58
Views
45
CrossRef citations to date
0
Altmetric
Article

R2D2 Organizes Small Regulatory RNA Pathways in Drosophila∇†

, , , &
Pages 884-896 | Received 28 Sep 2010, Accepted 24 Nov 2010, Published online: 20 Mar 2023

REFERENCES

  • Aliyari, R., and S. W. Ding. 2009. RNA-based viral immunity initiated by the Dicer family of host immune receptors. Immunol. Rev. 227:176–188.
  • Aliyari, R., Q. Wu, H. W. Li, X. H. Wang, F. Li, L. D. Green, C. S. Han, W. X. Li, and S. W. Ding. 2008. Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila. Cell Host Microbe 4:387–397.
  • Ameres, S. L., M. D. Horwich, J. H. Hung, J. Xu, M. Ghildiyal, Z. Weng, and P. D. Zamore. 2010. Target RNA-directed trimming and tailing of small silencing RNAs. Science 328:1534–1539.
  • Brennecke, J., A. A. Aravin, A. Stark, M. Dus, M. Kellis, R. Sachidanandam, and G. J. Hannon. 2007. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1089–1103.
  • Burroughs, A. M., Y. Ando, M. J. de Hoon, Y. Tomaru, T. Nishibu, R. Ukekawa, T. Funakoshi, T. Kurokawa, H. Suzuki, Y. Hayashizaki, et al. 2010. A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res. 20:1398–1410.
  • Campbell, C. L., W. C. Black IV, A. M. Hess, and B. D. Foy. 2008. Comparative genomics of small RNA regulatory pathway components in vector mosquitoes. BMC Genomics 9:425.
  • Chiang, H. R., L. W. Schoenfeld, J. G. Ruby, V. C. Auyeung, N. Spies, D. Baek, W. K. Johnston, C. Russ, S. Luo, J. E. Babiarz, et al. 2010. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 24:992–1009.
  • Chung, W. J., K. Okamura, R. Martin, and E. C. Lai. 2008. Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol. 18:795–802.
  • Czech, B., C. D. Malone, R. Zhou, A. Stark, C. Schlingeheyde, M. Dus, N. Perrimon, M. Kellis, J. Wohlschlegel, R. Sachidanandam, et al. 2008. An endogenous siRNA pathway in Drosophila. Nature 453:798–802.
  • Czech, B., R. Zhou, Y. Erlich, J. Brennecke, R. Binari, C. Villalta, A. Gordon, N. Perrimon, and G. J. Hannon. 2009. Hierarchical rules for Argonaute loading in Drosophila. Mol. Cell 36:445–456.
  • Flynt, A. S., and E. C. Lai. 2008. Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat. Rev. Genet. 9:831–842.
  • Flynt, A. S., N. Liu, and E. C. Lai. 2009. Dicing of viral replication intermediates during silencing of latent Drosophila viruses. Proc. Natl. Acad. Sci. U. S. A. 106:5270–5275.
  • Forstemann, K., M. D. Horwich, L. Wee, Y. Tomari, and P. D. Zamore. 2007. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by dicer-1. Cell 130:287–297.
  • Ghildiyal, M., H. Seitz, M. D. Horwich, C. Li, T. Du, S. Lee, J. Xu, E. L. Kittler, M. L. Zapp, Z. Weng, et al. 2008. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320:1077–1081.
  • Ghildiyal, M., J. Xu, H. Seitz, Z. Weng, and P. D. Zamore. 2010. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16:43–56.
  • Ghildiyal, M., and P. D. Zamore. 2009. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10:94–108.
  • Grishok, A., A. Pasquinelli, D. Conte, N. Li, S. Parrish, I. Ha, D. L. Baillie, A. Fire, G. Ruvkun, and C. C. Mello. 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106:23–34.
  • Gunawardane, L. S., K. Saito, K. M. Nishida, K. Miyoshi, Y. Kawamura, T. Nagami, H. Siomi, and M. C. Siomi. 2007. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315:1587–1590.
  • Hartig, J. V., S. Esslinger, R. Bottcher, K. Saito, and K. Forstemann. 2009. Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences. EMBO J. 28:2932–2944.
  • Horwich, M. D., C. Li, C. Matranga, V. Vagin, G. Farley, P. Wang, and P. D. Zamore. 2007. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol. 17:1265–1272.
  • Iwasaki, S., T. Kawamata, and Y. Tomari. 2009. Drosophila argonaute1 and argonaute2 employ distinct mechanisms for translational repression. Mol. Cell 34:58–67.
  • Jackson, A. L., J. Burchard, J. Schelter, B. N. Chau, M. Cleary, L. Lim, and P. S. Linsley. 2006. Widespread siRNA “off-target” transcript silencing mediated by seed region sequence complementarity. RNA 12:1179–1187.
  • Jurka, J., V. V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany, and J. Walichiewicz. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110:462–467.
  • Kalidas, S., C. Sanders, X. Ye, T. Strauss, M. Kuhn, Q. Liu, and D. P. Smith. 2008. Drosophila R2D2 mediates follicle formation in somatic tissues through interactions with Dicer-1. Mech. Dev. 125:475–485.
  • Kawamata, T., H. Seitz, and Y. Tomari. 2009. Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat. Struct. Mol. Biol. 16:953–960.
  • Kawamura, Y., K. Saito, T. Kin, Y. Ono, K. Asai, T. Sunohara, T. Okada, M. C. Siomi, and H. Siomi. 2008. Drosophila endogenous small RNAs bind to Argonaute2 in somatic cells. Nature 453:793–797.
  • Khan, A. A., D. Betel, M. L. Miller, C. Sander, C. S. Leslie, and D. S. Marks. 2009. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat. Biotechnol. 27:549–555.
  • Khvorova, A., A. Reynolds, and S. D. Jayasena. 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209–216.
  • Kim, V. N., J. Han, and M. C. Siomi. 2009. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10:126–139.
  • Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
  • Lau, N., N. Robine, R. Martin, W. J. Chung, Y. Niki, E. Berezikov, and E. C. Lai. 2009. Abundant primary piRNAs, endo-siRNAs and microRNAs in a Drosophila ovary cell line. Genome Res. 19:1776–1785.
  • Lee, Y. S., K. Nakahara, J. W. Pham, K. Kim, Z. He, E. J. Sontheimer, and R. W. Carthew. 2004. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117:69–81.
  • Li, H., W. X. Li, and S. W. Ding. 2002. Induction and suppression of RNA silencing by an animal virus. Science 296:1319–1321.
  • Liu, J., M. A. Carmell, F. V. Rivas, C. G. Marsden, J. M. Thomson, J. J. Song, S. M. Hammond, L. Joshua-Tor, and G. J. Hannon. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305:1437–1441.
  • Liu, Q., T. A. Rand, S. Kalidas, F. Du, H. E. Kim, D. P. Smith, and X. Wang. 2003. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301:1921–1925.
  • Lucchetta, E. M., R. W. Carthew, and R. F. Ismagilov. 2009. The endo-siRNA pathway is essential for robust development of the Drosophila embryo. PLoS One 4:e7576.
  • Ma, J., M. Flemr, P. Stein, P. Berninger, R. Malik, M. Zavolan, P. Svoboda, and R. M. Schultz. 2010. MicroRNA activity is suppressed in mouse oocytes. Curr. Biol. 20:265–270.
  • Marques, J. T., K. Kim, P. H. Wu, T. M. Alleyne, N. Jafari, and R. W. Carthew. 2010. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat. Struct. Mol. Biol. 17:24–30.
  • Meister, G., M. Landthaler, A. Patkaniowska, Y. Dorsett, G. Teng, and T. Tuschl. 2004. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15:185–197.
  • Meyer, W. J., S. Schreiber, Y. Guo, T. Volkmann, M. A. Welte, and H. A. Muller. 2006. Overlapping functions of argonaute proteins in patterning and morphogenesis of Drosophila embryos. PLoS Genet. 2:e134.
  • Miyoshi, K., T. Miyoshi, J. V. Hartig, H. Siomi, and M. C. Siomi. 2010. Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila. RNA 16:506–515.
  • Okamura, K., S. Balla, R. Martin, N. Liu, and E. C. Lai. 2008. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila. Nat. Struct. Mol. Biol. 15:581–590.
  • Okamura, K., W.-J. Chung, J. G. Ruby, H. Guo, D. P. Bartel, and E. C. Lai. 2008. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature 453:803–806.
  • Okamura, K., A. Ishizuka, H. Siomi, and M. C. Siomi. 2004. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 18:1655–1666.
  • Okamura, K., and E. C. Lai. 2008. Endogenous small interfering RNAs in animals. Nat. Rev. Mol. Cell Biol. 9:673–678.
  • Okamura, K., N. Liu, and E. C. Lai. 2009. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol. Cell 36:431–444.
  • Park, J. K., X. Liu, T. J. Strauss, D. M. McKearin, and Q. Liu. 2007. The miRNA pathway intrinsically controls self-renewal of Drosophila germline stem cells. Curr. Biol. 17:533–538.
  • Pham, J. W., and E. J. Sontheimer. 2005. Molecular requirements for RNA-induced silencing complex assembly in the Drosophila RNA interference pathway. J. Biol. Chem. 280:39278–39283.
  • Ruby, J. G., A. Stark, W. K. Johnston, M. Kellis, D. P. Bartel, and E. C. Lai. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17:1850–1864.
  • Saito, K., Y. Sakaguchi, T. Suzuki, T. Suzuki, H. Siomi, and M. C. Siomi. 2007. Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi-interacting RNAs at their 3′ ends. Genes Dev. 21:1603–1608.
  • Schwarz, D. S., G. Hutvagner, T. Du, Z. Xu, N. Aronin, and P. D. Zamore. 2003. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208.
  • Suh, N., L. Baehner, F. Moltzahn, C. Melton, A. Shenoy, J. Chen, and R. Blelloch. 2010. MicroRNA function is globally suppressed in mouse oocytes and early embryos. Curr. Biol. 20:271–277.
  • Tam, O. H., A. A. Aravin, P. Stein, A. Girard, E. P. Murchison, S. Cheloufi, E. Hodges, M. Anger, R. Sachidanandam, R. M. Schultz, et al. 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453:534–538.
  • Tomari, Y., T. Du, B. Haley, D. S. Schwarz, R. Bennett, H. A. Cook, B. S. Koppetsch, W. E. Theurkauf, and P. D. Zamore. 2004. RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116:831–841.
  • Tomari, Y., T. Du, and P. D. Zamore. 2007. Sorting of Drosophila small silencing RNAs. Cell 130:299–308.
  • Tomari, Y., C. Matranga, B. Haley, N. Martinez, and P. D. Zamore. 2004. A protein sensor for siRNA asymmetry. Science 306:1377–1380.
  • Tomari, Y., and P. D. Zamore. 2005. MicroRNA biogenesis: drosha can't cut it without a partner. Curr. Biol. 15:R61–R64.
  • Tomoyasu, Y., S. C. Miller, S. Tomita, M. Schoppmeier, D. Grossmann, and G. Bucher. 2008. Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol. 9:R10.
  • Vagin, V. V., A. Sigova, C. Li, H. Seitz, V. Gvozdev, and P. D. Zamore. 2006. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313:320–324.
  • Voinnet, O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687.
  • Watanabe, T., Y. Totoki, A. Toyoda, M. Kaneda, S. Kuramochi-Miyagawa, Y. Obata, H. Chiba, Y. Kohara, T. Kono, T. Nakano, et al. 2008. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453:539–543.
  • Wu, Q., Y. Luo, R. Lu, N. Lau, E. C. Lai, W. X. Li, and S. W. Ding. 2010. Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl. Acad. Sci. U. S. A. 107:1606–1611.
  • Yigit, E., P. J. Batista, Y. Bei, K. M. Pang, C. C. Chen, N. H. Tolia, L. Joshua-Tor, S. Mitani, M. J. Simard, and C. C. Mello. 2006. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 127:747–757.
  • Zhao, X. F., A. Fjose, N. Larsen, J. V. Helvik, and O. Drivenes. 2008. Treatment with small interfering RNA affects the microRNA pathway and causes unspecific defects in zebrafish embryos. FEBS J. 275:2177–2184.
  • Zhou, R., B. Czech, J. Brennecke, R. Sachidanandam, J. A. Wohlschlegel, N. Perrimon, and G. J. Hannon. 2009. Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA 15:1886–1895.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.