EGO-1, a C. elegans RdRP, modulates gene expression via production of mRNA-templated short antisense RNAs

Current Biology

Volumn 21, Issue 6, 2011, Pages 449-459

  Maniar, Jay M ^a   Fire, Andrew Z ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; EGO 1 PROTEIN, C ELEGANS; EGO-1 PROTEIN, C ELEGANS; MESSENGER RNA; RNA DIRECTED RNA POLYMERASE; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; BIOSYNTHESIS; CAENORHABDITIS ELEGANS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; RNA INTERFERENCE; SEQUENCE ANALYSIS;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; GENE EXPRESSION REGULATION; RNA INTERFERENCE; RNA REPLICASE; RNA, MESSENGER; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA;

ANIMALIA; CAENORHABDITIS ELEGANS;

EID: 79952818830     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2011.02.019     Document Type: Article

References (48)

1. C. Cogoni, and G. Macino Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase Nature 399 1999 166 169
2. H. Tabara, M. Sarkissian, W.G. Kelly, J. Fleenor, A. Grishok, L. Timmons, A. Fire, and C.C. Mello The rde-1 gene, RNA interference, and transposon silencing in C. elegans Cell 99 1999 123 132 (Pubitemid 29491779)
3. H. Vaucheret, C. Béclin, T. Elmayan, F. Feuerbach, C. Godon, J.B. Morel, P. Mourrain, J.C. Palauqui, and S. Vernhettes Transgene-induced gene silencing in plants Plant J. 16 1998 651 659
4. F. Ratcliff, B.D. Harrison, and D.C. Baulcombe A similarity between viral defense and gene silencing in plants Science 276 1997 1558 1560 (Pubitemid 27255318)
5. A. Fire, S. Xu, M.K. Montgomery, S.A. Kostas, S.E. Driver, and C.C. Mello Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans Nature 391 1998 806 811 (Pubitemid 28099681)
6. S.M. Elbashir, W. Lendeckel, and T. Tuschl RNA interference is mediated by 21- and 22-nucleotide RNAs Genes Dev. 15 2001 188 200 (Pubitemid 32107664)
7. A.J. Hamilton, and D.C. Baulcombe A species of small antisense RNA in posttranscriptional gene silencing in plants Science 286 1999 950 952
8. J.I. Gent, M. Schvarzstein, A.M. Villeneuve, S.G. Gu, V. Jantsch, A.Z. Fire, and A. Baudrimont A Caenorhabditis elegans RNA-directed RNA polymerase in sperm development and endogenous RNA interference Genetics 183 2009 1297 1314
9. J.I. Gent, A.T. Lamm, D.M. Pavelec, J.M. Maniar, P. Parameswaran, L. Tao, S. Kennedy, and A.Z. Fire Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma Mol. Cell 37 2010 679 689
10. T. Han, A.P. Manoharan, T.T. Harkins, P. Bouffard, C. Fitzpatrick, D.S. Chu, D. Thierry-Mieg, J. Thierry-Mieg, and J.K. Kim 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans Proc. Natl. Acad. Sci. USA 106 2009 18674 18679
11. J.J. Vasale, W. Gu, C. Thivierge, P.J. Batista, J.M. Claycomb, E.M. Youngman, T.F. Duchaine, C.C. Mello, and D. Conte Jr. Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway Proc. Natl. Acad. Sci. USA 107 2010 3582 3587
12. T. Sijen, J. Fleenor, F. Simmer, K.L. Thijssen, S. Parrish, L. Timmons, R.H. Plasterk, and A. Fire On the role of RNA amplification in dsRNA-triggered gene silencing Cell 107 2001 465 476 (Pubitemid 33152782)
13. J. Pak, and A. Fire Distinct populations of primary and secondary effectors during RNAi in C. elegans Science 315 2007 241 244 (Pubitemid 46166369)
14. A. Smardon, J.M. Spoerke, S.C. Stacey, M.E. Klein, N. Mackin, and E.M. Maine EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans Curr. Biol. 10 2000 169 178 (Pubitemid 30146781)
15. L. Qiao, J.L. Lissemore, P. Shu, A. Smardon, M.B. Gelber, and E.M. Maine Enhancers of glp-1, a gene required for cell-signaling in Caenorhabditis elegans, define a set of genes required for germline development Genetics 141 1995 551 569
16. V.E. Vought, M. Ohmachi, M.H. Lee, and E.M. Maine EGO-1, a putative RNA-directed RNA polymerase, promotes germline proliferation in parallel with GLP-1/notch signaling and regulates the spatial organization of nuclear pore complexes and germline P granules in Caenorhabditis elegans Genetics 170 2005 1121 1132 (Pubitemid 41105468)
17. E.M. Maine, J. Hauth, T. Ratliff, V.E. Vought, X. She, and W.G. Kelly EGO-1, a putative RNA-dependent RNA polymerase, is required for heterochromatin assembly on unpaired dna during C. elegans meiosis Curr. Biol. 15 2005 1972 1978 (Pubitemid 41566147)
18. X. She, X. Xu, A. Fedotov, W.G. Kelly, and E.M. Maine Regulation of heterochromatin assembly on unpaired chromosomes during Caenorhabditis elegans meiosis by components of a small RNA-mediated pathway PLoS Genet. 5 2009 e1000624
19. C.E. Rocheleau, K. Cullison, K. Huang, Y. Bernstein, A.C. Spilker, and M.V. Sundaram The Caenorhabditis elegans ekl (enhancer of ksr-1 lethality) genes include putative components of a germline small RNA pathway Genetics 178 2008 1431 1443
20. K. Aoki, H. Moriguchi, T. Yoshioka, K. Okawa, and H. Tabara In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans EMBO J. 26 2007 5007 5019 (Pubitemid 350261276)
21. J.M. Claycomb, P.J. Batista, K.M. Pang, W. Gu, J.J. Vasale, J.C. van Wolfswinkel, D.A. Chaves, M. Shirayama, S. Mitani, and R.F. Ketting The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation Cell 139 2009 123 134
22. A. Grishok, A.E. Pasquinelli, D. Conte, N. Li, S. Parrish, I. Ha, D.L. Baillie, A. Fire, G. Ruvkun, and C.C. Mello Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing Cell 106 2001 23 34 (Pubitemid 32709955)
23. V.J.P. Robert, T. Sijen, J. van Wolfswinkel, and R.H.A. Plasterk Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences Genes Dev. 19 2005 782 787
24. E. Yigit, 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 Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi Cell 127 2006 747 757 (Pubitemid 44716250)
25. T.F. Duchaine, J.A. Wohlschlegel, S. Kennedy, Y. Bei, D. Conte Jr., K. Pang, D.R. Brownell, S. Harding, S. Mitani, and G. Ruvkun Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways Cell 124 2006 343 354 (Pubitemid 43121982)
26. M. Mangone, A.P. Manoharan, D. Thierry-Mieg, J. Thierry-Mieg, T. Han, S.D. Mackowiak, E. Mis, C. Zegar, M.R. Gutwein, and V. Khivansara The landscape of C. elegans 3′UTRs Science 329 2010 432 435
27. A.T. Lamm, M.R. Stadler, H. Zhang, J.I. Gent, and A.Z. Fire Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome Genome Res. 21 2011 265 275
28. A. Stark, J. Brennecke, N. Bushati, R.B. Russell, and S.M. Cohen Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution Cell 123 2005 1133 1146 (Pubitemid 41785426)
29. B. Wightman, I. Ha, and G. Ruvkun Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans Cell 75 1993 855 862 (Pubitemid 24014543)
30. V. Reinke, I.S. Gil, S. Ward, and K. Kazmer Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans Development 131 2004 311 323 (Pubitemid 38181371)
31. M. Tijsterman, R.F. Ketting, K.L. Okihara, T. Sijen, and R.H.A. Plasterk RNA helicase MUT-14-dependent gene silencing triggered in C. elegans by short antisense RNAs Science 295 2002 694 697 (Pubitemid 34111831)
32. T. Sijen, and R.H.A. Plasterk Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi Nature 426 2003 310 314 (Pubitemid 37463152)
33. G. Wang, and V. Reinke A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis Curr. Biol. 18 2008 861 867
34. W. Gu, M. Shirayama, D. Conte Jr., J. Vasale, P.J. Batista, J.M. Claycomb, J.J. Moresco, E.M. Youngman, J. Keys, and M.J. Stoltz Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline Mol. Cell 36 2009 231 244
35. F.A. Steiner, K.L. Okihara, S.W. Hoogstrate, T. Sijen, and R.F. Ketting RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans Nat. Struct. Mol. Biol. 16 2009 207 211
36. S. Parrish, and A. Fire Distinct roles for RDE-1 and RDE-4 during RNA interference in Caenorhabditis elegans RNA 7 2001 1397 1402 (Pubitemid 32973225)
37. H. Tabara, E. Yigit, H. Siomi, and C.C. Mello The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans Cell 109 2002 861 871 (Pubitemid 34786001)
38. N.C. Lau, L.P. Lim, E.G. Weinstein, and D.P. Bartel An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 2001 858 862 (Pubitemid 33032104)
39. Kimble, J., and Crittenden, S.L. (2005). Germline proliferation and its control. In WormBook, The C. elegans Research Community, ed. doi/10.1895/wormbook.1.13.1. http://www.wormbook.org.
40. Greenstein, D. (2005). Control of oocyte meiotic maturation and fertilization. In WormBook, The C. elegans Research Community, ed. doi/10.1895/wormbook.1.53.1. http://www.wormbook.org.
41. Strome, S. (2005). Specification of the germ line. In WormBook, The C. elegans Research Community, ed. doi/10.1895/wormbook.1.9.1. http://www.wormbook. org.
42. H. Racher, and D. Hansen Translational control in the C. elegans hermaphrodite germ line Genome 53 2010 83 102
43. W.G. Dougherty, and T.D. Parks Transgenes and gene suppression: telling us something new? Curr. Opin. Cell Biol. 7 1995 399 405
44. W. Schiebel, T. Pélissier, L. Riedel, S. Thalmeir, R. Schiebel, D. Kempe, F. Lottspeich, H.L. Sänger, and M. Wassenegger Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato Plant Cell 10 1998 2087 2101
45. P.K.T. Shiu, and R.L. Metzenberg Meiotic silencing by unpaired DNA: properties, regulation and suppression Genetics 161 2002 1483 1495 (Pubitemid 35014750)
46. J. Zong, X. Yao, J. Yin, D. Zhang, and H. Ma Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups Gene 447 2009 29 39
47. M. Chao RNA recombination in hepatitis delta virus: implications regarding the abilities of mammalian RNA polymerases Virus Res. 127 2007 208 215 (Pubitemid 47058193)
48. E. Lehmann, F. Brueckner, and P. Cramer Molecular basis of RNA-dependent RNA polymerase II activity Nature 450 2007 445 449 (Pubitemid 350126752)