microRNA target predictions in animals (original) (raw)
Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. & Cohen, S.M. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell113, 25–36 (2003). ArticleCAS Google Scholar
Stark, A., Brennecke, J., Russell, R.B. & Cohen, S.M. Identification of Drosophila microRNA targets. PLoS Biol.1, E60 (2003). Article Google Scholar
Enright, A.J. et al. MicroRNA targets in Drosophila. Genome Biol.5, R1 (2003). Article Google Scholar
Rajewsky, N. & Socci, N.D. Computational identification of microRNA targets. Dev. Biol.267, 529–535 (2004). ArticleCAS Google Scholar
John, B. et al. Human MicroRNA targets. PLoS Biol.2, e363 (2004). Article Google Scholar
Kiriakidou, M. et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev.18, 1165–1178 (2004). ArticleCAS Google Scholar
Lai, E.C. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet.30, 363–364 (2002). ArticleCAS Google Scholar
Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). ArticleCAS Google Scholar
Bentwich, I. Prediction and validation of microRNAs and their targets. FEBS Lett.579, 5904–5910 (2005). ArticleCAS Google Scholar
Sood, P., Krek, A., Zavolan, M., Macino, G. & Rajewsky, N. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc. Natl. Acad. Sci. USA, published online 13 February 2006 (doi:10.1073/pnas.0511045103).
Wu, L., Fan, J. & Belasco, J.G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl. Acad. Sci. USA103, 4034–4039 (2006). ArticleCAS Google Scholar
Giraldez, A.J. et al. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science312, 75–79 (2006). ArticleCAS Google Scholar
Robins, H. & Press, W.H. Human microRNAs target a functionally distinct population of genes with AT-rich 3′ UTRs. Proc. Natl. Acad. Sci. USA102, 15557–15562 (2005). ArticleCAS Google Scholar
Brennecke, J., Stark, A., Russell, R.B. & Cohen, S.M. Principles of microRNA-target recognition. PLoS Biol.3, e85 (2005). Article Google Scholar
Grün, D., Wang, Y.L., Langenberger, D., Gunsalus, K.C. & Rajewsky, N. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol.1, e13 (2005). Article Google Scholar
Krek, A. et al. Combinatorial microRNA target predictions. Nat. Genet.37, 495–500 (2005). ArticleCAS Google Scholar
Lewis, B.P., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell120, 15–20 (2005). ArticleCAS Google Scholar
Stark, A., Brennecke, J., Bushati, N., Russell, R.B. & Cohen, S.M. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell123, 1133–1146 (2005). ArticleCAS Google Scholar
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature434, 338–345 (2005). ArticleCAS Google Scholar
Lall, S. et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol.16, 460–471 (2006). ArticleCAS Google Scholar
Robins, H., Li, Y. & Padgett, R.W. Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. USA102, 4006–4009 (2005). ArticleCAS Google Scholar
Zhao, Y., Samal, E. & Srivastava, D. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature436, 214–220 (2005). ArticleCAS Google Scholar
Farh, K.K. et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science310, 1817–1821 (2005). ArticleCAS Google Scholar
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res.31, 3406–3415 (2003). ArticleCAS Google Scholar
Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. Fast and effective prediction of microRNA/target duplexes. RNA10, 1507–1517 (2004). ArticleCAS Google Scholar
Chan, C.S., Elemento, O. & Tavazoie, S. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput. Biol.1, e69 (2005). Article Google Scholar
Watanabe, Y. et al. Computational analysis of microRNA targets in Caenorhabditis elegans. Gene365, 2–10 (2006). ArticleCAS Google Scholar
Sethupathy, P., Corda, B. & Hatzigeorgiou, A.G. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA12, 192–197 (2006). ArticleCAS Google Scholar
Shahi, P. et al. Argonaute–a database for gene regulation by mammalian microRNAs. Nucleic Acids Res.34, D115–D118 (2006). ArticleCAS Google Scholar
Hsu, P.W. et al. miRNAMAP: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res.34, D135–D139 (2006). ArticleCAS Google Scholar
Montgomery, S.B. et al. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics22, 637–640 (2006). ArticleCAS Google Scholar
Doench, J.G. & Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev.18, 504–511 (2004). ArticleCAS Google Scholar
Lindblad-Toh, K. et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature438, 803–819 (2005). ArticleCAS Google Scholar
Lim, L.P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature433, 769–773 (2005). ArticleCAS Google Scholar
Bagga, S. et al. Regulation by let-7 and lin-4 microRNAs results in target mRNA degradation. Cell122, 553–563 (2005). ArticleCAS Google Scholar
Krutzfeldt, J. et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature438, 685–689 (2005). Article Google Scholar
Bartel, D.P. & Chen, C.Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet.5, 396–400 (2004). ArticleCAS Google Scholar
Bussemaker, H.J., Li, H. & Siggia, E.D. Regulatory element detection using correlation with expression. Nat. Genet.27, 167–171 (2001). ArticleCAS Google Scholar
Foat, B.C., Houshmandi, S.S., Olivas, W.M. & Bussemaker, H.J. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl. Acad. Sci. USA102, 17675–17680 (2005). ArticleCAS Google Scholar
Aravin, A.A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell5, 337–350 (2003). ArticleCAS Google Scholar
Chen, P.Y. et al. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev.19, 1288–1293 (2005). ArticleCAS Google Scholar
Baskerville, S. & Bartel, D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA11, 241–247 (2005). ArticleCAS Google Scholar
Barad, O. et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res.14, 2486–2494 (2004). ArticleCAS Google Scholar
Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). ArticleCAS Google Scholar
Hammond, S.M. microRNA detection comes of age. Nat. Methods3, 12–3 (2006). ArticleCAS Google Scholar
Burgler, C. & Macdonald, P.M. Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. BMC Genomics6, 88 (2005). Article Google Scholar
Poy, M.N. et al. A pancreatic islet-specific microRNA regulates insulin secretion. Nature432, 226–230 (2004). ArticleCAS Google Scholar
Vella, M.C. et al. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′ UTR. Genes Dev.18, 132–137 (2004). ArticleCAS Google Scholar