Biogenesis of small RNAs in animals (original) (raw)
Lee, R. C., Feinbaum, R. L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell75, 843–854 (1993). ArticleCASPubMed Google Scholar
Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell75, 855–862 (1993). CASPubMed Google Scholar
Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science294, 858–862 (2001). CASPubMed Google Scholar
Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science294, 862–864 (2001). CASPubMed Google Scholar
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science294, 853–858 (2001). CASPubMed Google Scholar
Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science309, 1567–1569 (2005). CASPubMed Google Scholar
Lai, E. C., Tomancak, P., Williams, R. W. & Rubin, G. M. Computational identification of Drosophila microRNA genes. Genome Biol.4, R42 (2003). PubMedPubMed Central Google Scholar
Nam, J. W. et al. Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res.33, 3570–3581 (2005). CASPubMedPubMed Central Google Scholar
Li, S. C., Pan, C. Y. & Lin, W. C. Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics7, 164 (2006). CASPubMedPubMed Central Google Scholar
Huang, T. H. et al. MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics8, 341 (2007). PubMedPubMed Central Google Scholar
Chu, C. Y. & Rana, T. M. Small RNAs: regulators and guardians of the genome. J. Cell Physiol.213, 412–419 (2007). CASPubMed Google Scholar
Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet.9, 102–114 (2008). CASPubMed Google Scholar
Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science313, 320–324 (2006). The first paper to describe that piRNAs are produced in a Dicer-independent manner. The authors also reported thatD. melanogasterpiRNAs are modified at their 3′ ends. CASPubMed Google Scholar
Watanabe, T. et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature453, 539–543 (2008). CASPubMed Google Scholar
Tam, O. H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature453, 534–538 (2008). References 15 and 16 contributed to the identification of many endo-siRNAs in mouse oocytes and also to the proposal of the functions of pseudogenes in silencing the parental genes. CASPubMedPubMed Central Google Scholar
Babiarz, J. E., Ruby, J. G., Wang, Y., Bartel, D. P. & Blelloch, R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev.22, 2773–2785 (2008). CASPubMedPubMed Central Google Scholar
Okamura, K. et al. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature453, 803–806 (2008). CASPubMedPubMed Central Google Scholar
Kawamura, Y. et al. Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature453, 793–797 (2008). CASPubMed Google Scholar
Jones-Rhoades, M. W., Bartel, D. P. & Bartel, B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol.57, 19–53 (2006). CASPubMed Google Scholar
Mallory, A. C. & Vaucheret, H. Functions of microRNAs and related small RNAs in plants. Nature Genet.38, S31–S36 (2006). CASPubMed Google Scholar
Zhang, B., Pan, X., Cobb, G. P. & Anderson, T. A. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol.289, 3–16 (2006). CASPubMed Google Scholar
Verdel, A. & Moazed, D. RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett.579, 5872–5878 (2005). CASPubMed Google Scholar
Kim, V. N. MicroRNA biogenesis: coordinated cropping and dicing. Nature Rev. Mol. Cell Biol.6, 376–385 (2005). CAS Google Scholar
Kim, D. H., Saetrom, P., Snove, O. Jr. & Rossi, J. J. MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc. Natl Acad. Sci. USA105, 16230–16235 (2008). CASPubMedPubMed Central Google Scholar
Grimson, A. et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature455, 1193–1197 (2008). CASPubMed Google Scholar
Ibanez-Ventoso, C., Vora, M. & Driscoll, M. Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS ONE3, e2818 (2008). PubMedPubMed Central Google Scholar
Chapman, E. J. & Carrington, J. C. Specialization and evolution of endogenous small RNA pathways. Nature Rev. Genet.8, 884–896 (2007). CASPubMed Google Scholar
Millar, A. A. & Waterhouse, P. M. Plant and animal microRNAs: similarities and differences. Funct. Integr. Genomics5, 129–135 (2005). CASPubMed Google Scholar
Ventura, A. et al. Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell132, 875–886 (2008). CASPubMedPubMed Central Google Scholar
Lee, Y., Jeon, K., Lee, J. T., Kim, S. & Kim, V. N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J.21, 4663–4670 (2002). CASPubMedPubMed Central Google Scholar
Cai, X., Hagedorn, C. H. & Cullen, B. R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA10, 1957–1966 (2004). CASPubMedPubMed Central Google Scholar
Borchert, G. M., Lanier, W. & Davidson, B. L. RNA polymerase III transcribes human microRNAs. Nature Struct. Mol. Biol.13, 1097–1101 (2006). CAS Google Scholar
Lee, Y. S. & Dutta, A. MicroRNAs in cancer. Annu. Rev. Pathol. 25 Sep 2008 (doi:10.1146annurev.pathol.4.110807.092222).
Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature425, 415–419 (2003). CASPubMed Google Scholar
Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F. & Hannon, G. J. Processing of primary microRNAs by the Microprocessor complex. Nature432, 231–235 (2004). CASPubMed Google Scholar
Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature432, 235–240 (2004). CASPubMed Google Scholar
Landthaler, M., Yalcin, A. & Tuschl, T. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol.14, 2162–2167 (2004). CASPubMed Google Scholar
Wang, Y., Medvid, R., Melton, C., Jaenisch, R. & Blelloch, R. DGCR8 is essential for microRNA biogenesis and silencing of embryonic stem cell self-renewal. Nature Genet.39, 380–385 (2007). CASPubMed Google Scholar
Filippov, V., Solovyev, V., Filippova, M. & Gill, S. S. A novel type of RNase III family proteins in eukaryotes. Gene245, 213–221 (2000). CASPubMed Google Scholar
Wu, H., Xu, H., Miraglia, L. J. & Crooke, S. T. Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J. Biol. Chem.275, 36957–36965 (2000). CASPubMed Google Scholar
Fortin, K. R., Nicholson, R. H. & Nicholson, A. W. Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics3, 26 (2002). PubMedPubMed Central Google Scholar
Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha–DGCR8 complex. Cell125, 887–901 (2006). CASPubMed Google Scholar
Zeng, Y. & Cullen, B. R. Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J. Biol. Chem.280, 27595–27603 (2005). CASPubMed Google Scholar
Morlando, M. et al. Primary microRNA transcripts are processed co-transcriptionally. Nature Struct. Mol. Biol.15, 902–909 (2008). CAS Google Scholar
Pawlicki, J. M. & Steitz, J. A. Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. J. Cell Biol.182, 61–76 (2008). CASPubMedPubMed Central Google Scholar
Dye, M. J., Gromak, N. & Proudfoot, N. J. Exon tethering in transcription by RNA polymerase II. Mol. Cell21, 849–859 (2006). CASPubMed Google Scholar
Ruby, J. G., Jan, C. H. & Bartel, D. P. Intronic microRNA precursors that bypass Drosha processing. Nature448, 83–86 (2007). CASPubMedPubMed Central Google Scholar
Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M. & Lai, E. C. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell130, 89–100 (2007). CASPubMedPubMed Central Google Scholar
Berezikov, E., Chung, W. J., Willis, J., Cuppen, E. & Lai, E. C. Mammalian mirtron genes. Mol. Cell28, 328–336 (2007). CASPubMedPubMed Central Google Scholar
Ender, C. et al. A human snoRNA with microRNA-like functions. Mol. Cell32, 519–528 (2008). CASPubMed Google Scholar
Kim, V. N. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol.14, 156–159 (2004). CASPubMed Google Scholar
Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. & Kutay, U. Nuclear export of microRNA precursors. Science303, 95–98 (2004). CASPubMed Google Scholar
Yi, R., Doehle, B. P., Qin, Y., Macara, I. G. & Cullen, B. R. Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA11, 220–226 (2005). CASPubMedPubMed Central Google Scholar
Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA10, 185–191 (2004). CASPubMedPubMed Central Google Scholar
Bohnsack, M. T. et al. Exp5 exports eEF1A via tRNA from nuclei and synergizes with other transport pathways to confine translation to the cytoplasm. EMBO J.21, 6205–6215 (2002). CASPubMedPubMed Central Google Scholar
Calado, A., Treichel, N., Muller, E. C., Otto, A. & Kutay, U. Exportin-5-mediated nuclear export of eukaryotic elongation factor 1A and tRNA. EMBO J.21, 6216–6224 (2002). CASPubMedPubMed Central Google Scholar
Gwizdek, C. et al. Exportin-5 mediates nuclear export of minihelix-containing RNAs. J. Biol. Chem.278, 5505–5508 (2003). CASPubMed Google Scholar
Basyuk, E., Suavet, F., Doglio, A., Bordonne, R. & Bertrand, E. Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res.31, 6593–6597 (2003). CASPubMedPubMed Central Google Scholar
Zeng, Y. & Cullen, B. R. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res.32, 4776–4785 (2004). CASPubMedPubMed Central Google Scholar
Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature409, 363–366 (2001). CASPubMed Google Scholar
Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell106, 23–34 (2001). CASPubMed Google Scholar
Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science293, 834–838 (2001). CASPubMed Google Scholar
Ketting, R. F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev.15, 2654–2659 (2001). CASPubMedPubMed Central Google Scholar
Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science293, 2269–2271 (2001). CASPubMedPubMed Central Google Scholar
Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell117, 69–81 (2004). CASPubMed Google Scholar
Xie, Z. et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol.2, e104 (2004). PubMedPubMed Central Google Scholar
Forstemann, K. et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol.3, e236 (2005). PubMedPubMed Central Google Scholar
Saito, K., Ishizuka, A., Siomi, H. & Siomi, M. C. Processing of pre-microRNAs by the Dicer-1–Loquacious complex in Drosophila cells. PLoS Biol.3, e235 (2005). PubMedPubMed Central Google Scholar
Chendrimada, T. P. et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature436, 740–744 (2005). CASPubMedPubMed Central Google Scholar
Haase, A. D. et al. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep.6, 961–967 (2005). CASPubMedPubMed Central Google Scholar
Garcia, M. A., Meurs, E. F. & Esteban, M. The dsRNA protein kinase PKR: virus and cell control. Biochimie89, 799–811 (2007). CASPubMed Google Scholar
Aza-Blanc, P. et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell12, 627–637 (2003). CASPubMed Google Scholar
Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell115, 199–208 (2003). CASPubMed Google Scholar
Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell115, 209–216 (2003). CASPubMed Google Scholar
Maniataki, E. & Mourelatos, Z. A human, ATP-independent, RISC assembly machine fueled by pre-miRNA. Genes Dev.19, 2979–2990 (2005). CASPubMedPubMed Central Google Scholar
MacRae, I. J., Ma, E., Zhou, M., Robinson, C. V. & Doudna, J. A. In vitro reconstitution of the human RISC-loading complex. Proc. Natl Acad. Sci. USA105, 512–517 (2008). CASPubMedPubMed Central Google Scholar
Gregory, R. I., Chendrimada, T. P., Cooch, N. & Shiekhattar, R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell123, 631–640 (2005). CASPubMed Google Scholar
Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P. D. A protein sensor for siRNA asymmetry. Science306, 1377–1380 (2004). CASPubMed Google Scholar
Preall, J. B. & Sontheimer, E. J. RNAi: RISC gets loaded. Cell123, 543–545 (2005). CASPubMed Google Scholar
Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science301, 1921–1925 (2003). CASPubMed Google Scholar
Matranga, C., Tomari, Y., Shin, C., Bartel, D. P. & Zamore, P. D. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell123, 607–620 (2005). CASPubMed Google Scholar
Miyoshi, K., Tsukumo, H., Nagami, T., Siomi, H. & Siomi, M. C. Slicer function of Drosophila Argonautes and its involvement in RISC formation. Genes Dev.19, 2837–2848 (2005). CASPubMedPubMed Central Google Scholar
Leuschner, P. J., Ameres, S. L., Kueng, S. & Martinez, J. Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep.7, 314–320 (2006). CASPubMedPubMed Central Google Scholar
Diederichs, S. & Haber, D. A. Dual role for argonautes in microRNA processing and posttranscriptional regulation of microRNA expression. Cell131, 1097–1108 (2007). CASPubMed Google Scholar
Forstemann, K., Horwich, M. D., Wee, L., Tomari, Y. & Zamore, P. D. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell130, 287–297 (2007). PubMedPubMed Central Google Scholar
Steiner, F. A. et al. Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nature Struct. Mol. Biol.14, 927–933 (2007). CAS Google Scholar
Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science305, 1437–1441 (2004). CASPubMed Google Scholar
Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell15, 185–197 (2004). CASPubMed Google Scholar
Azuma-Mukai, A. et al. Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc. Natl Acad. Sci. USA105, 7964–7969 (2008). CASPubMedPubMed Central Google Scholar
Seitz, H., Ghildiyal, M. & Zamore, P. D. Argonaute loading improves the 5′ precision of both microRNAs and their miRNA strands in flies. Curr. Biol.18, 147–151 (2008). CASPubMedPubMed Central Google Scholar
Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell129, 1401–1414 (2007). CASPubMedPubMed Central Google Scholar
Jiang, Q. et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res.37, D98–D104 (2008). PubMedPubMed Central Google Scholar
Chen, J. F. et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nature Genet.38, 228–233 (2006). CASPubMed Google Scholar
Kim, H. K., Lee, Y. S., Sivaprasad, U., Malhotra, A. & Dutta, A. Muscle-specific microRNA miR-206 promotes muscle differentiation. J. Cell Biol.174, 677–687 (2006). CASPubMedPubMed Central Google Scholar
Rao, P. K., Kumar, R. M., Farkhondeh, M., Baskerville, S. & Lodish, H. F. Myogenic factors that regulate expression of muscle-specific microRNAs. Proc. Natl Acad. Sci. USA103, 8721–8726 (2006). CASPubMedPubMed Central Google Scholar
He, L., He, X., Lowe, S. W. & Hannon, G. J. microRNAs join the p53 network — another piece in the tumour-suppression puzzle. Nature Rev. Cancer7, 819–822 (2007). CAS Google Scholar
Chang, T. C. et al. Widespread microRNA repression by Myc contributes to tumorigenesis. Nature Genet.40, 43–50 (2008). CASPubMed Google Scholar
Bueno, M. J. et al. Genetic and epigenetic silencing of microRNA-203 enhances ABL1 and BCR-ABL1 oncogene expression. Cancer Cell13, 496–506 (2008). CASPubMed Google Scholar
Davis, B. N., Hilyard, A. C., Lagna, G. & Hata, A. SMAD proteins control DROSHA-mediated microRNA maturation. Nature454, 56–61 (2008). CASPubMedPubMed Central Google Scholar
Guil, S. & Caceres, J. F. The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nature Struct. Mol. Biol.14, 591–596 (2007). CAS Google Scholar
Michlewski, G., Guil, S., Semple, C. A. & Caceres, J. F. Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol. Cell32, 383–393 (2008). CASPubMedPubMed Central Google Scholar
Pasquinelli, A. E. et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature408, 86–89 (2000). CASPubMed Google Scholar
Suh, M. R. et al. Human embryonic stem cells express a unique set of microRNAs. Dev. Biol.270, 488–498 (2004). CASPubMed Google Scholar
Thomson, J. M. et al. Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev.20, 2202–2207 (2006). CASPubMedPubMed Central Google Scholar
Wulczyn, F. G. et al. Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB J.21, 415–426 (2007). CASPubMed Google Scholar
Newman, M. A., Thomson, J. M. & Hammond, S. M. Lin-28 interaction with the let-7 precursor loop mediates regulated microRNA processing. RNA14, 1539–1549 (2008). CASPubMedPubMed Central Google Scholar
Viswanathan, S. R., Daley, G. Q. & Gregory, R. I. Selective blockade of microRNA processing by Lin28. Science320, 97–100 (2008). CASPubMedPubMed Central Google Scholar
Rybak, A. et al. A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nature Cell Biol.10, 987–993 (2008). CASPubMed Google Scholar
Heo, I. et al. Lin28 mediates the terminal uridylation of let-7 precursor microRNA. Mol. Cell32, 276–284 (2008). CASPubMed Google Scholar
Balzer, E. & Moss, E. G. Localization of the developmental timing regulator Lin28 to mRNP complexes, P-bodies and stress granules. RNA Biol.4, 16–25 (2007). CASPubMed Google Scholar
Hwang, H. W., Wentzel, E. A. & Mendell, J. T. A hexanucleotide element directs microRNA nuclear import. Science315, 97–100 (2007). CASPubMed Google Scholar
Kennedy, S., Wang, D. & Ruvkun, G. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature427, 645–649 (2004). CASPubMed Google Scholar
Ramachandran, V. & Chen, X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science321, 1490–1492 (2008). CASPubMedPubMed Central Google Scholar
Yang, W. et al. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nature Struct. Mol. Biol.13, 13–21 (2006). CAS Google Scholar
Kawahara, Y., Zinshteyn, B., Chendrimada, T. P., Shiekhattar, R. & Nishikura, K. RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer–TRBP complex. EMBO Rep.8, 763–769 (2007). CASPubMedPubMed Central Google Scholar
Kawahara, Y. et al. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res.36, 5270–5280 (2008). CASPubMedPubMed Central Google Scholar
Obernosterer, G., Leuschner, P. J., Alenius, M. & Martinez, J. Post-transcriptional regulation of microRNA expression. RNA12, 1161–1167 (2006). CASPubMedPubMed Central Google Scholar
Lee, E. J. et al. Systematic evaluation of microRNA processing patterns in tissues, cell lines, and tumors. RNA14, 35–42 (2008). CASPubMedPubMed Central Google Scholar
Michael, M. Z., O'Connor, S. M., van Holst Pellekaan, N. G., Young, G. P. & James, R. J. Reduced accumulation of specific microRNAs in colorectal neoplasia. Mol. Cancer Res.1, 882–891 (2003). CASPubMed Google Scholar
Kefas, B. et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma. Cancer Res.68, 3566–3572 (2008). CASPubMed Google Scholar
Martinez, N. J. et al. A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev.22, 2535–2549 (2008). CASPubMedPubMed Central Google Scholar
Tokumaru, S., Suzuki, M., Yamada, H., Nagino, M. & Takahashi, T. let-7 regulates Dicer expression and constitutes a negative feedback loop. Carcinogenesis29, 2073–2077 (2008). CASPubMed Google Scholar
Forman, J. J., Legesse-Miller, A. & Coller, H. A. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc. Natl Acad. Sci. USA105, 14879–14884 (2008). CASPubMedPubMed Central Google Scholar
Piskounova, E. et al. Determinants of microRNA processing inhibition by the developmentally regulated RNA-binding protein Lin28. J. Biol. Chem.283, 21310–21314 (2008). CASPubMed Google Scholar
Bracken, C. P. et al. A double-negative feedback loop between ZEB1–SIP1 and the microRNA-200 family regulates epithelial–mesenchymal transition. Cancer Res.68, 7846–7854 (2008). CASPubMed Google Scholar
Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol.11, 1017–1027 (2001). CASPubMed Google Scholar
Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell5, 337–350 (2003). This was the herald of studies for a novel class of small RNAs of 24–29 nt (rasiRNAs or piRNAs) that are specifically expressed in germ lines. CASPubMed Google Scholar
Cox, D. N. et al. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev.12, 3715–3727 (1998). CASPubMedPubMed Central Google Scholar
Cox, D. N., Chao, A. & Lin, H. piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. Development127, 503–514 (2000). CASPubMed Google Scholar
Szakmary, A., Cox, D. N., Wang, Z. & Lin, H. Regulatory relationship among piwi, pumilio, and bag-of-marbles in Drosophila germline stem cell self-renewal and differentiation. Curr. Biol.15, 171–178 (2005). CASPubMed Google Scholar
Kalmykova, A. I., Klenov, M. S. & Gvozdev, V. A. Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline. Nucleic Acids Res.33, 2052–2059 (2005). CASPubMedPubMed Central Google Scholar
Sarot, E., Payen-Groschene, G., Bucheton, A. & Pelisson, A. Evidence for a _piwi_-dependent RNA silencing of the gypsy endogenous retrovirus by the Drosophila melanogaster flamenco gene. Genetics166, 1313–1321 (2004). CASPubMedPubMed Central Google Scholar
Harris, A. N. & Macdonald, P. M. aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C. Development128, 2823–2832 (2001). CASPubMed Google Scholar
Vagin, V. V. et al. The RNA interference proteins and vasa locus are involved in the silencing of retrotransposons in the female germline of Drosophila melanogaster. RNA Biol.1, 54–58 (2004). CASPubMed Google Scholar
Saito, K. et al. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev.20, 2214–2222 (2006). CASPubMedPubMed Central Google Scholar
Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell128, 1089–1103 (2007). CASPubMed Google Scholar
Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science315, 1587–1590 (2007). The ping-pong pathway for piRNA biogenesis was proposed on the basis of theseD. melanogasterstudies. CASPubMed Google Scholar
Nishida, K. M. et al. Gene silencing mechanisms mediated by Aubergine–piRNA complexes in Drosophila male gonad. RNA13, 1911–1922 (2007). Shows thatSuppressor of StellatepiRNAs are directly associated with AUB inD. melanogastertestes and that the complex can slice theStellatetranscripts. CASPubMedPubMed Central Google Scholar
Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature442, 203–207 (2006). CASPubMed Google Scholar
Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature442, 199–202 (2006). PubMed Google Scholar
Grivna, S. T., Beyret, E., Wang, Z. & Lin, H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev.20, 1709–1714 (2006). CASPubMedPubMed Central Google Scholar
Watanabe, T. et al. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev.20, 1732–1743 (2006). CASPubMedPubMed Central Google Scholar
Houwing, S. et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell129, 69–82 (2007). CASPubMed Google Scholar
Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell12, 503–514 (2007). CASPubMed Google Scholar
Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science316, 744–747 (2007). CASPubMed Google Scholar
Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev.22, 908–917 (2008). CASPubMedPubMed Central Google Scholar
Zamore, P. D. RNA silencing: genomic defence with a slice of pi. Nature446, 864–865 (2007). CASPubMed Google Scholar
Pane, A., Wehr, K. & Schupbach, T. zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev. Cell12, 851–862 (2007). CASPubMedPubMed Central Google Scholar
Lim, A. K. & Kai, T. Unique germ-line organelle, nuage, functions to repress selfish genetic elements in Drosophila melanogaster. Proc. Natl Acad. Sci. USA104, 6714–6719 (2007). CASPubMedPubMed Central Google Scholar
Findley, S. D., Tamanaha, M., Clegg, N. J. & Ruohola-Baker, H. Maelstrom, a _Drosophila spindle_-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage. Development130, 859–871 (2003). CASPubMed Google Scholar
Aravin, A. A., Hannon, G. J. & Brennecke, J. The Piwi–piRNA pathway provides an adaptive defense in the transposon arms race. Science318, 761–764 (2007). CASPubMed Google Scholar
Brennecke, J. et al. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science322, 1387–1392 (2008). CASPubMedPubMed Central Google Scholar
Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science313, 363–367 (2006). CASPubMed Google Scholar
Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell31, 785–799 (2008). CASPubMedPubMed Central Google Scholar
Saito, K., Sakaguchi, Y., Suzuki, T., Siomi, H. & Siomi, M. C. Pimet, the Drosophila homolog of HEN1, mediates 2′-_O_-methylation of Piwi-interacting RNAs at their 3′ ends. Genes Dev.21, 1603–1608 (2007). CASPubMedPubMed Central Google Scholar
Horwich, M. D. et al. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol.17, 1265–1272 (2007). CASPubMed Google Scholar
Kirino, Y. & Mourelatos, Z. Mouse Piwi-interacting RNAs are 2′-_O_-methylated at their 3′ termini. Nature Struct. Mol. Biol.14, 347–348 (2007). CAS Google Scholar
Ohara, T., Sakaguchi, Y., Suzuki, T., Ueda, H. & Miyauchi, K. The 3′ termini of mouse Piwi-interacting RNAs are 2′-_O_-methylated. Nature Struct. Mol. Biol.14, 349–350 (2007). CAS Google Scholar
Ghildiyal, M. et al. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science320, 1077–1081 (2008). CASPubMedPubMed Central Google Scholar
Chung, W. J., Okamura, K., Martin, R. & Lai, E. C. Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol.18, 795–802 (2008). CASPubMedPubMed Central Google Scholar
Okamura, K., Balla, S., Martin, R., Liu, N. & Lai, E. C. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nature Struct. Mol. Biol.15, 581–590 (2008). CAS Google Scholar
van Rij, R. P. et al. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes Dev.20, 2985–2995 (2006). CASPubMedPubMed Central Google Scholar
Wang, X. H. et al. RNA interference directs innate immunity against viruses in adult Drosophila. Science312, 452–454 (2006). CASPubMedPubMed Central Google Scholar
Nishikura, K. Editor meets silencer: crosstalk between RNA editing and RNA interference. Nature Rev. Mol. Cell Biol.7, 919–931 (2006). CAS Google Scholar
Fukuda, T. et al. DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nature Cell Biol.9, 604–611 (2007). CASPubMed Google Scholar
Shiohama, A., Sasaki, T., Noda, S., Minoshima, S. & Shimizu, N. Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins. Exp. Cell Res.313, 4196–4207 (2007). CASPubMed Google Scholar
Yu, B. et al. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl Acad. Sci. USA105, 10073–10078 (2008). CASPubMedPubMed Central Google Scholar
Neumuller, R. A. et al. Mei-P26 regulates microRNAs and cell growth in the Drosophila ovarian stem cell lineage. Nature454, 241–245 (2008). PubMedPubMed Central Google Scholar
Krol, J. et al. Ribonuclease dicer cleaves triplet repeat hairpins into shorter repeats that silence specific targets. Mol. Cell25, 575–586 (2007). CASPubMed Google Scholar
Ma, J. B., Ye, K. & Patel, D. J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature429, 318–322 (2004). CASPubMedPubMed Central Google Scholar
Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nature Struct. Mol. Biol.11, 576–577 (2004). CAS Google Scholar
Wang, Y. et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature456, 921–926 (2008). CASPubMedPubMed Central Google Scholar
Wang, Y., Sheng, G., Juranek, S., Tuschl, T. & Patel, D. J. Structure of the guide-strand-containing argonaute silencing complex. Nature456, 209–213 (2008). CASPubMedPubMed Central Google Scholar
Song, J. J., Smith, S. K., Hannon, G. J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science305, 1434–1437 (2004). CASPubMed Google Scholar
Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex. Nature434, 663–666 (2005). CASPubMedPubMed Central Google Scholar
Ma, J. B. et al. Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature434, 666–670 (2005). CASPubMedPubMed Central Google Scholar
Brower-Toland, B. et al. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev.21, 2300–2311 (2007). CASPubMedPubMed Central Google Scholar
Blaszczyk, J. et al. Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure9, 1225–1236 (2001). CASPubMed Google Scholar
Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell118, 57–68 (2004). CASPubMed Google Scholar
Yeom, K. H., Lee, Y., Han, J., Suh, M. R. & Kim, V. N. Characterization of DGCR8/Pasha, the essential cofactor for Drosha in primary miRNA processing. Nucleic Acids Res.34, 4622–4629 (2006). CASPubMedPubMed Central Google Scholar
Sohn, S. Y. et al. Crystal structure of human DGCR8 core. Nature Struct. Mol. Biol.14, 847–853 (2007). CAS Google Scholar
Faller, M., Matsunaga, M., Yin, S., Loo, J. A. & Guo, F. Heme is involved in microRNA processing. Nature Struct. Mol. Biol.14, 23–29 (2007). CAS Google Scholar
Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol.10, 1026–1032 (2003). CASPubMed Google Scholar
Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature426, 468–474 (2003). PubMed Google Scholar
Macrae, I. J. et al. Structural basis for double-stranded RNA processing by Dicer. Science311, 195–198 (2006). CASPubMed Google Scholar
Calin, G. A. et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl Acad. Sci. USA99, 15524–15529 (2002). CASPubMedPubMed Central Google Scholar
Tam, W. Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA. Gene274, 157–167 (2001). CASPubMed Google Scholar