J. Krol, I. Loedige, and W. Filipowicz, The widespread regulation of microRNA biogenesis, function and decay, Nat. Rev. Genet, vol.11, pp.597-610, 2010.

A. and V. , MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing, Cell, vol.113, pp.673-676, 2003.

B. Zhang, Q. Wang, and X. Pan, MicroRNAs and their regulatory roles in animals and plants, J. Cell. Physiol, vol.210, pp.279-289, 2007.

T. A. Farazi, J. I. Hoell, P. Morozov, and T. Tuschl, MicroRNAs in human cancer, Adv. Exp. Med. Biol, vol.774, pp.1-20, 2013.

T. Chang and J. T. Mendell, ) microRNAs in vertebrate physiology and human disease, Annu. Rev. Genomics Hum. Genet, vol.8, pp.215-239, 2007.

A. Rybak, H. Fuchs, L. Smirnova, C. Brandt, E. E. Pohl et al., A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment, Nat. Cell Biol, vol.10, pp.987-993, 2008.

M. A. Newman, J. M. Thomson, and S. M. Hammond, Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing, RNA, vol.14, pp.1539-1549, 2008.

S. R. Viswanathan, G. Q. Daley, and R. I. Gregory, Selective blockade of microRNA processing by Lin28, Science, vol.320, pp.97-100, 2008.

I. Heo, C. Joo, Y. Kim, M. Ha, M. Yoon et al., TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation, Cell, vol.138, pp.696-708, 2009.

I. Heo, C. Joo, J. Cho, M. Ha, J. Han et al., Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA, Mol. Cell, vol.32, pp.276-84, 2008.

H. Chang, R. Triboulet, J. E. Thornton, and R. I. Gregory, A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway, Nature, vol.497, pp.244-248, 2013.

X. Liu, Q. Zheng, N. Vrettos, M. Maragkakis, P. Alexiou et al., A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis, Mol. Cell, vol.55, pp.868-879, 2014.

A. Baccarini, H. Chauhan, T. J. Gardner, A. D. Jayaprakash, R. Sachidanandam et al., Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells, Curr. Biol, vol.21, pp.369-376, 2011.

M. P. Gantier, C. E. Mccoy, I. Rusinova, D. Saulep, D. Wang et al., Analysis of microRNA turnover in mammalian cells following Dicer1 ablation, Nucleic Acids Res, vol.39, pp.5692-5703, 2011.

D. 'ambrogio, A. Gu, W. Udagawa, T. Mello, C. C. Richter et al., Specific miRNA stabilization by Gld2-catalyzed monoadenylation, Cell Rep, vol.2, pp.1537-1545, 2012.

M. R. Jones, L. J. Quinton, M. T. Blahna, J. R. Neilson, S. Fu et al., Zcchc11-dependent uridylation of microRNA directs cytokine expression, Nat. Cell Biol, vol.11, pp.1157-1163, 2009.

R. ¨-uegger, S. Großhans, and H. , MicroRNA turnover: when, how, and why, Trends Biochem. Sci, vol.37, pp.436-446, 2012.

J. Krol, V. Busskamp, I. Markiewicz, M. B. Stadler, S. Ribi et al., Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs, Cell, vol.141, pp.618-631, 2010.

O. S. Rissland, S. Hong, and D. P. Bartel, MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes, Mol. Cell, vol.43, pp.993-1004, 2011.

L. Marcinowski, M. Tanguy, A. Krmpotic, B. Rädle, V. J. Lisni´clisni´c et al., Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathog, vol.8, p.1002510, 2012.

V. Libri, A. Helwak, P. Miesen, D. Santhakumar, J. G. Borger et al., Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.279-284, 2012.

D. Cazalla, T. Yario, J. A. Steitz, and J. Steitz, Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA, Science, vol.328, pp.1563-1566, 2010.

S. L. Ameres, M. D. Horwich, J. H. Hung, J. Xu, M. Ghildiyal et al., Target RNA-directed trimming and tailing of small silencing RNAs, Science, vol.328, pp.1534-1539, 2010.

M. De-la-mata, D. Gaidatzis, M. Vitanescu, M. B. Stadler, C. Wentzel et al., Potent degradation of neuronal miRNAs induced by highly complementary targets, EMBO Rep, vol.16, pp.500-511, 2015.

L. Ji and X. Chen, Regulation of small RNA stability: methylation and beyond, Cell Res, vol.22, pp.624-636, 2012.

J. Li, Z. Yang, B. Yu, J. Liu, and X. Chen, Methylation Protects miRNAs and siRNAs from a 3 ?-End Uridylation Activity in Arabidopsis, Curr Biol, vol.15, pp.1501-1507, 2005.

J. Lim, M. Ha, H. Chang, S. C. Kwon, D. K. Simanshu et al., Uridylation by TUT4 and TUT7 Marks mRNA for Degradation, Cell, vol.159, pp.1365-1376, 2014.

A. H. Buck, J. Perot, M. A. Chisholm, D. S. Kumar, L. Tuddenham et al., Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection, RNA, vol.16, pp.307-315, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00451207

J. A. Broderick, W. E. Salomon, S. P. Ryder, N. Aronin, and P. D. Zamore, Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing, RNA, vol.17, pp.1858-1869, 2011.

P. Saetrom, B. S. Heale, O. Snøve, L. Aagaard, J. Alluin et al., Distance constraints between microRNA target sites dictate efficacy and cooperativity, Nucleic Acids Res, vol.35, pp.2333-2342, 2007.

A. Grimson, K. K. Farh, W. K. Johnston, P. Garrett-engele, L. P. Lim et al., MicroRNA targeting specificity in mammals: determinants beyond seed pairing, Mol. Cell, vol.27, pp.91-105, 2007.

C. F. Flores-jasso, W. E. Salomon, and P. D. Zamore, Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates, RNA, vol.19, pp.271-279, 2013.

M. Malecki, S. C. Viegas, T. Carneiro, P. Golik, C. Dressaire et al., The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway, 2013.

, EMBO J, vol.32, pp.1842-1854

M. Lubas, C. K. Damgaard, R. Tomecki, D. Cysewski, T. H. Jensen et al., Exonuclease hDIS3L2 specifies an exosome-independent 3 ?-5 ? degradation pathway of human cytoplasmic mRNA, EMBO J, vol.32, pp.1855-1868, 2013.

S. K. Wyman, E. C. Knouf, R. K. Parkin, B. R. Fritz, D. W. Lin et al., Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity, Genome Res, vol.21, pp.1450-1461, 2011.

D. L. Mellman and R. A. Anderson, A novel gene expression pathway regulated by nuclear phosphoinositides, Adv. Enzyme Regul, vol.49, pp.11-28, 2009.

D. L. Mellman, M. L. Gonzales, C. Song, C. A. Barlow, P. Wang et al., , vol.4, pp.5-7, 2008.

C. R. Alarcón, H. Lee, H. Goodarzi, N. Halberg, and S. F. Tavazoie, N6-methyladenosine (m6A) marks primary microRNAs for processing, Nature, vol.519, pp.482-485, 2015.

S. L. Ameres, M. D. Horwich, J. H. Hung, J. Xu, M. Ghildiyal et al., Target RNA-directed trimming and tailing of small silencing RNAs, Science, vol.328, pp.1534-1539, 2010.

M. Ameyar-zazoua, C. Rachez, M. Souidi, P. Robin, L. Fritsch et al., Argonaute proteins couple chromatin silencing to alternative splicing, Nat. Struct. Mol. Biol, vol.19, pp.998-1004, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01393429

V. C. Auyeung, I. Ulitsky, S. E. Mcgeary, and D. P. Bartel, Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing, Cell, vol.152, pp.844-858, 2013.

J. E. Babiarz, J. G. Ruby, Y. Wang, D. P. Bartel, and R. Blelloch, Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicerdependent small RNAs, Genes Dev, vol.22, pp.2773-2785, 2008.

A. Baccarini, H. Chauhan, T. J. Gardner, A. D. Jayaprakash, R. Sachidanandam et al., Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells, Curr. Biol, vol.21, pp.369-376, 2011.

S. Backes, J. S. Shapiro, L. R. Sabin, A. M. Pham, I. Reyes et al., Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism, Cell Host Microbe, vol.12, pp.200-210, 2012.

D. Baek, J. Villen, C. Shin, F. D. Camargo, S. P. Gygi et al., The impact of microRNAs on protein output, Nature, vol.455, pp.64-71, 2008.

S. Bail, M. Swerdel, H. Liu, X. Jiao, L. A. Goff et al., , 2010.

, Differential regulation of microRNA stability, RNA N. Y. N, vol.16, pp.1032-1039

J. Baran-gale, E. E. Fannin, C. L. Kurtz, and P. Sethupathy, Beta Cell 5?-Shifted isomiRs Are Candidate Regulatory Hubs in Type 2 Diabetes, PLOS ONE, vol.8, p.73240, 2013.

D. P. Bartel, MicroRNAs: target recognition and regulatory functions, Cell, vol.136, pp.215-233, 2009.

D. P. Bartel, C. , and C. Z. , Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs, Nat Rev Genet, vol.5, pp.396-400, 2004.

S. Baskerville and D. P. Bartel, Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes, RNA, vol.11, pp.241-247, 2005.

A. A. Bazzini, M. T. Lee, and A. J. Giraldez, Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish, Science, vol.336, pp.233-237, 2012.

D. Beckett, E. Kovaleva, and P. J. Schatz, A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation, Protein Sci, vol.8, pp.921-929, 1999.

Y. Bennasser, C. Chable-bessia, R. Triboulet, D. Gibbings, C. Gwizdek et al., Competition for XPO5 binding between Dicer mRNA, pre-miRNA and viral RNA regulates human Dicer levels, Nat. Struct. Mol. Biol, vol.18, pp.323-327, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00575094

E. Berezikov, W. J. Chung, J. Willis, E. Cuppen, L. et al., Mammalian mirtron genes, Mol Cell, vol.28, pp.328-336, 2007.

H. Berndt, C. Harnisch, C. Rammelt, N. Stöhr, A. Zirkel et al., Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming, RNA, vol.18, pp.958-972, 2012.

E. Bernstein, S. Y. Kim, M. A. Carmell, E. P. Murchison, H. Alcorn et al., Dicer is essential for mouse development, Nat Genet, vol.35, pp.215-217, 2003.

J. G. Betancur and Y. Tomari, Dicer is dispensable for asymmetric RISC loading in mammals, RNA N. Y, vol.18, pp.24-30, 2012.

S. N. Bhattacharyya, R. Habermacher, U. Martine, E. I. Closs, and W. Filipowicz, Relief of microRNA-mediated translational repression in human cells subjected to stress, Cell, vol.125, pp.1111-1124, 2006.

V. A. Blomen, P. Májek, L. T. Jae, J. W. Bigenzahn, J. Nieuwenhuis et al., Gene essentiality and synthetic lethality in haploid human cells, Science, vol.350, pp.1092-1096, 2015.

M. J. Blow, R. J. Grocock, S. Van-dongen, A. J. Enright, E. Dicks et al., RNA editing of human microRNAs, Genome Biol, vol.7, p.27, 2006.

J. Boele, H. Persson, J. W. Shin, Y. Ishizu, I. S. Newie et al., PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease, Proc. Natl. Acad. Sci. U. S. A, vol.111, pp.11467-11472, 2014.

H. P. Bogerd, H. W. Karnowski, X. Cai, J. Shin, M. Pohlers et al., A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs, Mol. Cell, vol.37, pp.135-142, 2010.

M. T. Bohnsack, K. Czaplinski, G. , and D. , Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs, RNA, vol.10, pp.185-191, 2004.

D. Bortolamiol-becet, F. Hu, D. Jee, J. Wen, K. Okamura et al., Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor, Mol. Cell, vol.59, pp.217-228, 2015.

J. E. Braun, E. Huntzinger, M. Fauser, and E. Izaurralde, GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets, Mol. Cell, vol.44, pp.120-133, 2011.

J. E. Braun, V. Truffault, A. Boland, E. Huntzinger, C. Chang et al., A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation, Nat. Struct. Mol. Biol, vol.19, pp.1324-1331, 2012.

J. Brennecke, A. Stark, R. B. Russell, and S. M. Cohen, Principles of microRNAtarget recognition, PLoS Biol, vol.3, p.85, 2005.

J. L. Brenner, K. L. Jasiewicz, A. F. Fahley, B. J. Kemp, A. et al., Loss of Individual MicroRNAs Causes Mutant Phenotypes in Sensitized Genetic Backgrounds in C. elegans, Curr. Biol, vol.20, pp.1321-1325, 2010.

J. A. Broderick, W. E. Salomon, S. P. Ryder, N. Aronin, and P. D. Zamore, , 2011.

, Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing, RNA, vol.17, pp.1858-1869

A. Brückner, C. Polge, N. Lentze, D. Auerbach, and U. Schlattner, Yeast TwoHybrid, a Powerful Tool for Systems Biology, Int. J. Mol. Sci, vol.10, pp.2763-2788, 2009.

A. H. Buck, J. Perot, M. A. Chisholm, D. S. Kumar, L. Tuddenham et al., Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection, RNA, vol.16, pp.307-315, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00451207

A. M. Burroughs, Y. Ando, M. J. De-hoon, Y. Tomaru, T. Nishibu et al., , 2010.

X. Cai, C. H. Hagedorn, and B. R. Cullen, Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs, RNA, vol.10, pp.1957-1966, 2004.

G. A. Calin, M. Ferracin, A. Cimmino, G. Di-leva, M. Shimizu et al., A MicroRNA Signature Associated with Prognosis and Progression in Chronic Lymphocytic Leukemia, N. Engl. J. Med, vol.353, pp.1793-1801, 2005.

M. J. Cannon, D. S. Schmid, and T. B. Hyde, Review of cytomegalovirus seroprevalence and demographic characteristics associated with infection, Rev. Med. Virol, vol.20, pp.202-213, 2010.

M. A. Carmell, Z. Xuan, M. Q. Zhang, and G. J. Hannon, The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis, Genes Dev, vol.16, pp.2733-2742, 2002.

D. Cazalla, T. Yario, J. A. Steitz, and J. Steitz, Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA, Science, vol.328, pp.1563-1566, 2010.

D. Cazalla, M. Xie, and J. A. Steitz, A primate herpesvirus uses the integrator complex to generate viral microRNAs, Mol. Cell, vol.43, pp.982-992, 2011.

Y. Chan, Y. Lin, R. Lin, H. Kuo, W. Thang et al., Concordant and Discordant Regulation of Target Genes by miR-31 and Its Isoforms, PLOS ONE, vol.8, p.58169, 2013.

H. Chang, R. Triboulet, J. E. Thornton, G. , and R. I. , A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway, Nature, vol.497, pp.244-248, 2013.

T. Chang, D. Yu, Y. Lee, E. A. Wentzel, D. E. Arking et al., Widespread microRNA repression by Myc contributes to tumorigenesis, Nat. Genet, vol.40, pp.43-50, 2008.
DOI : 10.1038/ng.2007.30

URL : http://europepmc.org/articles/pmc2628762?pdf=render

S. Chatterjee and H. Grosshans, Active turnover modulates mature microRNA activity in Caenorhabditis elegans, Nature, vol.461, pp.546-549, 2009.

S. Chatterjee, M. Fasler, I. Büssing, and H. Grosshans, Target-mediated protection of endogenous microRNAs in C. elegans, Dev. Cell, vol.20, pp.388-396, 2011.

M. Chekulaeva, H. Mathys, J. T. Zipprich, J. Attig, M. Colic et al., miRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs, Nat. Struct. Mol. Biol, vol.18, pp.1218-1226, 2011.

S. Cheloufi, C. O. Santos, M. M. Chong, and G. J. Hannon, A dicerindependent miRNA biogenesis pathway that requires Ago catalysis, Nature, vol.465, pp.584-589, 2010.

C. Chen, Y. Hu, N. D. Udeshi, T. Y. Lau, F. Wirtz-peitz et al., Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase, Proc. Natl. Acad. Sci. U. S. A, vol.112, pp.12093-12098, 2015.

Y. Chen, A. Boland, D. Kuzuo?lu-Öztürk, P. Bawankar, B. Loh et al., A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing, Mol. Cell, vol.54, pp.737-750, 2014.

T. P. Chendrimada, R. I. Gregory, E. Kumaraswamy, J. Norman, N. Cooch et al., TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing, Nature, vol.436, pp.740-744, 2005.

S. W. Chi, J. B. Zang, A. Mele, D. , and R. B. , Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps, Nature, vol.460, pp.479-486, 2009.

H. R. Chiang, L. W. Schoenfeld, J. G. Ruby, V. C. Auyeung, N. Spies et al., Mammalian microRNAs: experimental evaluation of novel and previously annotated genes, Genes Dev, vol.24, pp.992-1009, 2010.

J. Chicher, A. Simonetti, L. Kuhn, L. Schaeffer, P. Hammann et al., Purification of mRNA-programmed translation initiation complexes suitable for mass spectrometry analysis, Proteomics, vol.15, pp.2417-2425, 2015.

D. Cifuentes, H. Xue, D. W. Taylor, H. Patnode, Y. Mishima et al., A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity, Science, vol.328, pp.1694-1698, 2010.

N. Cloonan, S. Wani, Q. Xu, J. Gu, K. Lea et al., MicroRNAs and their isomiRs function cooperatively to target common biological pathways, Genome Biol, vol.12, p.126, 2011.

W. Coley, R. Van-duyne, L. Carpio, I. Guendel, K. Kehn-hall et al., Absence of DICER in monocytes and its regulation by HIV-1, J. Biol. Chem, vol.285, pp.31930-31943, 2010.

L. Cong, F. A. Ran, D. Cox, S. Lin, R. Barretto et al., Multiplex genome engineering using CRISPR/Cas systems, Science, vol.339, pp.819-823, 2013.

E. Coyaud, M. Mis, E. M. Laurent, W. H. Dunham, A. L. Couzens et al., BioID-based Identification of Skp Cullin F-box (SCF)?-TrCP1/2 E3 Ligase Substrates, Mol. Cell. Proteomics MCP, vol.14, pp.1781-1795, 2015.

S. K. Das, U. K. Sokhi, S. K. Bhutia, B. Azab, Z. Su et al., , 2010.

, Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells, Proc. Natl. Acad. Sci, vol.107, pp.11948-11953

B. N. Davis, A. C. Hilyard, G. Lagna, and A. Hata, SMAD proteins control DROSHA-mediated microRNA maturation, Nature, vol.454, pp.56-61, 2008.

B. N. Davis, A. C. Hilyard, P. H. Nguyen, G. Lagna, and A. Hata, Smad Proteins Bind a Conserved RNA Sequence to Promote MicroRNA Maturation by Drosha, Mol. Cell, vol.39, pp.373-384, 2010.

A. J. Davison, Overview of classification, Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis, 2007.

A. J. Davison and D. Bhella, Comparative genome and virion structure, Human Herpesviruses: Biology, Therapy, and Immunoprophylaxis, 2007.

N. De, L. Young, P. Lau, N. Meisner, D. V. Morrissey et al., , 2013.

, Mol. Cell, vol.50, pp.344-355

A. M. Denli, B. B. Tops, R. H. Plasterk, R. F. Ketting, and G. J. Hannon, Processing of primary microRNAs by the microprocessor complex, Nature, vol.432, pp.231-235, 2004.

D. Didiano, H. , and O. , Molecular architecture of a miRNA-regulated 3? UTR, RNA, vol.14, pp.1297-1317, 2008.

S. Diederichs and D. A. Haber, Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression, Cell, vol.131, pp.1097-1108, 2007.

D. Dingar, M. Kalkat, P. Chan, T. Srikumar, S. D. Bailey et al., BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors, J. Proteomics, vol.118, pp.95-111, 2015.

J. G. Doench and P. A. Sharp, Specificity of microRNA target selection in translational repression, Genes Dev, vol.18, pp.504-511, 2004.

J. G. Doench, C. P. Petersen, and P. A. Sharp, siRNAs can function as miRNAs, 2003.

, Genes Dev, vol.17, pp.438-442

L. Dölken, J. Perot, V. Cognat, A. Alioua, M. John et al., Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation, J. Virol, vol.81, pp.13771-13782, 2007.

L. Dölken, A. Krmpotic, S. Kothe, L. Tuddenham, M. Tanguy et al., Cytomegalovirus microRNAs Facilitate Persistent Virus Infection in Salivary Glands, PLoS Pathog, vol.6, 2010.

L. Dölken, G. Malterer, F. Erhard, S. Kothe, C. C. Friedel et al., Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay, Cell Host Microbe, vol.7, pp.324-334, 2010.

M. S. Ebert and P. A. Sharp, Roles for microRNAs in conferring robustness to biological processes, Cell, vol.149, pp.515-524, 2012.

M. S. Ebert, J. R. Neilson, and P. A. Sharp, MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells, Nat. Methods, vol.4, pp.721-726, 2007.

S. W. Eichhorn, H. Guo, S. E. Mcgeary, R. A. Rodriguez-mias, C. Shin et al., mRNA Destabilization Is the Dominant Effect of Mammalian MicroRNAs by the Time Substantial Repression Ensues, Mol. Cell, vol.56, pp.104-115, 2014.

I. Elcheva, S. Goswami, F. K. Noubissi, and V. S. Spiegelman, CRD-BP protects the coding region of betaTrCP1 mRNA from miR-183-mediated degradation, Mol. Cell, vol.35, pp.240-246, 2009.

E. Elkayam, C. Kuhn, A. Tocilj, A. D. Haase, E. M. Greene et al., The Structure of Human Argonaute-2 in Complex with miR-20a, Cell, vol.150, pp.100-110, 2012.

C. Ender, A. Krek, M. R. Friedlander, M. Beitzinger, L. Weinmann et al., A human snoRNA with microRNA-like functions, Mol Cell, vol.32, pp.519-528, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00347390

A. Esquela-kerscher and F. J. Slack, Oncomirs-microRNAs with a role in cancer, Nat. Rev. Cancer, vol.6, pp.259-269, 2006.

A. Eulalio, I. Behm-ansmant, D. Schweizer, and E. Izaurralde, P-body formation is a consequence, not the cause, of RNA-mediated gene silencing, Mol Cell Biol, vol.27, pp.3970-3981, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01738446

A. Eulalio, E. Huntzinger, and E. Izaurralde, , 2008.

M. R. Fabian and N. Sonenberg, The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC, Nat. Struct. Mol. Biol, vol.19, pp.586-593, 2012.

M. R. Fabian, M. K. Cieplak, F. Frank, M. Morita, J. Green et al., miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT, Nat. Struct. Mol. Biol, vol.18, pp.1211-1217, 2011.

C. R. Faehnle, J. Walleshauser, J. , and L. , Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway, Nature, vol.514, pp.252-256, 2014.

W. Fang and D. P. Bartel, The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes, Mol. Cell, vol.60, pp.131-145, 2015.

K. K. Farh, A. Grimson, C. Jan, B. P. Lewis, W. K. Johnston et al., The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution, Science, 2005.

S. Fields and O. Song, A novel genetic system to detect protein-protein interactions, Nature, vol.340, pp.245-246, 1989.

E. N. Firat-karalar, N. Rauniyar, J. R. Yates, and T. Stearns, Proximity interactions among centrosome components identify regulators of centriole duplication, Curr. Biol. CB, vol.24, pp.664-670, 2014.

C. F. Flores-jasso, W. E. Salomon, and P. D. Zamore, Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates, RNA, vol.19, pp.271-279, 2013.

J. J. Forman, A. Legesse-miller, and H. A. Coller, A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence, Proc. Natl. Acad. Sci. U. S. A, vol.105, pp.14879-14884, 2008.

R. C. Friedman, K. K. Farh, C. B. Burge, and D. P. Bartel, Most mammalian mRNAs are conserved targets of microRNAs, Genome Res, vol.19, pp.92-105, 2009.

A. Frohn, H. C. Eberl, J. Stöhr, E. Glasmacher, S. Rüdel et al., Dicer-dependent and-independent Argonaute2 Protein Interaction Networks in Mammalian Cells, Mol. Cell. Proteomics, vol.11, pp.1442-1456, 2012.

T. Fukuda, K. Yamagata, S. Fujiyama, T. Matsumoto, I. Koshida et al., , 2007.

D. Gaidatzis, E. Van-nimwegen, J. Hausser, and M. Zavolan, Inference of miRNA targets using evolutionary conservation and pathway analysis, BMC Bioinformatics, vol.8, p.69, 2007.

A. Galgano, M. Forrer, L. Jaskiewicz, A. Kanitz, M. Zavolan et al., , 2008.

, Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System, PLOS ONE, vol.3, p.3164

M. P. Gantier, C. E. Mccoy, I. Rusinova, D. Saulep, D. Wang et al., Analysis of microRNA turnover in mammalian cells following Dicer1 ablation, Nucleic Acids Res, vol.39, pp.5692-5703, 2011.

G. K. Geiss, R. E. Bumgarner, B. Birditt, T. Dahl, N. Dowidar et al., Direct multiplexed measurement of gene expression with color-coded probe pairs, Nat. Biotechnol, vol.26, pp.317-325, 2008.

D. Gibbings, S. Mostowy, F. Jay, Y. Schwab, P. Cossart et al., , 2012.

, Selective autophagy degrades DICER and AGO2 and regulates miRNA activity, Nat. Cell Biol, vol.14, pp.1314-1321

D. R. Gill, S. E. Smyth, C. A. Goddard, I. A. Pringle, C. F. Higgins et al., Increased persistence of lung gene expression using plasmids containing the ubiquitin C or elongation factor 1alpha promoter, Gene Ther, vol.8, pp.1539-1546, 2001.

M. L. Gonzales, D. L. Mellman, A. , and R. A. , CKIalpha is associated with and phosphorylates star-PAP and is also required for expression of select star-PAP target messenger RNAs, J. Biol. Chem, vol.283, pp.12665-12673, 2008.

R. I. Gregory, K. P. Yan, G. Amuthan, T. Chendrimada, B. Doratotaj et al., The Microprocessor complex mediates the genesis of microRNAs, Nature, vol.432, pp.235-240, 2004.

R. I. Gregory, T. P. Chendrimada, N. Cooch, and R. Shiekhattar, Human RISC couples microRNA biogenesis and posttranscriptional gene silencing, Cell, vol.123, pp.631-640, 2005.

N. M. Griffin, J. Yu, F. Long, P. Oh, S. Shore et al., Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis, Nat. Biotechnol, vol.28, pp.83-89, 2010.

A. Grimson, K. K. Farh, W. K. Johnston, P. Garrett-engele, L. P. Lim et al., MicroRNA targeting specificity in mammals: determinants beyond seed pairing, Mol. Cell, vol.27, pp.91-105, 2007.

S. Guil and J. F. Caceres, The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a, Nat Struct Mol Biol, vol.14, pp.591-596, 2007.

L. Guo, C. , and F. , A challenge for miRNA: multiple isomiRs in miRNAomics, Gene, vol.544, pp.1-7, 2014.

H. Guo, N. T. Ingolia, J. S. Weissman, and D. P. Bartel, Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature, vol.466, pp.835-840, 2010.

H. Ha, M. , K. , and V. N. , Regulation of microRNA biogenesis, Nat. Rev. Mol. Cell Biol, vol.15, pp.509-524, 2014.

G. Haas, S. Cetin, M. Messmer, B. Chane-woon-ming, O. Terenzi et al., Identification of factors involved in target RNAdirected microRNA degradation, Nucleic Acids Res, vol.44, pp.2873-2887, 2016.

A. D. Haase, L. Jaskiewicz, H. Zhang, S. Laine, R. Sack et al., TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing, EMBO Rep, vol.6, pp.961-967, 2005.

M. Hafner, M. Landthaler, L. Burger, M. Khorshid, J. Hausser et al., Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP, Cell, vol.141, pp.129-141, 2010.

J. P. Hagan, E. Piskounova, G. , and R. I. , Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells, Nat. Struct. Mol. Biol, vol.16, pp.1021-1025, 2009.

S. M. Hammond, MicroRNAs as tumor suppressors, Nat. Genet, vol.39, pp.582-583, 2007.

B. W. Han, J. Hung, Z. Weng, P. D. Zamore, A. et al., , 2011.

, Exoribonuclease Nibbler Shapes the 3? Ends of MicroRNAs Bound to Drosophila Argonaute1, Curr. Biol, vol.21, pp.1878-1887

J. Han, Y. Lee, K. Yeom, Y. Kim, H. Jin et al., The DroshaDGCR8 complex in primary microRNA processing, Genes Dev, vol.18, pp.3016-3027, 2004.

J. Han, Y. Lee, K. H. Yeom, J. W. Nam, I. Heo et al., Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex, Cell, vol.125, pp.887-901, 2006.

J. Han, J. S. Pedersen, S. C. Kwon, C. D. Belair, Y. Kim et al., Posttranscriptional crossregulation between Drosha and DGCR8, Cell, vol.136, pp.75-84, 2009.

T. B. Hansen, T. I. Jensen, B. H. Clausen, J. B. Bramsen, B. Finsen et al., Natural RNA circles function as efficient microRNA sponges, Nature, vol.495, pp.384-388, 2013.

L. He, X. He, S. W. Lowe, and G. J. Hannon, microRNAs join the p53 networkanother piece in the tumour-suppression puzzle, Nat Rev Cancer, vol.7, pp.819-822, 2007.

M. Y. Hein, N. C. Hubner, I. Poser, J. Cox, N. Nagaraj et al., A human interactome in three quantitative dimensions organized by stoichiometries and abundances, Cell, vol.163, pp.712-723, 2015.

I. Heo, C. Joo, J. Cho, M. Ha, J. Han et al., Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA, Mol Cell, vol.32, pp.276-284, 2008.

I. Heo, C. Joo, Y. Kim, M. Ha, M. Yoon et al., TUT4 in concert with Lin28 suppresses microRNA biogenesis through premicroRNA uridylation, Cell, vol.138, pp.696-708, 2009.

I. Heo, M. Ha, J. Lim, M. Yoon, J. Park et al., Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs, Cell, vol.151, pp.521-532, 2012.

K. M. Herbert, G. Pimienta, S. J. Degregorio, A. Alexandrov, and J. A. Steitz, Phosphorylation of DGCR8 Increases Its Intracellular Stability and Induces a Progrowth miRNA Profile, Cell Rep, vol.5, pp.1070-1081, 2013.

A. Heyam, D. Lagos, and M. Plevin, Dissecting the roles of TRBP and PACT in double-stranded RNA recognition and processing of noncoding RNAs, Wiley Interdiscip. Rev. RNA, vol.6, pp.271-289, 2015.

J. Höck, L. Weinmann, C. Ender, S. Rüdel, E. Kremmer et al., Proteomic and functional analysis of Argonaute-containing mRNAprotein complexes in human cells, EMBO Rep, vol.8, pp.1052-1060, 2007.

K. Hodge, S. T. Have, L. Hutton, and A. I. Lamond, Cleaning up the masses: exclusion lists to reduce contamination with HPLC-MS/MS, J. Proteomics, vol.88, pp.92-103, 2013.

M. J. Hoon, . De, R. J. Taft, T. Hashimoto, M. Kanamori-katayama et al., Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries, Genome Res, vol.20, pp.257-264, 2010.

S. R. Horman, M. M. Janas, C. Litterst, B. Wang, I. J. Macrae et al., Akt-Mediated Phosphorylation of Argonaute 2 Downregulates Cleavage and Upregulates Translational Repression of MicroRNA Targets, Mol. Cell, vol.50, pp.356-367, 2013.

M. D. Horwich, C. Li, C. Matranga, V. Vagin, G. Farley et al., The Drosophila RNA Methyltransferase, DmHen1, Modifies Germline piRNAs and Single-Stranded siRNAs in RISC, Curr. Biol, vol.17, pp.1265-1272, 2007.

N. C. Hubner, A. W. Bird, J. Cox, B. Splettstoesser, P. Bandilla et al., Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions, J. Cell Biol, vol.189, pp.739-754, 2010.

D. T. Humphreys, C. J. Hynes, H. R. Patel, G. H. Wei, L. Cannon et al., Complexity of Murine Cardiomyocyte miRNA Biogenesis, Sequence Variant Expression and Function, PLOS ONE, vol.7, p.30933, 2012.

V. Hung, P. Zou, H. Rhee, N. D. Udeshi, V. Cracan et al., Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging, Mol. Cell, vol.55, pp.332-341, 2014.

V. Hung, N. D. Udeshi, S. S. Lam, K. H. Loh, K. J. Cox et al., Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2, Nat. Protoc, vol.11, pp.456-475, 2016.

E. Huntzinger and E. Izaurralde, Gene silencing by microRNAs: contributions of translational repression and mRNA decay, Nat. Rev. Genet, vol.12, pp.99-110, 2011.

E. Huntzinger, J. E. Braun, S. Heimstädt, L. Zekri, and E. Izaurralde, Two PABPC1-binding sites in GW182 proteins promote miRNA-mediated gene silencing, EMBO J, vol.29, pp.4146-4160, 2010.

E. L. Huttlin, L. Ting, R. J. Bruckner, F. Gebreab, M. P. Gygi et al., The BioPlex Network: A Systematic Exploration of the Human Interactome, Cell, vol.162, pp.425-440, 2015.

G. Hutvágner, J. Mclachlan, A. E. Pasquinelli, E. Balint, T. Tuschl et al., A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA, Science, vol.293, pp.834-838, 2001.

G. Hutvagner, M. J. Simard, C. C. Mello, and P. D. Zamore, Sequence-specific inhibition of small RNA function, PLoS Biol, vol.2, p.98, 2004.

H. Hwang, E. A. Wentzel, and J. T. Mendell, A hexanucleotide element directs microRNA nuclear import, Science, vol.315, pp.97-100, 2007.

F. Ibrahim, L. A. Rymarquis, E. Kim, J. Becker, E. Balassa et al., Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas, Proc. Natl. Acad. Sci. U. S. A, vol.107, pp.3906-3911, 2010.

S. Iwasaki, M. Kobayashi, M. Yoda, Y. Sakaguchi, S. Katsuma et al., Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes, Mol. Cell, vol.39, pp.292-299, 2010.

Y. W. Iwasaki, K. Kiga, H. Kayo, Y. Fukuda-yuzawa, J. Weise et al., Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry, RNA, vol.19, pp.490-497, 2013.

A. Jakymiw, S. Lian, T. Eystathioy, S. Li, M. Satoh et al., Disruption of GW bodies impairs mammalian RNA interference, Nat. Cell Biol, vol.7, pp.1267-1274, 2005.

K. Jazdzewski, E. L. Murray, K. Franssila, B. Jarzab, D. R. Schoenberg et al., Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma, Proc. Natl. Acad. Sci. 105, pp.7269-7274, 2008.

K. Jazdzewski, S. Liyanarachchi, M. Swierniak, J. Pachucki, M. D. Ringel et al., Polymorphic mature microRNAs from passenger strand of premiR-146a contribute to thyroid cancer, Proc. Natl. Acad. Sci, vol.106, pp.1502-1505, 2009.

P. Jiang, C. , and H. , Functional interactions between microRNAs and RNA binding proteins, vol.1, pp.70-79, 2012.

H. Jin, M. R. Suh, J. Han, K. Yeom, Y. Lee et al., Human UPF1 participates in small RNA-induced mRNA downregulation, Mol. Cell. Biol, vol.29, pp.5789-5799, 2009.

M. Jinek, M. R. Fabian, S. M. Coyle, N. Sonenberg, and J. A. Doudna, Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation, Nat. Struct. Mol. Biol, vol.17, pp.238-240, 2010.

M. Johnston, M. Geoffroy, A. Sobala, R. Hay, and G. Hutvagner, HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells, Mol. Biol. Cell, vol.21, pp.1462-1469, 2010.

S. Jonas and E. Izaurralde, The role of disordered protein regions in the assembly of decapping complexes and RNP granules, Genes Dev, vol.27, pp.2628-2641, 2013.

S. Jonas and E. Izaurralde, Towards a molecular understanding of microRNAmediated gene silencing, Nat. Rev. Genet, vol.16, pp.421-433, 2015.

M. R. Jones, L. J. Quinton, M. T. Blahna, J. R. Neilson, S. Fu et al., Zcchc11-dependent uridylation of microRNA directs cytokine expression, Nat. Cell Biol, vol.11, pp.1157-1163, 2009.

M. R. Jones, M. T. Blahna, E. Kozlowski, K. Y. Matsuura, J. D. Ferrari et al., Zcchc11 uridylates mature miRNAs to enhance neonatal IGF-1 expression, growth, and survival, PLoS Genet, vol.8, p.1003105, 2012.

M. W. Jones-rhoades, D. P. Bartel, B. , and B. , MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS, Annu. Rev. Plant Biol, vol.57, pp.19-53, 2006.

J. Lisnic, V. Babic-cac, M. Lisnic, B. Trsan, T. Mefferd et al., , 2013.

R. Kalantari, J. A. Hicks, L. Li, K. T. Gagnon, V. Sridhara et al., Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells, vol.22, pp.1085-1098, 2016.

T. Katoh, Y. Sakaguchi, K. Miyauchi, T. Suzuki, S. Kashiwabara et al., Selective stabilization of mammalian microRNAs by 3? adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2, Genes Dev, vol.23, pp.433-438, 2009.

Y. Kawahara, B. Zinshteyn, T. P. Chendrimada, R. Shiekhattar, and K. Nishikura, , 2007.

, RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex, EMBO Rep, vol.8, pp.763-769

Y. Kawahara, B. Zinshteyn, P. Sethupathy, H. Iizasa, A. G. Hatzigeorgiou et al., Redirection of silencing targets by adenosine-to-inosine editing of miRNAs, Science, vol.315, pp.1137-1140, 2007.

T. Kawamata, H. Seitz, and Y. Tomari, Structural determinants of miRNAs for RISC loading and slicer-independent unwinding, Nat. Struct. Mol. Biol, vol.16, pp.953-960, 2009.

M. Kedde, M. J. Strasser, B. Boldajipour, J. A. Vrielink, K. Slanchev et al., RNA-Binding Protein Dnd1 Inhibits MicroRNA Access to Target mRNA, Cell, vol.131, pp.1273-1286, 2007.

M. Kedde, M. Van-kouwenhove, W. Zwart, J. A. Oude-vrielink, R. Elkon et al., A Pumilio-induced RNA structure switch in p27-3? UTR controls miR-221 and miR-222 accessibility, Nat. Cell Biol, vol.12, pp.1014-1020, 2010.

A. Khvorova, A. Reynolds, J. , and S. D. , Functional siRNAs and miRNAs exhibit strand bias, Cell, vol.115, pp.209-216, 2003.

Y. Kim, K. , and V. N. , Processing of intronic microRNAs, EMBO J, vol.26, pp.775-783, 2007.

B. Kim, M. Ha, L. Loeff, H. Chang, D. K. Simanshu et al., TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms, EMBO J, vol.34, pp.1801-1815, 2015.

D. I. Kim, K. C. Birendra, W. Zhu, K. Motamedchaboki, V. Doye et al., Probing nuclear pore complex architecture with proximity-dependent biotinylation, Proc. Natl. Acad. Sci. U. S. A, vol.111, pp.2453-2461, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01059687

D. I. Kim, S. C. Jensen, K. A. Noble, B. Kc, K. H. Roux et al., An improved smaller biotin ligase for BioID proximity labeling, Mol. Biol. Cell, vol.27, pp.1188-1196, 2016.

H. H. Kim, Y. Kuwano, S. Srikantan, E. K. Lee, J. L. Martindale et al., , 2009.

, HuR recruits let-7/RISC to repress c-Myc expression, Genes Dev, vol.23, pp.1743-1748

Y. Kim, J. Yeo, J. H. Lee, J. Cho, D. Seo et al., Deletion of Human tarbp2 Reveals Cellular MicroRNA Targets and Cell-Cycle Function of, TRBP. Cell Rep, vol.9, pp.1061-1074, 2014.

Y. Kim, B. Kim, K. , and V. N. , Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis, Proc. Natl. Acad. Sci. U. S. A, vol.113, pp.1881-1889, 2016.

E. C. Knouf, S. K. Wyman, and M. Tewari, The human TUT1 nucleotidyl transferase as a global regulator of microRNA abundance, PloS One, vol.8, p.69630, 2013.

H. Kobayashi and Y. Tomari, RISC assembly: Coordination between small RNAs and Argonaute proteins, Biochim. Biophys. Acta BBA-Gene Regul. Mech, vol.1859, pp.71-81, 2016.

M. Van-kouwenhove, M. Kedde, A. , and R. , MicroRNA regulation by RNAbinding proteins and its implications for cancer, Nat. Rev. Cancer, vol.11, pp.644-656, 2011.

A. Krek, D. Grun, M. N. Poy, R. Wolf, L. Rosenberg et al., Combinatorial microRNA target predictions, Nat Genet, vol.37, pp.495-500, 2005.

A. Krmpotic, I. Bubic, B. Polic, P. Lucin, J. et al., Pathogenesis of murine cytomegalovirus infection, Microbes Infect, vol.5, pp.1263-1277, 2003.

J. Krol, V. Busskamp, I. Markiewicz, M. B. Stadler, S. Ribi et al., Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs, Cell, vol.141, pp.618-631, 2010.

J. Krutzfeldt, N. Rajewsky, R. Braich, K. G. Rajeev, T. Tuschl et al., Silencing of microRNAs in vivo with "antagomirs, Nature, vol.438, pp.685-689, 2005.

P. Kundu, M. R. Fabian, N. Sonenberg, S. N. Bhattacharyya, and W. Filipowicz, , 2012.

, HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA, Nucleic Acids Res, vol.40, pp.5088-5100

J. E. Kwak and M. Wickens, A family of poly(U) polymerases, RNA, vol.13, pp.860-867, 2007.

P. B. Kwak and Y. Tomari, The N domain of Argonaute drives duplex unwinding during RISC assembly, Nat. Struct. Mol. Biol, vol.19, pp.145-151, 2012.

K. Kwon and D. Beckett, Function of a conserved sequence motif in biotin holoenzyme synthetases, Protein Sci. Publ. Protein Soc, vol.9, pp.1530-1539, 2000.

S. C. Kwon, T. A. Nguyen, Y. Choi, M. H. Jo, S. Hohng et al., Structure of Human DROSHA. Cell, vol.164, pp.81-90, 2016.

A. ?abno, Z. Warkocki, T. Kuli?ski, P. S. Krawczyk, K. Bijata et al., Perlman syndrome nuclease DIS3L2 controls cytoplasmic noncoding RNAs and provides surveillance pathway for maturing snRNAs, Nucleic Acids Res, 2016.

D. H. Lackner, A. Carré, P. M. Guzzardo, C. Banning, R. Mangena et al., A generic strategy for CRISPR-Cas9-mediated gene tagging, Nat. Commun, vol.6, 2015.

R. S. Laishram, A. , and R. A. , The poly A polymerase Star-PAP controls 3'-end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA, EMBO J, vol.29, pp.4132-4145, 2010.

S. S. Lam, J. D. Martell, K. J. Kamer, T. J. Deerinck, M. H. Ellisman et al., Directed evolution of APEX2 for electron microscopy and proximity labeling, Nat. Methods, vol.12, pp.51-54, 2015.

J. Lambert, M. Tucholska, C. Go, J. D. Knight, and A. Gingras, Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes, J. Proteomics, vol.118, pp.81-94, 2015.

P. Landgraf, M. Rusu, R. Sheridan, A. Sewer, N. Iovino et al., A mammalian microRNA expression atlas based on small RNA library sequencing, Cell, vol.129, pp.1401-1414, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00159802

M. Landthaler, A. Yalcin, and T. Tuschl, The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis, Curr Biol, vol.14, pp.2162-2167, 2004.

M. Landthaler, D. Gaidatzis, A. Rothballer, P. Y. Chen, S. J. Soll et al., Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs, Rna, vol.14, pp.2580-2596, 2008.

D. Lazzaretti, I. Tournier, and E. Izaurralde, The C-terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins, RNA N. Y. N, vol.15, pp.1059-1066, 2009.

M. Lee, Y. Choi, K. Kim, H. Jin, J. Lim et al., Adenylation of Maternally Inherited MicroRNAs by Wispy, 2014.

, Mol. Cell, vol.56, pp.696-707

S. Lee, J. Song, S. Kim, J. Kim, Y. Hong et al., Selective degradation of host MicroRNAs by an intergenic HCMV noncoding RNA accelerates virus production, Cell Host Microbe, vol.13, pp.678-690, 2013.

Y. Lee, K. Jeon, J. T. Lee, S. Kim, K. et al., MicroRNA maturation: stepwise processing and subcellular localization, Embo J, vol.21, pp.4663-4670, 2002.

Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim et al., The nuclear RNase III Drosha initiates microRNA processing, Nature, vol.425, pp.415-419, 2003.

Y. Lee, M. Kim, J. Han, K. H. Yeom, S. Lee et al., , 2004.

, MicroRNA genes are transcribed by RNA polymerase II, Embo J, vol.23, pp.4051-4060

Y. Lee, I. Hur, S. Y. Park, Y. K. Kim, M. R. Suh et al., The role of PACT in the RNA silencing pathway, Embo J, vol.25, pp.522-532, 2006.

L. Sage, V. Cinti, A. Valiente-echeverría, F. Mouland, and A. J. , Proteomic analysis of HIV-1 Gag interacting partners using proximity-dependent biotinylation, Virol. J, vol.12, p.138, 2015.

A. K. Leung, A. G. Young, A. Bhutkar, G. X. Zheng, A. D. Bosson et al., , 2011.

, Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs, Nat. Struct. Mol. Biol, vol.18, pp.237-244

A. K. Leung, S. Vyas, J. E. Rood, A. Bhutkar, P. A. Sharp et al., , 2011.

. Poly, ADP-Ribose) Regulates Stress Responses and MicroRNA Activity in the Cytoplasm

, Mol. Cell, vol.42, pp.489-499

B. P. Lewis, I. Shih, M. W. Jones-rhoades, D. P. Bartel, and C. B. Burge, Prediction of mammalian microRNA targets, Cell, vol.115, pp.787-798, 2003.

B. P. Lewis, C. B. Burge, and D. P. Bartel, Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets, Cell, vol.120, pp.15-20, 2005.

J. Li, Z. Yang, B. Yu, J. Liu, C. et al., Methylation Protects miRNAs and siRNAs from a 3'-End Uridylation Activity in Arabidopsis, Curr Biol, vol.15, pp.1501-1507, 2005.

W. Li, R. S. Laishram, Z. Ji, C. A. Barlow, B. Tian et al., Star-PAP control of BIK expression and apoptosis is regulated by nuclear PIPKI? and PKC? signaling, 2012.

, Mol. Cell, vol.45, pp.25-37

S. L. Lian, S. Li, G. X. Abadal, B. A. Pauley, M. J. Fritzler et al., The Cterminal half of human Ago2 binds to multiple GW-rich regions of GW182 and requires GW182 to mediate silencing, RNA, vol.15, pp.804-813, 2009.

V. Libri, A. Helwak, P. Miesen, D. Santhakumar, J. G. Borger et al., Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.279-284, 2012.

J. Lim, M. Ha, H. Chang, S. C. Kwon, D. K. Simanshu et al., , 2014.

, Uridylation by TUT4 and TUT7 Marks mRNA for Degradation, Cell, vol.159, pp.1365-1376

A. Lingel, B. Simon, E. Izaurralde, and M. Sattler, Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain, Nat Struct Mol Biol, vol.11, pp.576-577, 2004.

J. Liu, M. A. Carmell, F. V. Rivas, C. G. Marsden, J. M. Thomson et al., Argonaute2 is the catalytic engine of mammalian RNAi, Science, vol.305, pp.1437-1441, 2004.

J. Liu, M. A. Valencia-sanchez, G. J. Hannon, P. , and R. , MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies, Nat Cell Biol, 2005.

J. Liu, F. V. Rivas, J. Wohlschlegel, J. R. Yates, R. Parker et al., A role for the P-body component GW182 in microRNA function, Nat Cell Biol, vol.7, pp.1261-1266, 2005.

N. Liu, M. Abe, L. R. Sabin, G. Hendriks, A. S. Naqvi et al., The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila, Curr. Biol. CB, vol.21, pp.1888-1893, 2011.

X. Liu, D. Jin, M. T. Mcmanus, M. , and Z. , Precursor MicroRNAProgrammed Silencing Complex Assembly Pathways in Mammals, Mol. Cell, vol.46, pp.507-517, 2012.

X. Liu, Q. Zheng, N. Vrettos, M. Maragkakis, P. Alexiou et al., A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis, Mol. Cell, vol.55, pp.868-879, 2014.

A. Loffreda, A. Rigamonti, S. M. Barabino, and S. C. Lenzken, RNA-Binding Proteins in the Regulation of miRNA Activity: A Focus on Neuronal Functions, Biomolecules, vol.5, pp.2363-2387, 2015.

S. Lu and B. R. Cullen, Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and MicroRNA biogenesis, J. Virol, vol.78, pp.12868-12876, 2004.

J. Lu, G. Getz, E. A. Miska, E. Alvarez-saavedra, J. Lamb et al., MicroRNA expression profiles classify human cancers, Nature, vol.435, pp.834-838, 2005.

M. Lubas, C. K. Damgaard, R. Tomecki, D. Cysewski, T. H. Jensen et al., Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA, EMBO J, vol.32, pp.1855-1868, 2013.

D. J. Luciano, H. Mirsky, N. J. Vendetti, and S. Maas, RNA editing of a miRNA precursor, RNA, vol.10, pp.1174-1177, 2004.

E. Lund, S. Guttinger, A. Calado, J. E. Dahlberg, and U. Kutay, Nuclear export of microRNA precursors, Science, vol.303, pp.95-98, 2004.

J. B. Ma, K. Ye, P. , and D. J. , Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain, Nature, vol.429, pp.318-322, 2004.

L. Ma, J. Young, H. Prabhala, E. Pan, P. Mestdagh et al., miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis, Nat. Cell Biol, vol.12, pp.247-256, 2010.

I. J. Macrae, K. Zhou, F. Li, A. Repic, A. N. Brooks et al., Structural basis for double-stranded RNA processing by Dicer, Science, vol.311, pp.195-198, 2006.

M. Malecki, S. C. Viegas, T. Carneiro, P. Golik, C. Dressaire et al., The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway, EMBO J, vol.32, pp.1842-1854, 2013.

P. Mali, L. Yang, K. M. Esvelt, J. Aach, M. Guell et al., RNA-Guided Human Genome Engineering via Cas9, Science, vol.339, pp.823-826, 2013.

E. Maniataki, M. , and Z. , A human, ATP-independent, RISC assembly machine fueled by pre-miRNA, Genes Dev, vol.19, pp.2979-2990, 2005.

L. Marcinowski, M. Tanguy, A. Krmpotic, B. Rädle, V. J. Lisni? et al., Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathog, vol.8, p.1002510, 2012.

J. D. Martell, T. J. Deerinck, Y. Sancak, T. L. Poulos, V. K. Mootha et al., Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy, Nat. Biotechnol, vol.30, pp.1143-1148, 2012.

G. Martin and W. Keller, RNA-specific ribonucleotidyl transferases, RNA, vol.13, pp.1834-1849, 2007.

N. J. Martinez, G. , and R. I. , Argonaute2 expression is post-transcriptionally coupled to microRNA abundance, RNA, vol.19, pp.605-612, 2013.

M. De-la-mata, D. Gaidatzis, M. Vitanescu, M. B. Stadler, C. Wentzel et al., Potent degradation of neuronal miRNAs induced by highly complementary targets, EMBO Rep, vol.16, pp.500-511, 2015.

H. Mathys, J. Basquin, S. Ozgur, M. Czarnocki-cieciura, F. Bonneau et al., Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression, Mol. Cell, vol.54, pp.751-765, 2014.

A. Mazumder, M. Bose, A. Chakraborty, S. Chakrabarti, and S. N. Bhattacharyya, , 2013.

, A transient reversal of miRNA-mediated repression controls macrophage activation, EMBO Rep, vol.14, pp.1008-1016

V. Mehta and L. Trinkle-mulcahy, Recent advances in large-scale protein interactome mapping, 2016.

N. Meisner and W. Filipowicz, Properties of the Regulatory RNA-Binding Protein HuR and its Role in Controlling miRNA Repression, Adv. Exp. Med. Biol, vol.700, pp.106-123, 2011.

G. Meister, M. Landthaler, A. Patkaniowska, Y. Dorsett, G. Teng et al., , 2004.

, Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs, Mol Cell, vol.15, pp.185-197

G. Meister, M. Landthaler, L. Peters, P. Y. Chen, H. Urlaub et al., Identification of novel argonaute-associated proteins, Curr. Biol. CB, vol.15, pp.2149-2155, 2005.

D. Mellacheruvu, Z. Wright, A. L. Couzens, J. Lambert, N. A. St-denis et al., The CRAPome: a contaminant repository for affinity purification-mass spectrometry data, Nat. Methods, vol.10, pp.730-736, 2013.

D. L. Mellman, M. L. Gonzales, C. Song, C. A. Barlow, P. Wang et al., A PtdIns4,5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs, Nature, vol.451, pp.1013-1017, 2008.

S. A. Melo, S. Ropero, C. Moutinho, L. A. Aaltonen, H. Yamamoto et al., A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function, Nat. Genet, vol.41, pp.365-370, 2009.

S. A. Melo, C. Moutinho, S. Ropero, G. A. Calin, S. Rossi et al., A Genetic Defect in Exportin-5 Traps Precursor MicroRNAs in the Nucleus of Cancer Cells, Cancer Cell, vol.18, pp.303-315, 2010.

S. Memczak, M. Jens, A. Elefsinioti, F. Torti, J. Krueger et al., Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, vol.495, pp.333-338, 2013.

A. Mencia, S. Modamio-hoybjor, N. Redshaw, M. Morin, F. Mayo-merino et al., , 2009.

W. M. Merritt, Y. G. Lin, L. Y. Han, A. A. Kamat, W. A. Spannuth et al., Dicer, Drosha, and outcomes in patients with ovarian cancer, N. Engl. J. Med, vol.359, pp.2641-2650, 2008.

G. Michlewski, S. Guil, C. A. Semple, C. , and J. F. , Posttranscriptional regulation of miRNAs harboring conserved terminal loops, Mol. Cell, vol.32, pp.383-393, 2008.

D. U. Mick, R. B. Rodrigues, R. D. Leib, C. M. Adams, A. S. Chien et al., Proteomics of Primary Cilia by Proximity Labeling, vol.35, pp.497-512, 2015.

H. Min, Y. , and S. , Got target?: computational methods for microRNA target prediction and their extension, Exp. Mol. Med, vol.42, pp.233-244, 2010.

E. A. Miska, E. Alvarez-saavedra, A. L. Abbott, N. C. Lau, A. B. Hellman et al., Most Caenorhabditis elegans microRNAs Are Individually Not Essential for Development or Viability, PLOS Genet, vol.3, p.215, 2007.

N. Mohan, S. Ap, N. Francis, R. Anderson, and R. S. Laishram, Phosphorylation regulates the Star-PAP-PIPKI? interaction and directs specificity toward mRNA targets, Nucleic Acids Res, vol.43, pp.7005-7020, 2015.

A. M. Monteys, R. M. Spengler, J. Wan, L. Tecedor, K. A. Lennox et al., Structure and activity of putative intronic miRNA promoters, RNA, vol.16, pp.495-505, 2010.

R. D. Morin, M. D. O'connor, M. Griffith, F. Kuchenbauer, A. Delaney et al., Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells, Genome Res, vol.18, pp.610-621, 2008.

C. Much, T. Auchynnikava, D. Pavlinic, A. Buness, J. Rappsilber et al., Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein, PLOS Genet, vol.12, 2016.

N. Mukherjee, D. L. Corcoran, J. D. Nusbaum, D. W. Reid, S. Georgiev et al., Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability, Mol. Cell, vol.43, pp.327-339, 2011.

T. Nakanishi, H. Kubota, N. Ishibashi, S. Kumagai, H. Watanabe et al., Possible role of mouse poly(A) polymerase mGLD-2 during oocyte maturation, Dev. Biol, vol.289, pp.115-126, 2006.

C. T. Neilsen, G. J. Goodall, and C. P. Bracken, IsomiRs-the overlooked repertoire in the dynamic microRNAome, Trends Genet, vol.28, pp.544-549, 2012.

M. A. Newman, J. M. Thomson, and S. M. Hammond, Lin-28 interaction with the Let7 precursor loop mediates regulated microRNA processing, RNA, vol.14, pp.1539-1549, 2008.

M. A. Newman, V. Mani, and S. M. Hammond, Deep sequencing of microRNA precursors reveals extensive 3? end modification, RNA, vol.17, pp.1795-1803, 2011.

T. A. Nguyen, M. H. Jo, Y. Choi, J. Park, S. C. Kwon et al., Functional Anatomy of the Human Microprocessor, vol.161, pp.1374-1387, 2015.

K. Nishikura, Functions and regulation of RNA editing by ADAR deaminases, Annu. Rev. Biochem, vol.79, pp.321-349, 2010.

K. Nishikura, A-to-I editing of coding and non-coding RNAs by ADARs, Nat. Rev, 2016.

, Mol. Cell Biol, vol.17, pp.83-96

O. Donnell, K. A. Wentzel, E. A. Zeller, K. I. Dang, C. V. Mendell et al., c-Mycregulated microRNAs modulate E2F1 expression, Nature, vol.435, pp.839-843, 2005.

C. Okada, E. Yamashita, S. J. Lee, S. Shibata, J. Katahira et al., A high-resolution structure of the pre-microRNA nuclear export machinery, Science, vol.326, pp.1275-1279, 2009.

K. Okamura, A. Ishizuka, H. Siomi, and M. C. Siomi, Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways, Genes Dev, vol.18, pp.1655-1666, 2004.

K. Okamura, J. W. Hagen, H. Duan, D. M. Tyler, L. et al., The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila, Cell, vol.130, pp.89-100, 2007.

P. H. Olsen, A. , and V. , The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation, Dev Biol, vol.216, pp.671-680, 1999.

F. Ozsolak, L. L. Poling, Z. Wang, H. Liu, X. S. Liu et al., A Resource for the Conditional Ablation of microRNAs in the Mouse, Genes Dev, vol.22, pp.385-391, 2008.

J. Park, I. Heo, Y. Tian, D. K. Simanshu, H. Chang et al., Dicer recognizes the 5? end of RNA for efficient and accurate processing, Nature, vol.475, pp.201-205, 2011.

J. S. Parker, S. M. Roe, and D. Barford, Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex, Nature, vol.434, pp.663-666, 2005.

Z. Paroo, X. Ye, S. Chen, and Q. Liu, Phosphorylation of the Human MicroRNAGenerating Complex Mediates MAPK/Erk Signaling, Cell, vol.139, pp.112-122, 2009.

A. E. Pasquinelli, MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship, Nat. Rev. Genet, vol.13, pp.271-282, 2012.

R. F. Pass, K. B. Fowler, S. B. Boppana, W. J. Britt, and S. Stagno, Congenital cytomegalovirus infection following first trimester maternal infection: symptoms at birth and outcome, J. Clin. Virol. Off. Publ. Pan Am. Soc. Clin. Virol, vol.35, pp.216-220, 2006.

P. Pawlica, W. N. Moss, and J. A. Steitz, Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region, RNA, vol.22, pp.1181-1189, 2016.

Z. Peng, Y. Cheng, B. C. Tan, L. Kang, Z. Tian et al., Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome, Nat. Biotechnol, vol.30, pp.253-260, 2012.

J. Pfaff, J. Hennig, F. Herzog, R. Aebersold, M. Sattler et al., Structural features of Argonaute-GW182 protein interactions. Proc. Natl. Acad. Sci, 2013.

U. S. , , vol.110, pp.3770-3779

S. Pfeffer, A. Sewer, M. Lagos-quintana, R. Sheridan, C. Sander et al., Identification of microRNAs of the herpesvirus family, Nat. Methods, vol.2, pp.269-276, 2005.

D. Piedade and J. M. Azevedo-pereira, The Role of microRNAs in the Pathogenesis of Herpesvirus Infection, Viruses, vol.8, 2016.

R. S. Pillai, S. N. Bhattacharyya, C. G. Artus, T. Zoller, N. Cougot et al., Inhibition of translational initiation by Let-7 MicroRNA in human cells, Science, vol.309, pp.1573-1576, 2005.

R. S. Pillai, S. N. Bhattacharyya, and W. Filipowicz, Repression of protein synthesis by miRNAs: how many mechanisms?, Trends Cell Biol, vol.17, pp.118-126, 2007.

M. Pirouz, P. Du, M. Munafò, G. , and R. I. , Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs, Cell Rep, 2016.

L. De-pontual, E. Yao, P. Callier, L. Faivre, V. Drouin et al., Germline deletion of the miR17[sim]92 cluster causes skeletal and growth defects in humans, Nat. Genet, vol.43, pp.1026-1030, 2011.

I. Poser, M. Sarov, J. R. Hutchins, J. Hériché, Y. Toyoda et al., BAC TransgeneOmics: a highthroughput method for exploration of protein function in mammals, Nat. Methods, vol.5, pp.409-415, 2008.

O. Puig, F. Caspary, G. Rigaut, B. Rutz, E. Bouveret et al., The tandem affinity purification (TAP) method: a general procedure of protein complex purification, Methods, vol.24, pp.218-229, 2001.

H. H. Qi, P. P. Ongusaha, J. Myllyharju, D. Cheng, O. Pakkanen et al., Prolyl 4-hydroxylation regulates Argonaute 2 stability, Nature, vol.455, pp.421-424, 2008.

P. Rajasethupathy, F. Fiumara, R. Sheridan, D. Betel, S. V. Puthanveettil et al., Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB, Neuron, vol.63, pp.803-817, 2009.

V. Ramachandran, C. , and X. , Degradation of microRNAs by a family of exoribonucleases in Arabidopsis, Science, vol.321, pp.1490-1492, 2008.

T. A. Reese, J. Xia, L. S. Johnson, X. Zhou, W. Zhang et al., Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts, J. Virol, vol.84, pp.10344-10353, 2010.

M. M. Reimão-pinto, V. Ignatova, T. R. Burkard, J. Hung, R. A. Manzenreither et al., , 2015.

, Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila, Mol. Cell, vol.59, pp.203-216

B. J. Reinhart, F. J. Slack, M. Basson, A. E. Pasquinelli, J. C. Bettinger et al., The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans, Nature, vol.403, pp.901-906, 2000.

G. Ren, X. Chen, Y. , and B. , Uridylation of miRNAs by hen1 suppressor1 in Arabidopsis, Curr. Biol. CB, vol.22, pp.695-700, 2012.

H. Rhee, P. Zou, N. D. Udeshi, J. D. Martell, V. K. Mootha et al., Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging, Science, vol.339, pp.1328-1331, 2013.

G. Rigaut, A. Shevchenko, B. Rutz, M. Wilm, M. Mann et al., A generic protein purification method for protein complex characterization and proteome exploration, Nat Biotechnol, vol.17, pp.1030-1032, 1999.

O. S. Rissland, A. Mikulasova, and C. J. Norbury, Efficient RNA Polyuridylation by Noncanonical Poly(A) Polymerases, Mol. Cell. Biol, vol.27, pp.3612-3624, 2007.

O. S. Rissland, S. Hong, and D. P. Bartel, MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes, Mol. Cell, vol.43, pp.993-1004, 2011.

A. Rodriguez, S. Griffiths-jones, J. L. Ashurst, B. , and A. , Identification of mammalian microRNA host genes and transcription units, Genome Res, vol.14, pp.1902-1910, 2004.

C. Romilly, C. Lays, A. Tomasini, I. Caldelari, Y. Benito et al., A non-coding RNA promotes bacterial persistence and decreases virulence by regulating a regulator in Staphylococcus aureus, PLoS Pathog, vol.10, p.1003979, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00965591

E. Rooij, . Van, L. B. Sutherland, X. Qi, J. A. Richardson et al., , 2007.

, Control of Stress-Dependent Cardiac Growth and Gene Expression by a MicroRNA, Science, vol.316, pp.575-579

K. J. Roux, Marked by association: techniques for proximity-dependent labeling of proteins in eukaryotic cells, Cell. Mol. Life Sci. CMLS, vol.70, pp.3657-3664, 2013.

K. J. Roux, D. I. Kim, M. Raida, B. , and B. , A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells, J. Cell Biol, vol.196, pp.801-810, 2012.

K. J. Roux, D. I. Kim, B. , and B. , BioID: a screen for protein-protein interactions, 2013.

, Curr. Protoc. Protein Sci. Editor. Board John E Coligan Al, vol.74

J. G. Ruby, C. H. Jan, and D. P. Bartel, Intronic microRNA precursors that bypass Drosha processing, Nature, vol.448, pp.83-86, 2007.

S. Rüdel, Y. Wang, R. Lenobel, R. Körner, H. Hsiao et al., Phosphorylation of human Argonaute proteins affects small RNA binding, Nucleic Acids Res, vol.39, pp.2330-2343, 2011.

S. Rüegger and H. Großhans, MicroRNA turnover: when, how, and why, Trends Biochem. Sci, vol.37, pp.436-446, 2012.

S. Ruegger, T. S. Miki, D. Hess, and H. Grosshans, The ribonucleotidyl transferase USIP-1 acts with SART3 to promote U6 snRNA recycling, Nucleic Acids Res, vol.43, pp.3344-3357, 2015.

T. Ruggiero, M. Trabucchi, F. De-santa, S. Zupo, B. D. Harfe et al., LPS induces KH-type splicing regulatory proteindependent processing of microRNA-155 precursors in macrophages, FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol, vol.23, pp.2898-2908, 2009.

B. M. Ryan, A. I. Robles, H. , and C. C. , Genetic variation in microRNA networks: the implications for cancer research, Nat. Rev. Cancer, vol.10, pp.389-402, 2010.

A. Rybak, H. Fuchs, L. Smirnova, C. Brandt, E. E. Pohl et al., A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment, Nat Cell Biol, vol.10, pp.987-993, 2008.

A. Rybak, H. Fuchs, K. Hadian, L. Smirnova, E. A. Wulczyn et al., 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, vol.11, p.1411, 2009.

P. Saetrom, B. S. Heale, O. Snøve, L. Aagaard, J. Alluin et al., Distance constraints between microRNA target sites dictate efficacy and cooperativity, Nucleic Acids Res, vol.35, pp.2333-2342, 2007.

D. Santhakumar, T. Forster, N. N. Laqtom, R. Fragkoudis, P. Dickinson et al., Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs, Proc. Natl. Acad. Sci. U. S. A, vol.107, pp.13830-13835, 2010.

N. T. Schirle and I. J. Macrae, The Crystal Structure of Human Argonaute2, Science, vol.336, pp.1037-1040, 2012.

M. Schmidt, S. West, and C. J. Norbury, The human cytoplasmic RNA terminal Utransferase ZCCHC11 targets histone mRNAs for degradation, RNA, vol.17, pp.39-44, 2011.

D. S. Schwarz, G. Hutvágner, T. Du, Z. Xu, N. Aronin et al., , 2003.

, Asymmetry in the assembly of the RNAi enzyme complex, Cell, vol.115, pp.199-208

D. S. Schwarz, Y. Tomari, and P. D. Zamore, The RNA-induced silencing complex Is a Mg(2+)-dependent endonuclease, Curr Biol, vol.14, pp.787-791, 2004.

C. Schweingruber, P. Soffientini, M. Ruepp, A. Bachi, and O. Mühlemann, Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID), PLOS ONE, vol.11, p.150239, 2016.

G. L. Sen and H. M. Blau, Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies, Nat. Cell Biol, vol.7, pp.633-636, 2005.

G. J. Seo, R. P. Kincaid, T. Phanaksri, J. M. Burke, J. M. Pare et al., Reciprocal inhibition between intracellular antiviral signaling and the RNAi machinery in mammalian cells, Cell Host Microbe, vol.14, pp.435-445, 2013.

P. Sethi and W. J. Lukiw, Micro-RNA abundance and stability in human brain: specific alterations in Alzheimer's disease temporal lobe neocortex, Neurosci. Lett, vol.459, pp.100-104, 2009.

B. Shen and H. M. Goodman, Uridine addition after microRNA-directed cleavage, Science, vol.306, p.997, 2004.

J. Shen, W. Xia, Y. B. Khotskaya, L. Huo, K. Nakanishi et al., EGFR modulates microRNA maturation in response to hypoxia through phosphorylation of AGO2, Nature, vol.497, pp.383-387, 2013.

C. Shin, Cleavage of the star strand facilitates assembly of some microRNAs into Ago2-containing silencing complexes in mammals, Mol. Cells, vol.26, pp.308-313, 2008.

P. Smibert, J. Yang, G. Azzam, J. Liu, L. et al., Homeostatic control of Argonaute stability by microRNA availability, Nat. Struct. Mol. Biol, vol.20, pp.789-795, 2013.

J. J. Song, S. K. Smith, G. J. Hannon, J. , and L. , Crystal structure of Argonaute and its implications for RISC slicer activity, Science, vol.305, pp.1434-1437, 2004.

A. Stark, J. Brennecke, N. Bushati, R. B. Russell, and S. M. Cohen, , 2005.

A. L. Stevenson and C. J. Norbury, The Cid1 family of non-canonical poly(A) polymerases, Yeast, vol.23, pp.991-1000, 2006.

W. Su, S. V. Slepenkov, M. K. Slevin, S. M. Lyons, M. Ziemniak et al., mRNAs containing the histone 3? stem-loop are degraded primarily by decapping mediated by oligouridylation of the 3? end, RNA, vol.19, pp.1-16, 2013.

M. R. Suh, Y. Lee, J. Y. Kim, S. K. Kim, S. H. Moon et al., Human embryonic stem cells express a unique set of microRNAs, Dev Biol, vol.270, pp.488-498, 2004.

H. I. Suzuki, K. Yamagata, K. Sugimoto, T. Iwamoto, S. Kato et al., Modulation of microRNA processing by p53, Nature, vol.460, pp.529-533, 2009.

H. I. Suzuki, A. Katsura, T. Yasuda, T. Ueno, H. Mano et al., Small-RNA asymmetry is directly driven by mammalian Argonautes, 2015.

, Mol. Biol, vol.22, pp.512-521

E. Svobodova, J. Kubikova, and P. Svoboda, , 2016.

X. Tang, Y. Zhang, L. Tucker, R. , and B. , Phosphorylation of the RNase III enzyme Drosha at Serine300 or Serine302 is required for its nuclear localization, Nucleic Acids Res, vol.38, pp.6610-6619, 2010.

X. Tang, M. Li, L. Tucker, R. , and B. , Glycogen Synthase Kinase 3 Beta (GSK3?) Phosphorylates the RNAase III Enzyme Drosha at S300 and S302, PLOS ONE, vol.6, 2011.

X. Tang, S. Wen, D. Zheng, L. Tucker, L. Cao et al., Acetylation of Drosha on the N-Terminus Inhibits Its Degradation by Ubiquitination, PLOS ONE, vol.8, 2013.

H. Thiele, J. Glandorf, and P. Hufnagel, Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction, J. Integr. Bioinforma, vol.7, p.141, 2010.

M. F. Thomas, S. Abdul-wajid, M. Panduro, J. E. Babiarz, M. Rajaram et al., Eri1 regulates microRNA homeostasis and mouse lymphocyte development and antiviral function, Blood, vol.120, pp.130-142, 2012.

M. P. Thomas, X. Liu, J. Whangbo, G. Mccrossan, K. B. Sanborn et al., Apoptosis Triggers Specific, Rapid, and Global mRNA Decay with 3? Uridylated Intermediates Degraded by DIS3L2, Cell Rep, vol.11, pp.1079-1089, 2015.

J. M. Thomson, M. Newman, J. S. Parker, E. M. Morin-kensicki, T. Wright et al., Extensive Post-Transcriptional Regulation of microRNAs and Its Implications for Cancer, Genes Dev, vol.20, pp.2202-2207, 2006.

J. E. Thornton, H. Chang, E. Piskounova, G. , and R. I. , Lin28-mediated control of let-7 microRNA expression by alternative TUTases Zcchc11 (TUT4) and Zcchc6 (TUT7), RNA, vol.18, pp.1875-1885, 2012.

S. Till, E. Lejeune, R. Thermann, M. Bortfeld, M. Hothorn et al., A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain, 2007.

, Mol. Biol, vol.14, pp.897-903

M. Trabucchi, P. Briata, M. Garcia-mayoral, A. D. Haase, W. Filipowicz et al., The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs, Nature, vol.459, pp.1010-1014, 2009.

R. Triboulet, H. Chang, R. J. Lapierre, G. , and R. I. , Post-transcriptional control of DGCR8 expression by the Microprocessor, RNA N. Y. N, vol.15, pp.1005-1011, 2009.

R. Trippe, H. Richly, and B. Benecke, Biochemical characterization of a U6 small nuclear RNA-specific terminal uridylyltransferase, Eur. J. Biochem, vol.270, pp.971-980, 2003.

R. Trippe, E. Guschina, M. Hossbach, H. Urlaub, R. Lührmann et al., , 2006.

, Identification, cloning, and functional analysis of the human U6 snRNA-specific terminal uridylyl transferase, RNA, vol.12, pp.1494-1504

L. Tuddenham and S. Pfeffer, Roles and regulation of microRNAs in cytomegalovirus infection, Biochim. Biophys. Acta, vol.1809, pp.613-622, 2011.

D. Ustianenko, D. Hrossova, D. Potesil, K. Chalupnikova, K. Hrazdilova et al., Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs, RNA, vol.19, pp.1632-1638, 2013.

S. V-vasudevan and J. A. Steitz, AU-Rich-Element-Mediated Upregulation of Translation by FXR1 and Argonaute 2, Cell, vol.128, pp.1105-1118, 2007.

S. Vasudevan, Y. Tong, and J. A. Steitz, Switching from repression to activation: microRNAs can up-regulate translation, Science, vol.318, pp.1931-1934, 2007.

S. R. Viswanathan, G. Q. Daley, G. , and R. I. , Selective blockade of microRNA processing by Lin28, Science, vol.320, pp.97-100, 2008.

T. Wada, J. Kikuchi, and Y. Furukawa, Histone deacetylase 1 enhances microRNA processing via deacetylation of DGCR8, EMBO Rep, vol.13, pp.142-149, 2012.

E. Wahle and G. S. Winkler, RNA decay machines: Deadenylation by the Ccr4-Not and Pan2-Pan3 complexes, Biochim. Biophys. Acta BBA-Gene Regul. Mech, vol.1829, pp.561-570, 2013.

G. Wan, X. Zhang, R. R. Langley, Y. Liu, X. Hu et al., DNA-Damage-Induced Nuclear Export of Precursor MicroRNAs Is Regulated by the ATM-AKT Pathway, Cell Rep, vol.3, pp.2100-2112, 2013.

S. Wang, T. Toda, R. Maccallum, A. L. Harris, and C. Norbury, Cid1, a Fission Yeast Protein Required for S-M Checkpoint Control when DNA Polymerase ? or ? Is Inactivated, Mol. Cell. Biol, vol.20, pp.3234-3244, 2000.

T. Wang, K. Birsoy, N. W. Hughes, K. M. Krupczak, Y. Post et al., Identification and characterization of essential genes in the human genome, Science, vol.350, pp.1096-1101, 2015.

X. Wang, S. Zhang, Y. Dou, C. Zhang, X. Chen et al., Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis, PLoS Genet, vol.11, p.1005091, 2015.

Y. Wang, R. Medvid, C. Melton, R. Jaenisch, and R. Blelloch, DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal, Nat. Genet, vol.39, pp.380-385, 2007.

Y. Wang, S. Juranek, H. Li, G. Sheng, G. S. Wardle et al., , 2009.

, Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes, Nature, vol.461, pp.754-761

E. A. White and D. H. Spector, Early viral gene expression and function, Human Herpesviruses: Biology, Therapy, 2007.

E. White, M. Schlackow, K. Kamieniarz-gdula, N. J. Proudfoot, and M. Gullerova, , 2014.

, Human nuclear Dicer restricts the deleterious accumulation of endogenous double-stranded RNA, Nat. Struct. Mol. Biol, vol.21, pp.552-559

M. Wickens and J. E. Kwak, A Tail Tale for U, Science, vol.319, pp.1344-1345, 2008.

R. C. Wilson, A. Tambe, M. A. Kidwell, C. L. Noland, C. P. Schneider et al., Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis, 2015.

, Mol. Cell, vol.57, pp.397-407

C. J. Wilusz and J. Wilusz, New ways to meet your (3?) end-oligouridylation as a step on the path to destruction, Genes Dev, vol.22, pp.1-7, 2008.

C. Wu, J. So, B. N. Davis-dusenbery, H. H. Qi, D. B. Bloch et al., Hypoxia Potentiates MicroRNA-Mediated Gene Silencing through Posttranslational Modification of Argonaute2, Mol. Cell. Biol, vol.31, pp.4760-4774, 2011.

H. Wu, C. Ye, D. Ramirez, and N. Manjunath, Alternative Processing of Primary microRNA Transcripts by Drosha Generates 5? End Variation of Mature microRNA, PLOS ONE, vol.4, p.7566, 2009.

S. K. Wyman, E. C. Knouf, R. K. Parkin, B. R. Fritz, D. W. Lin et al., , 2011.

B. Xhemalce, S. C. Robson, and T. Kouzarides, Human RNA Methyltransferase BCDIN3D Regulates MicroRNA Processing, Cell, vol.151, pp.278-288, 2012.

J. Xie, S. L. Ameres, R. Friedline, J. Hung, Y. Zhang et al., Long-term, efficient inhibition of microRNA function in mice using rAAV vectors, Nat. Methods, vol.9, pp.403-409, 2012.

M. Xie, M. Li, A. Vilborg, N. Lee, M. Shu et al., Mammalian 5?-Capped MicroRNA Precursors that Generate a Single MicroRNA, Cell, vol.155, pp.1568-1580, 2013.

Z. Xue, H. Yuan, J. Guo, and Y. Liu, Reconstitution of an Argonaute-dependent small RNA biogenesis pathway reveals a handover mechanism involving the RNA exosome and the exonuclease QIP, Mol. Cell, vol.46, pp.299-310, 2012.

K. S. Yan, S. Yan, A. Farooq, A. Han, L. Zeng et al., Structure and conserved RNA binding of the PAZ domain, Nature, vol.426, pp.468-474, 2003.

J. Yang, T. Maurin, N. Robine, K. D. Rasmussen, K. L. Jeffrey et al., Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis, Proc. Natl. Acad. Sci, vol.107, pp.15163-15168, 2010.

W. Yang, T. P. Chendrimada, Q. Wang, M. Higuchi, P. H. Seeburg et al., Modulation of microRNA processing and expression through RNA editing by ADAR deaminases, Nat Struct Mol Biol, vol.13, pp.13-21, 2006.

S. Yekta, I. H. Shih, and D. P. Bartel, MicroRNA-directed cleavage of HOXB8 mRNA, Science, vol.304, pp.594-596, 2004.

K. Yeom, Y. Lee, J. Han, M. R. Suh, K. et al., Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing, Nucleic Acids Res, vol.34, pp.4622-4629, 2006.

R. Yi, Y. Qin, I. G. Macara, and B. R. Cullen, Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs, Genes Dev, vol.17, pp.3011-3016, 2003.

M. Yoda, D. Cifuentes, N. Izumi, Y. Sakaguchi, T. Suzuki et al., Poly(A)-Specific Ribonuclease Mediates 3?-End Trimming of Argonaute2-Cleaved Precursor MicroRNAs, Cell Rep, vol.5, pp.715-726, 2013.

B. Yu, Z. Yang, J. Li, S. Minakhina, M. Yang et al., Methylation as a crucial step in plant microRNA biogenesis, Science, vol.307, pp.932-935, 2005.

L. Zekri, E. Huntzinger, S. Heimstädt, and E. Izaurralde, The Silencing Domain of GW182 Interacts with PABPC1 To Promote Translational Repression and Degradation of MicroRNA Targets and Is Required for Target Release, Mol. Cell. Biol, vol.29, pp.6220-6231, 2009.

Y. Zeng and B. R. Cullen, Structural requirements for pre-microRNA binding and nuclear export by Exportin 5, Nucleic Acids Res, vol.32, pp.4776-4785, 2004.

Y. Zeng, H. Sankala, X. Zhang, and P. R. Graves, Phosphorylation of Argonaute 2 at serine-387 facilitates its localization to processing bodies, Biochem. J, vol.413, pp.429-436, 2008.

P. Zhang and H. Zhang, Autophagy modulates miRNA-mediated gene silencing and selectively degrades AIN-1/GW182 in C. elegans, EMBO Rep, vol.14, pp.568-576, 2013.

H. Zhang, F. A. Kolb, L. Jaskiewicz, E. Westhof, and W. Filipowicz, Single processing center models for human Dicer and bacterial RNase III, 2004.

Z. Zhang, J. Zou, G. Wang, J. Zhang, S. Huang et al., , 2011.

, Uracils at nucleotide position 9-11 are required for the rapid turnover of miR-29 family, Nucleic Acids Res, vol.39, pp.4387-4395

Y. Zhao, Y. Yu, J. Zhai, V. Ramachandran, T. T. Dinh et al., The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation, Curr. Biol, vol.22, pp.689-694, 2012.

H. Zhou, M. L. Arcila, Z. Li, E. J. Lee, C. Henzler et al., Deep annotation of mouse iso-miR and iso-moR variation, Nucleic Acids Res, 2012.

J. T. Zipprich, S. Bhattacharyya, H. Mathys, and W. Filipowicz, Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression, RNA N. Y. N, vol.15, pp.781-793, 2009.

, MiR-30a-3p Negatively Regulates BAFF Synthesis in Systemic Sclerosis and Rheumatoid Arthritis Fibroblasts

, Lucas Philippe 1 , Ya-Zhuo Gong 1 , Seiamak Bahram 1, Jacques-Eric Gottenberg, vol.2, issue.1

I. Immunorhumatologie-moléculaire and . Umr-s_1109, France Abstract We evaluated micro (mi) RNA-mediated regulation of BAFF expression in fibroblasts using two concomitant models: (i) synovial fibroblasts (FLS) isolated from healthy controls (N) or Rheumatoid Arthritis (RA) patients; (ii) human dermal fibroblasts (HDF) isolated from healthy controls (N) or Systemic Sclerosis (SSc) patients. Using RT-qPCR and ELISA, we first showed that SScHDF synthesized and released BAFF in response to Poly(I:C) or IFN-c treatment, as previously observed in RAFLS, whereas NHDF released BAFF preferentially in response to IFN-c. Next, we demonstrated that miR-30a-3p expression was down regulated in RAFLS and SScHDF stimulated with Poly(I:C) or IFN-c. Moreover, we demonstrated that transfecting miR-30a-3p mimic in Poly(I:C)-and IFN-c-activated RAFLS and SScHDF showed a strong decrease on BAFF synthesis and release and thus B cells survival in our model. Interestingly, FLS and HDF isolated from healthy subjects express higher levels of miR-30a-3p and lower levels of BAFF than RAFLS and SScHDF. Transfection of miR-30a-3p antisense in Poly(I:C)-and IFNc-activated NFLS and NHDF upregulated BAFF secretion, confirming that this microRNA is a basal repressors of BAFF expression in cells from healthy donors. Our data suggest a critical role of miR, Centre National de Référence pour les Maladies Systémiques Autoimmunes Rares

G. Alsaleh, A. François, L. Philippe, Y. Gong, and S. Bahram, MiR-30a-3p Negatively Regulates BAFF Synthesis in Systemic Sclerosis and Rheumatoid Arthritis Fibroblasts, PLoS ONE, vol.9, issue.10, p.111266, 2014.

. Alsaleh, This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited, 2014.

, Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files

, Jean Sibilia's work was supported by grants from Bristol Myers Squibb, Roche, Pfizer, Courtin Foundation and CAMPLP. Sébastien Pfeffer's work was supported by the European Research Council (ERC-StG-260767) and Agence Nationale pour la Recherche (labex netRNA, ANR-10-LABX-36). The funders had no role in study design, data collection and analysis

, Competing Interests: The authors have declared that no competing interests exist

, Email: galfarhan@unistra.fr . These authors contributed equally to this work

, L-glutamine, penicillin, streptomycin, amphotericin B, TRIzol reagent and DiOC 6 (3,39-Dihexyloxacarbocyanine Iodide) were from Invitrogen, LPS from Salmonella abortus equi and Propidium Iodide (PI) solution was obtained from Sigma Aldrich

, The miScript System, miRNA mimc and Allstars negative control siRNA were obtained from Qiagen (Courtabeuf, France). miR-30a-3p antagonists were from Fisher scientific (Illkirch Cedex, France), The enzyme immunoassay kits for human BAFF, APRIL and IL-6 detection and recombinant IFN-c were from R&D systems

F. Mackay, P. Schneider, P. Rennert, and J. Browning, BAFF AND APRIL: a tutorial on B cell survival, Annu Rev Immunol, vol.21, pp.231-264, 2003.

B. Nardelli, O. Belvedere, V. Roschke, P. A. Moore, and H. S. Olsen, Synthesis and release of B-lymphocyte stimulator from myeloid cells, Blood, vol.97, pp.198-204, 2001.

P. Scapini, B. Nardelli, G. Nadali, F. Calzetti, and G. Pizzolo, G-CSFstimulated neutrophils are a prominent source of functional BLyS, J Exp Med, vol.197, pp.297-302, 2003.

M. Krumbholz, D. Theil, T. Derfuss, A. Rosenwald, and F. Schrader, BAFF is produced by astrocytes and up-regulated in multiple sclerosis lesions and primary central nervous system lymphoma, J Exp Med, vol.201, pp.195-200, 2005.

S. L. Kalled, The role of BAFF in immune function and implications for autoimmunity, Immunol Rev, vol.204, pp.43-54, 2005.

F. Mackay, S. A. Woodcock, P. Lawton, C. Ambrose, and M. Baetscher, Mice Transgenic for Baff Develop Lymphocytic Disorders along with Autoimmune Manifestations, Journal of Experimental Medicine, vol.190, pp.1697-1710, 1999.

T. M. Seyler, Y. W. Park, S. Takemura, R. J. Bram, and P. J. Kurtin, BLyS and APRIL in rheumatoid arthritis, J Clin Invest, vol.115, pp.3083-3092, 2005.

F. Mackay and P. Schneider, Cracking the BAFF code, Nat Rev Immunol, vol.9, pp.491-502, 2009.

J. Pers, C. Daridon, V. Devauchelle, S. Jousse, and A. Saraux, BAFF overexpression is associated with autoantibody production in autoimmune diseases, Ann N Y Acad Sci, vol.1050, pp.34-39, 2005.

T. Matsushita, M. Hasegawa, Y. Matsushita, T. Echigo, and T. Wayaku, Elevated serum BAFF levels in patients with localized scleroderma in contrast to other organ-specific autoimmune diseases, Exp Dermatol, vol.16, pp.87-93, 2007.

T. Matsushita, M. Fujimoto, M. Hasegawa, C. Tanaka, and S. Kumada, Elevated serum APRIL levels in patients with systemic sclerosis: distinct profiles of systemic sclerosis categorized by APRIL and BAFF, J Rheumatol, vol.34, pp.2056-2062, 2007.

M. Zhang, K. Ko, Q. Lam, C. Lo, and G. Srivastava, Expression and function of TNF family member B cell-activating factor in the development of autoimmune arthritis, Int Immunol, vol.17, pp.1081-1092, 2005.

G. Alsaleh, A. François, A. Knapp, J. Schickel, and J. Sibilia, Synovial fibroblasts promote immunoglobulin class switching by a mechanism involving BAFF, Eur J Immunol, vol.41, pp.2113-2122, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00605025

K. P. Baker, B. M. Edwards, S. H. Main, G. H. Choi, and R. E. Wager, Generation and characterization of LymphoStat-B, a human monoclonal antibody that antagonizes the bioactivities of B lymphocyte stimulator, Arthritis Rheum, vol.48, pp.3253-3265, 2003.

A. C. Chan, B cell immunotherapy in autoimmunity-2010 update, Mol Immunol, vol.48, pp.1344-1347, 2011.

P. K. Chugh and B. S. Kalra, Belimumab: targeted therapy for lupus, Int J Rheum Dis, vol.16, pp.4-13, 2013.

Q. Jing, S. Huang, S. Guth, T. Zarubin, and A. Motoyama, Involvement of microRNA in AU-rich element-mediated mRNA instability, Cell, vol.120, pp.623-634, 2005.

A. J. Asirvatham, W. J. Magner, and T. B. Tomasi, ) miRNA regulation of cytokine genes, Cytokine, vol.45, pp.58-69, 2009.

L. Philippe, G. Alsaleh, A. Pichot, E. Ostermann, and G. Zuber, MiR-20a regulates ASK1 expression and TLR4-dependent cytokine release in rheumatoid fibroblast-like synoviocytes, Ann Rheum Dis, vol.72, pp.1071-1079, 2013.

G. Alsaleh, G. Suffert, N. Semaan, T. Juncker, and L. Frenzel, Bruton's tyrosine kinase is involved in miR-346-related regulation of IL-18 release by lipopolysaccharide-activated rheumatoid fibroblast-like synoviocytes, J Immunol, vol.182, pp.5088-5097, 2009.

N. Zamzami, P. Marchetti, M. Castedo, C. Zanin, and J. L. Vayssière, Reduction in mitochondrial potential constitutes an early irreversible step of programmed lymphocyte death in vivo, J Exp Med, vol.181, pp.1661-1672, 1995.

G. Alsaleh, L. Messer, N. Semaan, N. Boulanger, and J. Gottenberg, BAFF synthesis by rheumatoid synoviocytes is positively controlled by alpha5beta1 integrin stimulation and is negatively regulated by tumor necrosis factor alpha and Toll-like receptor ligands, Arthritis Rheum, vol.56, pp.3202-3214, 2007.

T. Kishimoto, Interleukin-6: from basic science to medicine-40 years in immunology, Annu Rev Immunol, vol.23, pp.1-21, 2005.

A. Finnegan, S. Ashaye, and K. M. Hamel, B effector cells in rheumatoid arthritis and experimental arthritis, Autoimmunity, vol.45, pp.353-363, 2012.

I. Moisini and A. Davidson, BAFF: a local and systemic target in autoimmune diseases, Clin Exp Immunol, vol.158, pp.155-163, 2009.

J. Ohata, N. J. Zvaifler, M. Nishio, D. L. Boyle, and S. L. Kalled, Fibroblastlike synoviocytes of mesenchymal origin express functional B cell-activating factor of the TNF family in response to proinflammatory cytokines, J Immunol, vol.174, pp.864-870, 2005.

M. Ittah, C. Miceli-richard, J. Gottenberg, J. Sellam, and P. Eid, Viruses induce high expression of BAFF by salivary gland epithelial cells through TLRand type-I IFN-dependent and-independent pathways, Eur J Immunol, vol.38, pp.1058-1064, 2008.

A. Kato, A. Q. Truong-tran, A. L. Scott, K. Matsumoto, and R. P. Schleimer, Airway epithelial cells produce B cell-activating factor of TNF family by an IFNbeta-dependent mechanism, J Immunol, vol.177, pp.7164-7172, 2006.

S. Zhang, E. Jouanguy, V. Sancho-shimizu, V. Bernuth, H. Yang et al., Human Toll-like receptor-dependent induction of interferons in protective immunity to viruses, Immunol Rev, vol.220, pp.225-236, 2007.

G. Ferraccioli and B. Tolusso, Infections, B cell receptor activation and autoimmunity: different check-point impairments lead to autoimmunity, clonal B cell expansion and fibrosis in different immunological settings, Autoimmun Rev, vol.7, pp.109-113, 2007.

M. Ittah, C. Miceli-richard, J. Gottenberg, J. Sellam, and C. Lepajolec, B-cell-activating factor expressions in salivary epithelial cells after dsRNA virus infection depends on RNA-activated protein kinase activation, Eur J Immunol, vol.39, pp.1271-1279, 2009.

S. Mukherji, M. S. Ebert, G. Zheng, J. S. Tsang, and P. A. Sharp, MicroRNAs can generate thresholds in target gene expression, Nat Genet, vol.43, pp.854-859, 2011.

J. Stanczyk, D. Pedrioli, F. Brentano, O. Sanchez-pernaute, and C. Kolling, Altered expression of MicroRNA in synovial fibroblasts and synovial tissue in rheumatoid arthritis, Arthritis Rheum, vol.58, pp.1001-1009, 2008.

A. Ceribelli, M. A. Nahid, M. Satoh, and E. Chan, MicroRNAs in rheumatoid arthritis, FEBS Lett, vol.585, pp.3667-3674, 2011.

Y. Dai, Y. Huang, M. Tang, T. Lv, and C. Hu, Microarray analysis of microRNA expression in peripheral blood cells of systemic lupus erythematosus patients, Lupus, vol.16, pp.939-946, 2007.

Y. Tang, X. Luo, H. Cui, X. Ni, and M. Yuan, MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins, Arthritis Rheum, vol.60, pp.1065-1075, 2009.

H. Li, R. Yang, X. Fan, T. Gu, and Z. Zhao, MicroRNA array analysis of microRNAs related to systemic scleroderma, Rheumatol Int, vol.32, pp.307-313, 2012.

B. Maurer, J. Stanczyk, A. Jüngel, A. Akhmetshina, and M. Trenkmann, MicroRNA-29, a key regulator of collagen expression in systemic sclerosis, Arthritis Rheum, vol.62, pp.1733-1743, 2010.

O. Neill, L. A. Sheedy, F. J. Mccoy, and C. E. , MicroRNAs: the fine-tuners of Tolllike receptor signalling, Nat Rev Immunol, vol.11, pp.163-175, 2011.

G. Alsaleh, G. Suffert, N. Semaan, T. Juncker, and L. Frenzel, Bruton's tyrosine kinase is involved in miR-346-related regulation of IL-18 release by lipopolysaccharide-activated rheumatoid fibroblast-like synoviocytes, J Immunol, vol.182, pp.5088-5097, 2009.

N. Semaan, L. Frenzel, G. Alsaleh, G. Suffert, and J. Gottenberg, miR346 controls release of TNF-a protein and stability of its mRNA in rheumatoid arthritis via tristetraprolin stabilization, PLoS ONE, vol.6, 2011.

W. Stohl, J. T. Merrill, J. D. Mckay, J. R. Lisse, and Z. J. Zhong, Efficacy and safety of belimumab in patients with rheumatoid arthritis: a phase II, randomized, double-blind, placebo-controlled, dose-ranging Study, J Rheumatol, vol.40, pp.579-589, 2013.

H. Janssen, H. W. Reesink, E. J. Lawitz, S. Zeuzem, and M. Rodriguez-torres, Treatment of HCV Infection by Targeting MicroRNA, N Engl J Med, 2013.

. Lee, Introduction Les microARN (miARN) sont des petits ARN non codants d'environ 22 nucléotides III Drosha, 2003.

(. Chendrimada, Maniataki and Mourelatos, 2005) qui va guider le complexe effecteur RISC (RNA des miARN, protéine Argonaute (AGO), 2005.

;. Cependant and . Baccarini, information concernant la régulation de la stabilité des miARN. Ces derniers ont en effet longtemps été considérés comme des molécules très stables, 2007.

. Marcinowski, Ainsi, il a été observé au laboratoire qu'au cours d'une infection par le cytomégalovirus murin (MCMV), un transcrit viral (m169) induit la dégradation spécifique d'un miARN cellulaire (miR-27) suite à la formation d'espèces plus courtes ('trimming') et plus longues ('tailing') de, Toutefois, plusieurs exemples illustrant la nécessité de contrôler la stabilité des miARN, notamment en cas d'adaptation aux stress biotiques et abiotiques, commencent à apparaître dans la littérature, 2012.

. Lian, régulation des messagers cibles comme TNRC6B, p.4, 2009.

J. and I. Jinek, , 2009.

, Par la suite, nous avons voulu créer une lignée stable exprimant la protéine de fusion

*. Bira and . Liu, Pour créer cette lignée, nous sommes partis d'une lignée cellulaire appelée MEF-AGO2-/-, une lignée de fibroblastes embryonnaires de souris (MEF) issue de souris 'knock-out' pour AGO2, 2004.

S. L. Ameres, M. D. Horwich, J. H. Hung, J. Xu, M. Ghildiyal et al., Target RNA-directed trimming and tailing of small silencing RNAs, Science, vol.328, pp.1534-1539, 2010.

A. Baccarini, H. Chauhan, T. J. Gardner, A. D. Jayaprakash, R. Sachidanandam et al., Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells, Curr. Biol, vol.21, pp.369-376, 2011.

S. Bail, M. Swerdel, H. Liu, X. Jiao, L. A. Goff et al., , 2010.

, Differential regulation of microRNA stability, RNA N. Y. N, vol.16, pp.1032-1039

H. Chang, R. Triboulet, J. E. Thornton, G. , and R. I. , A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway, Nature, vol.497, pp.244-248, 2013.

T. P. Chendrimada, R. I. Gregory, E. Kumaraswamy, J. Norman, N. Cooch et al., TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing, Nature, vol.436, pp.740-744, 2005.

C. R. Faehnle, J. Walleshauser, J. , and L. , Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway, Nature, vol.514, pp.252-256, 2014.

M. P. Gantier, C. E. Mccoy, I. Rusinova, D. Saulep, D. Wang et al., Analysis of microRNA turnover in mammalian cells following Dicer1 ablation, Nucleic Acids Res, vol.39, pp.5692-5703, 2011.

R. I. Gregory, T. P. Chendrimada, N. Cooch, and R. Shiekhattar, Human RISC couples microRNA biogenesis and posttranscriptional gene silencing, Cell, vol.123, pp.631-640, 2005.

M. Ha, K. , and V. N. , Regulation of microRNA biogenesis, Nat. Rev. Mol. Cell Biol, vol.15, pp.509-524, 2014.

G. Haas, S. Cetin, M. Messmer, B. Chane-woon-ming, O. Terenzi et al., Identification of factors involved in target RNAdirected microRNA degradation, Nucleic Acids Res, vol.44, pp.2873-2887, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02294219

G. Hutvágner, J. Mclachlan, A. E. Pasquinelli, E. Balint, T. Tuschl et al., A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA, Science, vol.293, pp.834-838, 2001.

S. Iwasaki, M. Kobayashi, M. Yoda, Y. Sakaguchi, S. Katsuma et al., Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes, Mol. Cell, vol.39, pp.292-299, 2010.

M. Jinek, M. R. Fabian, S. M. Coyle, N. Sonenberg, and J. A. Doudna, Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation, Nat. Struct. Mol. Biol, vol.17, pp.238-240, 2010.

M. Johnston, M. Geoffroy, A. Sobala, R. Hay, and G. Hutvagner, HSP90 protein stabilizes unloaded argonaute complexes and microscopic P-bodies in human cells, Mol. Biol. Cell, vol.21, pp.1462-1469, 2010.

S. Jonas and E. Izaurralde, The role of disordered protein regions in the assembly of decapping complexes and RNP granules, Genes Dev, vol.27, pp.2628-2641, 2013.

S. Jonas and E. Izaurralde, Towards a molecular understanding of microRNAmediated gene silencing, Nat. Rev. Genet, vol.16, pp.421-433, 2015.

A. ?abno, Z. Warkocki, T. Kuli?ski, P. S. Krawczyk, K. Bijata et al., Perlman syndrome nuclease DIS3L2 controls cytoplasmic noncoding RNAs and provides surveillance pathway for maturing snRNAs, Nucleic Acids Res, 2016.

Y. Lee, C. Ahn, J. Han, H. Choi, J. Kim et al., The nuclear RNase III Drosha initiates microRNA processing, Nature, vol.425, pp.415-419, 2003.

S. L. Lian, S. Li, G. X. Abadal, B. A. Pauley, M. J. Fritzler et al., The Cterminal half of human Ago2 binds to multiple GW-rich regions of GW182 and requires GW182 to mediate silencing, RNA, vol.15, pp.804-813, 2009.

J. Liu, M. A. Carmell, F. V. Rivas, C. G. Marsden, J. M. Thomson et al., Argonaute2 is the catalytic engine of mammalian RNAi, Science, vol.305, pp.1437-1441, 2004.

M. Lubas, C. K. Damgaard, R. Tomecki, D. Cysewski, T. H. Jensen et al., Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA, EMBO J, vol.32, pp.1855-1868, 2013.

M. Malecki, S. C. Viegas, T. Carneiro, P. Golik, C. Dressaire et al., The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway, EMBO J, vol.32, pp.1842-1854, 2013.

E. Maniataki, M. , and Z. , A human, ATP-independent, RISC assembly machine fueled by pre-miRNA, Genes Dev, vol.19, pp.2979-2990, 2005.

L. Marcinowski, M. Tanguy, A. Krmpotic, B. Rädle, V. J. Lisni? et al., Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathog, vol.8, p.1002510, 2012.

V. Mehta and L. Trinkle-mulcahy, Recent advances in large-scale protein interactome mapping, 2016.

J. Pfaff, J. Hennig, F. Herzog, R. Aebersold, M. Sattler et al., Structural features of Argonaute-GW182 protein interactions. Proc. Natl. Acad. Sci, 2013.

U. S. , , vol.110, pp.3770-3779

M. Pirouz, P. Du, M. Munafò, G. , and R. I. , Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs, Cell Rep, 2016.

E. Rooij, . Van, L. B. Sutherland, X. Qi, J. A. Richardson et al., , 2007.

, Control of Stress-Dependent Cardiac Growth and Gene Expression by a MicroRNA, Science, vol.316, pp.575-579

K. J. Roux, D. I. Kim, M. Raida, B. , and B. , A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells, J. Cell Biol, vol.196, pp.801-810, 2012.

D. Ustianenko, D. Hrossova, D. Potesil, K. Chalupnikova, K. Hrazdilova et al., Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs, RNA, vol.19, pp.1632-1638, 2013.

L. Zekri, E. Huntzinger, S. Heimstädt, and E. Izaurralde, The Silencing Domain of GW182 Interacts with PABPC1 To Promote Translational Repression and Degradation of MicroRNA Targets and Is Required for Target Release, Mol. Cell. Biol, vol.29, pp.6220-6231, 2009.