature03514

Lewis, 2005, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120, 15, 10.1016/j.cell.2004.12.035

Frank, 2010, Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2, Nature, 465, 818, 10.1038/nature09039

Khvorova, 2003, Functional siRNAs and miRNAs exhibit strand bias, Cell, 115, 209, 10.1016/S0092-8674(03)00801-8

Schwarz, 2003, Asymmetry in the assembly of the RNAi enzyme complex, Cell, 115, 199, 10.1016/S0092-8674(03)00759-1

Frank, 2012, Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs, EMBO J., 31, 3588, 10.1038/emboj.2012.204

Bartel, 2009, MicroRNAs: target recognition and regulatory functions, Cell, 136, 215, 10.1016/j.cell.2009.01.002

Lewis, 2003, Prediction of mammalian microRNA targets, Cell, 115, 787, 10.1016/S0092-8674(03)01018-3

Brennecke, 2003, Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila, Cell, 113, 25, 10.1016/S0092-8674(03)00231-9

Doench, 2003, siRNAs can function as miRNAs, Genes Dev., 17, 438, 10.1101/gad.1064703

Lai, 2002, Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation, Nat. Genet., 30, 363, 10.1038/ng865

Krek, 2005, Combinatorial microRNA target predictions, Nat. Genet., 37, 495, 10.1038/ng1536

Nakanishi, 2013, Eukaryote-specific insertion elements control human ARGONAUTE slicer activity, Cell Rep., 3, 1893, 10.1016/j.celrep.2013.06.010

Ma, 2004, Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain, Nature, 429, 318, 10.1038/nature02519

Baccarini, 2011, Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells, Curr. Biol., 21, 369, 10.1016/j.cub.2011.01.067

van Rooij, 2007, Control of stress-dependent cardiac growth and gene expression by a microRNA, Science, 316, 575, 10.1126/science.1139089

Hill, 2009, DICER1 mutations in familial pleuropulmonary blastoma, Science, 325, 965, 10.1126/science.1174334

Heravi-Moussavi, 2012, Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers, N. Engl. J. Med., 366, 234, 10.1056/NEJMoa1102903

Foulkes, 2014, DICER1: mutations, microRNAs and mechanisms, Nat. Rev. Cancer, 10.1038/nrc3802

Wu, 2013, Biallelic DICER1 mutations occur in Wilms tumours, J. Pathol., 230, 154, 10.1002/path.4196

Doros, 2014, DICER1 mutations in childhood cystic nephroma and its relationship to DICER1-renal sarcoma, Mod. Pathol., 27, 1267, 10.1038/modpathol.2013.242

de Kock, 2014, Pituitary blastoma: a pathognomonic feature of germ-line DICER1 mutations, Acta Neuropathol., 128, 111, 10.1007/s00401-014-1285-z

Slade, 2011, DICER1 syndrome: clarifying the diagnosis, clinical features and management implications of a pleiotropic tumour predisposition syndrome, J. Med. Genet., 48, 273, 10.1136/jmg.2010.083790

Foulkes, 2011, Extending the phenotypes associated with DICER1 mutations, Hum. Mutat., 32, 1381, 10.1002/humu.21600

Wegert, 2015, Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA Microprocessor complex underlie high-risk blastemal type Wilms tumors, Cancer Cell, 27, 298, 10.1016/j.ccell.2015.01.002

Torrezan, 2014, Recurrent somatic mutation in DROSHA induces microRNA profile changes in Wilms tumour, Nat. Commun., 5, 4039, 10.1038/ncomms5039

Kobayashi, 1859, RISC assembly: coordination between small RNAs and Argonaute proteins, Biochim. Biophys. Acta, 2016, 71

Tomari, 2007, Sorting of Drosophila small silencing RNAs, Cell, 130, 299, 10.1016/j.cell.2007.05.057

Forstemann, 2007, Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1, Cell, 130, 287, 10.1016/j.cell.2007.05.056

Lee, 2004, Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways, Cell, 117, 69, 10.1016/S0092-8674(04)00261-2

Pham, 2004, A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila, Cell, 117, 83, 10.1016/S0092-8674(04)00258-2

Zhou, 2008, Comparative analysis of argonaute-dependent small RNA pathways in Drosophila, Mol. Cell, 32, 592, 10.1016/j.molcel.2008.10.018

Czech, 2009, Hierarchical rules for Argonaute loading in Drosophila, Mol. Cell, 36, 445, 10.1016/j.molcel.2009.09.028

Yoda, 2010, ATP-dependent human RISC assembly pathways, Nat. Struct. Mol. Biol., 17, 17, 10.1038/nsmb.1733

Yekta, 2004, MicroRNA-directed cleavage of HOXB8 mRNA, Science, 304, 594, 10.1126/science.1097434

Tomari, 2004, A protein sensor for siRNA asymmetry, Science, 306, 1377, 10.1126/science.1102755

Liu, 2006, Dicer-2 and R2D2 coordinately bind siRNA to promote assembly of the siRISC complexes, RNA, 12, 1514, 10.1261/rna.101606

Ameres, 2010, Target RNA-directed trimming and tailing of small silencing RNAs, Science, 328, 1534, 10.1126/science.1187058

Marques, 2010, Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila, Nat. Struct. Mol. Biol., 17, 24, 10.1038/nsmb.1735

Okamura, 2011, R2D2 organizes small regulatory RNA pathways in Drosophila, Mol. Cell. Biol., 31, 884, 10.1128/MCB.01141-10

Iwasaki, 2015, Defining fundamental steps in the assembly of the Drosophila RNAi enzyme complex, Nature, 521, 533, 10.1038/nature14254

Nishida, 2013, Roles of R2D2, a cytoplasmic D2 body component, in the endogenous siRNA pathway in Drosophila, Mol. Cell, 10.1016/j.molcel.2012.12.024

Kawamata, 2009, Structural determinants of miRNAs for RISC loading and slicer-independent unwinding, Nat. Struct. Mol. Biol., 16, 953, 10.1038/nsmb.1630

Betancur, 2012, Dicer is dispensable for asymmetric RISC loading in mammals, RNA, 18, 24, 10.1261/rna.029785.111

Murchison, 2005, Characterization of Dicer-deficient murine embryonic stem cells, Proc. Natl. Acad. Sci. U. S. A., 102, 12135, 10.1073/pnas.0505479102

Suzuki, 2015, Small-RNA asymmetry is directly driven by mammalian Argonautes, Nat. Struct. Mol. Biol., 22, 512, 10.1038/nsmb.3050

Noland, 2013, Multiple sensors ensure guide strand selection in human RNAi pathways, RNA, 19, 639, 10.1261/rna.037424.112

Kwak, 2012, The N domain of Argonaute drives duplex unwinding during RISC assembly, Nat. Struct. Mol. Biol., 10.1038/nsmb.2232

Wang, 2009, Nucleation, propagation and cleavage of target RNAs in ago silencing complexes, Nature, 461, 754, 10.1038/nature08434

Liu, 2009, C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation, Science, 325, 750, 10.1126/science.1176325

Ye, 2011, Structure of C3PO and mechanism of human RISC activation, Nat. Struct. Mol. Biol., 10.1038/nsmb.2032

Wee, 2012, Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties, Cell, 151, 1055, 10.1016/j.cell.2012.10.036

Kawamata, 2011, Multilayer checkpoints for microRNA authenticity during RISC assembly, EMBO Rep., 12, 944, 10.1038/embor.2011.128

Gu, 2012, Slicing-independent RISC activation requires the Argonaute PAZ domain, Curr. Biol, 22, 1536, 10.1016/j.cub.2012.06.040

Nykanen, 2001, ATP requirements and small interfering RNA structure in the RNA interference pathway, Cell, 107, 309, 10.1016/S0092-8674(01)00547-5

Iki, 2010, In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90, Mol. Cell, 39, 282, 10.1016/j.molcel.2010.05.014

Iwasaki, 2010, Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes, Mol. Cell, 39, 292, 10.1016/j.molcel.2010.05.015

Smibert, 2013, Homeostatic control of Argonaute stability by microRNA availability, Nat. Struct. Mol. Biol., 20, 789, 10.1038/nsmb.2606

Olivieri, 2012, The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila, Mol. Cell, 47, 954, 10.1016/j.molcel.2012.07.021

Xiol, 2012, A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing, Mol. Cell, 47, 970, 10.1016/j.molcel.2012.07.019

Izumi, 2013, Hsp90 facilitates accurate loading of precursor piRNAs into PIWI proteins, RNA, 19, 896, 10.1261/rna.037200.112

Specchia, 2010, Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons, Nature, 463, 662, 10.1038/nature08739

Gangaraju, 2011, Drosophila Piwi functions in Hsp90-mediated suppression of phenotypic variation, Nat. Genet., 43, 153, 10.1038/ng.743

Yao, 2015, Single-molecule analysis of the target cleavage reaction by the Drosophila RNAi enzyme complex, Mol. Cell, 59, 125, 10.1016/j.molcel.2015.05.015

Pearl, 2006, Structure and mechanism of the Hsp90 molecular chaperone machinery, Annu. Rev. Biochem., 75, 271, 10.1146/annurev.biochem.75.103004.142738

Grimson, 2007, MicroRNA targeting specificity in mammals: determinants beyond seed pairing, Mol. Cell, 27, 91, 10.1016/j.molcel.2007.06.017

Parker, 2009, Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein, Mol. Cell, 33, 204, 10.1016/j.molcel.2008.12.012

Filipowicz, 2005, RNAi: the nuts and bolts of the RISC machine, Cell, 122, 17, 10.1016/j.cell.2005.06.023

Tomari, 2005, Perspective: machines for RNAi, Genes Dev., 19, 517, 10.1101/gad.1284105

Faehnle, 2013, The making of a slicer: activation of human Argonaute-1, Cell Rep., 3, 1901, 10.1016/j.celrep.2013.05.033

Willkomm, 2017, Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein, Nat. Microbiol., 2, 17035, 10.1038/nmicrobiol.2017.35

Kaya, 2016, A bacterial Argonaute with noncanonical guide RNA specificity, Proc. Natl. Acad. Sci. U. S. A., 113, 4057, 10.1073/pnas.1524385113

Chandradoss, 2015, A dynamic search process underlies microRNA targeting, Cell, 162, 96, 10.1016/j.cell.2015.06.032

Ragunathan, 2012, RecA filament sliding on DNA facilitates homology search, elife, 1, e00067, 10.7554/eLife.00067

Sternberg, 2014, DNA interrogation by the CRISPR RNA-guided endonuclease Cas9, Nature, 507, 62, 10.1038/nature13011

Klein, 2017, Why Argonaute is needed to make microRNA target search fast and reliable, Semin. Cell Dev. Biol., 65, 20, 10.1016/j.semcdb.2016.05.017

Ameres, 2007, Molecular basis for target RNA recognition and cleavage by human RISC, Cell, 130, 101, 10.1016/j.cell.2007.04.037

Hammar, 2012, The <em>lac</em> repressor displays facilitated diffusion in living cells, Science (New York, N.Y.), 336, 1595, 10.1126/science.1221648

Stratmann, 2015, The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex, elife, 4, e11721, 10.7554/eLife.11721

Leith, 2012, Sequence-dependent sliding kinetics of p53, Proc. Natl. Acad. Sci., 109, 16552, 10.1073/pnas.1120452109

Blainey, 2009, Nonspecifically bound proteins spin while diffusing along DNA, Nat. Struct. Mol. Biol., 16, 1224, 10.1038/nsmb.1716

Gorman, 2012, Single-molecule imaging reveals target-search mechanisms during DNA mismatch repair, Proc. Natl. Acad. Sci. U. S. A., 109, E3074, 10.1073/pnas.1211364109

Graneli, 2006, Long-distance lateral diffusion of human Rad51 on double-stranded DNA, Proc. Natl. Acad. Sci. U. S. A., 103, 1221, 10.1073/pnas.0508366103

Bailey, 2007, The crystal structure of the Thermus aquaticus DnaB helicase monomer, Nucleic Acids Res., 35, 4728, 10.1093/nar/gkm507

Broderick, 2011, Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing, RNA, 17, 1858, 10.1261/rna.2778911

Grosswendt, 2014, Unambiguous identification of miRNA:target site interactions by different types of ligation reactions, Mol. Cell, 54, 1042, 10.1016/j.molcel.2014.03.049

Schirle, 2015, Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets, elife, 4, 10.7554/eLife.07646

Haley, 2004, Kinetic analysis of the RNAi enzyme complex, Nat. Struct. Mol. Biol., 11, 599, 10.1038/nsmb780

Goh, 2015, piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis, Genes Dev, 29, 1032, 10.1101/gad.260455.115

Nishida, 2015, Respective functions of two distinct Siwi complexes assembled during PIWI-interacting RNA biogenesis in Bombyx germ cells, Cell Rep., 10, 193, 10.1016/j.celrep.2014.12.013

Helwak, 2013, Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding, Cell, 153, 654, 10.1016/j.cell.2013.03.043

Boudreau, 2014, Transcriptome-wide discovery of microRNA binding sites in human brain, Neuron, 81, 294, 10.1016/j.neuron.2013.10.062

Wang, 2014, Composition of seed sequence is a major determinant of microRNA targeting patterns, Bioinformatics, 30, 1377, 10.1093/bioinformatics/btu045

Broughton, 2016, Pairing beyond the seed supports microRNA targeting specificity, Mol. Cell, 64, 320, 10.1016/j.molcel.2016.09.004

Chi, 2009, Argonaute HITS–CLIP decodes microRNA–mRNA interaction maps, Nature, 460, 479, 10.1038/nature08170

Chi, 2012, An alternative mode of microRNA target recognition, Nat. Struct. Mol. Biol., 19, 321, 10.1038/nsmb.2230

Swarts, 2014, DNA-guided DNA interference by a prokaryotic Argonaute, Nature, 507, 258, 10.1038/nature12971

Nowotny, 2005, Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis, Cell, 121, 1005, 10.1016/j.cell.2005.04.024

Song, 2006, Argonaute and RNA—getting into the groove, Curr. Opin. Struct. Biol., 16, 5, 10.1016/j.sbi.2006.01.010

Sheng, 2014, Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage, Proc. Natl. Acad. Sci. U. S. A., 111, 652, 10.1073/pnas.1321032111

Swarts, 2014, The evolutionary journey of Argonaute proteins, Nat. Struct. Mol. Biol., 21, 743, 10.1038/nsmb.2879

Hauptmann, 2013, Turning catalytically inactive human Argonaute proteins into active slicer enzymes, Nat. Struct. Mol. Biol., 20, 814, 10.1038/nsmb.2577

Bagga, 2005, Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation, Cell, 122, 553, 10.1016/j.cell.2005.07.031

Bazzini, 2012, Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish, Science, 336, 233, 10.1126/science.1215704

Djuranovic, 2012, miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay, Science, 336, 237, 10.1126/science.1215691

Guo, 2010, Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature, 466, 835, 10.1038/nature09267

Lim, 2005, Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs, Nature, 433, 769, 10.1038/nature03315

Selbach, 2008, Widespread changes in protein synthesis induced by microRNAs, Nature, 455, 58, 10.1038/nature07228

Jonas, 2015, Towards a molecular understanding of microRNA-mediated gene silencing, Nat. Rev. Genet., 16, 421, 10.1038/nrg3965

Meister, 2005, Identification of novel argonaute-associated proteins, Curr. Biol., 15, 2149, 10.1016/j.cub.2005.10.048

Ding, 2005, The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans, Mol. Cell, 19, 437, 10.1016/j.molcel.2005.07.013

Rehwinkel, 2005, A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing, RNA, 11, 1640, 10.1261/rna.2191905

Liu, 2005, A role for the P-body component GW182 in microRNA function, Nat. Cell Biol., 7, 1261, 10.1038/ncb1333

Chen, 2009, Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps, Nat. Struct. Mol. Biol., 16, 1160, 10.1038/nsmb.1709

Braun, 2011, GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets, Mol. Cell, 44, 120, 10.1016/j.molcel.2011.09.007

Behm-Ansmant, 2006, mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes, Genes Dev., 20, 1885, 10.1101/gad.1424106

Chekulaeva, 2011, miRNA repression involves GW182-mediated recruitment of CCR4–NOT through conserved W-containing motifs, Nat. Struct. Mol. Biol, 18, 1218, 10.1038/nsmb.2166

Fabian, 2011, miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4–NOT, Nat. Struct. Mol. Biol, 18, 1211, 10.1038/nsmb.2149

Chen, 2014, A DDX6–CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing, Mol. Cell, 54, 737, 10.1016/j.molcel.2014.03.034

Mathys, 2014, Structural and biochemical insights to the role of the CCR4–NOT complex and DDX6 ATPase in microRNA repression, Mol. Cell, 54, 751, 10.1016/j.molcel.2014.03.036

Baillat, 2009, Functional dissection of the human TNRC6 (GW182-related) family of proteins, Mol. Cell. Biol., 29, 4144, 10.1128/MCB.00380-09

Boland, 2011, Crystal structure of the MID–PIWI lobe of a eukaryotic Argonaute protein, Proc. Natl. Acad. Sci. U. S. A., 10.1073/pnas.1103946108

El-Shami, 2007, Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components, Genes Dev., 21, 2539, 10.1101/gad.451207

Eulalio, 2009, A C-terminal silencing domain in GW182 is essential for miRNA function, RNA, 15, 1067, 10.1261/rna.1605509

Pfaff, 2013, Structural features of Argonaute–GW182 protein interactions, Proc. Natl. Acad. Sci. U. S. A., 110, E3770, 10.1073/pnas.1308510110

Takimoto, 2009, Mammalian GW182 contains multiple Argonaute-binding sites and functions in microRNA-mediated translational repression, RNA, 15, 1078, 10.1261/rna.1363109

Till, 2007, A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain, Nat. Struct. Mol. Biol., 14, 897, 10.1038/nsmb1302

Kuzuoglu-Ozturk, 2016, miRISC and the CCR4–NOT complex silence mRNA targets independently of 43S ribosomal scanning, EMBO J., 35, 1186, 10.15252/embj.201592901

Eulalio, 2008, GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay, Nat. Struct. Mol. Biol., 15, 346, 10.1038/nsmb.1405

Boland, 2011, Crystal structure of the MID–PIWI lobe of a eukaryotic Argonaute protein, Proc. Natl. Acad. Sci. U. S. A., 108, 10466, 10.1073/pnas.1103946108

Christie, 2013, Structure of the PAN3 pseudokinase reveals the basis for interactions with the PAN2 deadenylase and the GW182 proteins, Mol. Cell, 51, 360, 10.1016/j.molcel.2013.07.011

Boland, 2013, Structure and assembly of the NOT module of the human CCR4–NOT complex, Nat. Struct. Mol. Biol., 20, 1289, 10.1038/nsmb.2681

Jinek, 2010, Structural insights into the human GW182–PABC interaction in microRNA-mediated deadenylation, Nat. Struct. Mol. Biol., 17, 238, 10.1038/nsmb.1768

Wolf, 2014, Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation, EMBO J., 33, 1514, 10.15252/embj.201488373

Schafer, 2014, The structure of the Pan2–Pan3 core complex reveals cross-talk between deadenylase and pseudokinase, Nat. Struct. Mol. Biol., 21, 591, 10.1038/nsmb.2834

Jonas, 2014, An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay, Nat. Struct. Mol. Biol., 21, 599, 10.1038/nsmb.2837

Petit, 2012, The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4–NOT deadenylase complex, Nucleic Acids Res., 40, 11058, 10.1093/nar/gks883

Kozlov, 2010, Structural basis of binding of P-body-associated proteins GW182 and ataxin-2 by the Mlle domain of poly(A)-binding protein, J. Biol. Chem., 285, 13599, 10.1074/jbc.M109.089540

Eystathioy, 2002, A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles, Mol. Biol. Cell, 13, 1338, 10.1091/mbc.01-11-0544

Eystathioy, 2003, The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies, RNA, 9, 1171, 10.1261/rna.5810203

Jagannath, 2009, Localization of double-stranded small interfering RNA to cytoplasmic processing bodies is Ago2 dependent and results in up-regulation of GW182 and Argonaute-2, Mol. Biol. Cell, 20, 521, 10.1091/mbc.e08-08-0796

Eulalio, 2007, P-body formation is a consequence, not the cause, of RNA-mediated gene silencing, Mol. Cell. Biol., 27, 3970, 10.1128/MCB.00128-07

Gatfield, 2009, Integration of microRNA miR-122 in hepatic circadian gene expression, Genes Dev., 23, 1313, 10.1101/gad.1781009

Hwang, 2007, A hexanucleotide element directs microRNA nuclear import, Science, 315, 97, 10.1126/science.1136235

De, 2013, Highly complementary target RNAs promote release of guide RNAs from human Argonaute2, Mol. Cell, 50, 344, 10.1016/j.molcel.2013.04.001

Cazalla, 2010, Down-regulation of a host microRNA by a viral noncoding RNA, Cold Spring Harb. Symp. Quant. Biol., 75, 321, 10.1101/sqb.2010.75.009

Buck, 2010, Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection, RNA, 16, 307, 10.1261/rna.1819210

Marcinowski, 2012, Degradation of cellular miR-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathog, 8, e1002510, 10.1371/journal.ppat.1002510

Lee, 2013, Selective degradation of host MicroRNAs by an intergenic HCMV noncoding RNA accelerates virus production, Cell Host Microbe, 13, 678, 10.1016/j.chom.2013.05.007

Krol, 2010, Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs, Cell, 141, 618, 10.1016/j.cell.2010.03.039

Rissland, 2011, MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes, Mol. Cell, 43, 993, 10.1016/j.molcel.2011.08.021

Monticelli, 2005, MicroRNA profiling of the murine hematopoietic system, Genome Biol., 6, R71, 10.1186/gb-2005-6-8-r71

Sethi, 2009, Micro-RNA abundance and stability in human brain: specific alterations in Alzheimer's disease temporal lobe neocortex, Neurosci. Lett., 459, 100, 10.1016/j.neulet.2009.04.052

Rajasethupathy, 2009, Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB, Neuron, 63, 803, 10.1016/j.neuron.2009.05.029

de la Mata, 2015, Potent degradation of neuronal miRNAs induced by highly complementary targets, EMBO Rep., 16, 500, 10.15252/embr.201540078

Cazalla, 2010, Down-regulation of a host microRNA by a herpesvirus saimiri noncoding RNA, Science, 328, 1563, 10.1126/science.1187197

Park, 2017, Non-canonical targets destabilize microRNAs in human Argonautes, Nucleic Acids Res., 45, 1569

Denzler, 2016, Impact of microRNA levels, target-site complementarity, and cooperativity on competing endogenous RNA-regulated gene expression, Mol. Cell, 64, 565, 10.1016/j.molcel.2016.09.027

Horman, 2013, Akt-mediated phosphorylation of Argonaute 2 downregulates cleavage and upregulates translational repression of microRNA targets, Mol. Cell, 50, 356, 10.1016/j.molcel.2013.03.015

Zeng, 2008, Phosphorylation of Argonaute 2 at serine-387 facilitates its localization to processing bodies, Biochem. J., 413, 429, 10.1042/BJ20080599

Rüdel, 2011, Phosphorylation of human Argonaute proteins affects small RNA binding, Nucleic Acids Res., 39, 2330, 10.1093/nar/gkq1032

Mazumder, 2013, A transient reversal of miRNA-mediated repression controls macrophage activation, EMBO Rep., 14, 1008, 10.1038/embor.2013.149

Shen, 2013, EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2, Nature, 497, 383, 10.1038/nature12080

Golden, 2017, An Argonaute phosphorylation cycle promotes microRNA-mediated silencing, Nature, 542, 197, 10.1038/nature21025

Leung, 2011, Poly(ADP-ribose) regulates stress responses and microRNA activity in the cytoplasm, Mol. Cell, 42, 489, 10.1016/j.molcel.2011.04.015

Seo, 2013, Reciprocal inhibition between intracellular antiviral signaling and the RNAi machinery in mammalian cells, Cell Host Microbe, 14, 435, 10.1016/j.chom.2013.09.002

Qi, 2008, Prolyl 4-hydroxylation regulates Argonaute 2 stability, Nature, 455, 421, 10.1038/nature07186

Wu, 2011, Hypoxia potentiates microRNA-mediated gene silencing through posttranslational modification of Argonaute2, Mol. Cell. Biol., 31, 4760, 10.1128/MCB.05776-11

Rybak, 2009, The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2, Nat. Cell Biol., 11, 1411, 10.1038/ncb1987

Loedige, 2013, The mammalian TRIM–NHL protein TRIM71/LIN-41 is a repressor of mRNA function, Nucleic Acids Res., 41, 518, 10.1093/nar/gks1032

Chang, 2012, Trim71 cooperates with microRNAs to repress Cdkn1a expression and promote embryonic stem cell proliferation, Nat. Commun, 3, 923, 10.1038/ncomms1909

Chen, 2012, The ubiquitin ligase mLin41 temporally promotes neural progenitor cell maintenance through FGF signaling, Genes Dev., 26, 803, 10.1101/gad.187641.112

Martinez, 2013, Argonaute2 expression is post-transcriptionally coupled to microRNA abundance, RNA, 19, 605, 10.1261/rna.036434.112

Gibbings, 2012, Selective autophagy degrades DICER and AGO2 and regulates miRNA activity, Nat. Cell Biol., 14, 1314, 10.1038/ncb2611