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The impact of microRNAs on protein output Nature 455, 64-71 47. Gottesman, S sof Escherichia coli roles and mechanism 13. Selbach,Meta. Widespread changes in protein synthesis induced by microRNAs. 48. Huelsken, J, vogel, R- Erdmann, B, Cotsarelis, G. Birchmeier, W. B-Cat 14. Bartel, D P MicroRNAs: target recognition and regulatory functions. Cell 136, 49. Park, H C et al Analysis of upstream elements in the HuC promoter leads to the 15. Krek, A et al. Combinatorial microRNA target predictions. Nature Genet 37, establishment of transgenic zebrafish with fluorescent neurons. Dev Biol. 227. 79-293(2000 . 6.Lewis,BP, Burge,CB&Bartel, D.P. Conserved seed pairing, often flanked by 50. Peri, F& Nusslein- Volhard, C Live imaging of neuronal degradation by microglia that thousands of human genes are microRNA targets. Cell reveals a role for vo-ATPase al in phagosomal fusion in vivo Ce/l 133, 916-927 edma r c. nsn of several mamm4343835)and3y51)水WR成C四,厂 RNAs are abundant, conserved, and associated with ALU 18mBN19.228 Supplementary Information is available in the online version of the cular human CDRlas for our zebrafish experiments We t ndependent function of gene and pseudogene mRNAs facility. We thankA. lvanov for assisting in bioinformaticanalysis. NRtha 22. Tay. suppressor PTEN by ing funding sources: PhD program endogenous mRNAs Cell 147, 344-357(2011). Mr:RM project 1210182, MIRNAs as therapeutic targets(AE): DFG trog@T M, F.T. LH.G): the 23. Cesana, M. et al A long noncoding RNA controls muscle differentiation b functioning as a competing endogenous RNA Cell 147, 358-369(2011) KF0218(UZ): Helmholtz Association for the ' MDC Systems Biology Network, MSBI 24. 2b R&&-R85ha P A Emerging roles for natural microRNA sponges. CulT. Biol Bertin(K. FIN.). Funding for the group of ML is supported by BMBF-funding for the 25. Vivancos deep sequencing of the transcriptome Genome Res 20, 989-999(2010) Author Contributions S M, MJ, AE and F T contributed equally. S M. performed 26. Huang, R et al. An RNA-Seq strategy to detect the complete co nscriptome including full-length imprinted macro ncRNAs. PLOS ONE 6, man out most of the computation, 27. Kent W.J.etal. The human genome browser at UcSC Genome Res, 12.,996-1006 AG pARC P R, erformed all northem experiments. LH.G. and M. M. designed and carried out the single molecule experi sova, T& Maglott, D R NCBI Reference Sequence(Refseq): a UZ. performed the mouse part together with A L K contributed the zebrafish experiments upervised by FIN N.R. designed and supervised the project N.R. and MJ. wrote the Nucleic Acids Res. 33, D501-D504(2005) 29. Cabili, M. N. et al. Integrative a RNAs reveals global properties and specific subclasses. Genes Dev. 25, Author Information Sequencing data have been de 1915-1927(2011) 30.SuzukiH.etal.CharacterizationofRnaSeR-digestedcellularRnasourcethatwww.nature.coma are no competing financial interests. consists of lariat and circular RNAs from splicing. Nucleic Acids Res 34, Readers are welcome to comment on the online version of the paper Correspondence e63(2006 and requests for materials should be addressed to N.R. (rajewsky@mdc- berlin. de). 6I NATURE I VOL 00000 MONTH 2013 @2013 Macmillan Publishers Limited. All rights reservedwere injected. Confocal imaging was performed using Carl Zeiss MicroImaging. Reduced midbrain development was defined as .50% smaller than the mean size of controls. Each experimental group was evaluated in at least three independent experiments; a minimum of 80 individual embryos per group was examined. Full Methods and any associated references are available in the online version of the paper. Received 11 September 2012; accepted 24 January 2013. 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AcknowledgementsWe thankM. Feldkamp and C. Langnick (laboratory ofW. Chen) for Illumina sequencing runs. We thank J. Kjems for sending us a plasmid encoding circular human CDR1as for our zebrafish experiments. We thank K. Meier for technical assistance with zebrafish experiments and A. Sporbert from the confocal imaging facility.We thank A. Ivanov for assisting in bioinformatic analysis. N.R. thanks E. Westhof for useful discussions. We acknowledge the following funding sources: PhD program of the Max-Delbru¨ck-Center (MDC) (S.M., F.T., L.H.G.); the MDC-NYU exchange program (M.M.); BMBF project 1210182, ‘MiRNAs as therapeutic targets’ (A.E.); DFG for KFO218 (U.Z.); Helmholtz Association for the ‘MDC Systems Biology Network’, MSBN (S.D.M.); BMBF support for the DZHK (F.l.N. and N.R.); Center for Stroke Research Berlin (J.K., F.l.N.). Funding for the group of M.L. is supported by BMBF-funding for the Berlin Institute for Medical Systems Biology (0315362C). Author Contributions S.M., M.J., A.E. and F.T. contributed equally. S.M. performed many experiments, assisted by L.M. M.J. and A.E. carried out most of the computation, with contributions from N.R. and S.D.M. F.T. performed the circRNA validation experiments. A.R. performed all northern experiments. L.H.G. and M.M. contributed AGO PAR-CLIP experiments and HEK293 ribominus data, supervised by M.L. C.K. designed and carried out the single molecule experiments, in part together with A.L. U.Z. performed the mouse experiments. J.K. contributed the zebrafish experiments, supervised by F.l.N. N.R. designed and supervised the project. N.R. and M.J. wrote the paper. Author Information Sequencing data have been deposited at GEO under accession number GSE43574. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests. Readers are welcome to comment on the online version of the paper. Correspondence and requests for materials should be addressed to N.R. (rajewsky@mdc-berlin.de). RESEARCH ARTICLE 6 | NATURE | VOL 000 | 00 MONTH 2013 ©2013 Macmillan Publishers Limited. All rights reserved