Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

Cell

Volumn 133, Issue 1, 2008, Pages 128-141

  Montgomery, Taiowa A ^a   Howell, Miya D ^a   Cuperus, Josh T ^a   Li, Dawei ^b   Hansen, Jesse E ^a   Alexander, Amanda L ^a   Chapman, Elisabeth J ^a   Fahlgren, Noah ^a   Allen, Edwards ^a   Carrington, James C ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

DEVBIO; RNA

Indexed keywords

ARGONAUTE PROTEIN; DICER; MICRORNA; RNA DIRECTED RNA POLYMERASE; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; GENE EXPRESSION; IMMUNOPRECIPITATION; MUTANT; NONHUMAN; NORTHERN BLOTTING; PLANT; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN RNA BINDING; RHIZOBIUM; RNA INTERFERENCE; RNA SEQUENCE; STATISTICAL ANALYSIS; TRANSGENE; WILD TYPE;

EID: 41149158475     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2008.02.033     Document Type: Article

References (48)

1. Adenot X., Elmayan T., Lauressergues D., Boutet S., Bouche N., Gasciolli V., and Vaucheret H. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr. Biol. 16 (2006) 927-932
2. Allen E., Xie Z., Gustafson A.M., Sung G.H., Spatafora J.W., and Carrington J.C. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 36 (2004) 1282-1290
3. Allen E., Xie Z., Gustafson A.M., and Carrington J.C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121 (2005) 207-221
4. Axtell M.J., Jan C., Rajagopalan R., and Bartel D.P. A two-hit trigger for siRNA biogenesis in plants. Cell 127 (2006) 565-577
5. Axtell M.J., Snyder J.A., and Bartel D.P. Common functions for diverse small RNAs of land plants. Plant Cell 19 (2007) 1750-1769
6. Baumberger N., and Baulcombe D.C. Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc. Natl. Acad. Sci. USA 102 (2005) 11928-11933
7. Chapman E.J., and Carrington J.C. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8 (2007) 884-896
8. Chapman E.J., Prokhnevsky A.I., Gopinath K., Dolja V.V., and Carrington J.C. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev. 18 (2004) 1179-1186
9. Chen H.M., Li Y.H., and Wu S.H. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc. Natl. Acad. Sci. USA 104 (2007) 3318-3323
10. Clough S.J., and Bent A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16 (1998) 735-743
11. Curtis M.D., and Grossniklaus U. A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133 (2003) 462-469
12. Dunoyer P., Himber C., and Voinnet O. DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat. Genet. 37 (2005) 1356-1360
13. El-Shami M., Pontier D., Lahmy S., Braun L., Picart C., Vega D., Hakimi M.A., Jacobsen S.E., Cooke R., and Lagrange T. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21 (2007) 2539-2544
14. Fagard M., Boutet S., Morel J.B., Bellini C., and Vaucheret H. AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl. Acad. Sci. USA 97 (2000) 11650-11654
15. Fahlgren N., Montgomery T.A., Howell M.D., Allen E., Dvorak S.K., Alexander A.L., and Carrington J.C. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr. Biol. 16 (2006) 939-944
16. Forstemann K., Horwich M.D., Wee L., Tomari Y., and Zamore P.D. Drosophila microRNAs are sorted into functionally distinct Argonaute complexes after production by Dicer-1. Cell 130 (2007) 287-297
17. Garcia D., Collier S.A., Byrne M.E., and Martienssen R.A. Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr. Biol. 16 (2006) 933-938
18. Gasciolli V., Mallory A.C., Bartel D.P., and Vaucheret H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr. Biol. 15 (2005) 1494-1500
19. Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., and Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77 (1989) 51-59
20. Howell M.D., Fahlgren N., Chapman E.J., Cumbie J.S., Sullivan C.M., Givan S.A., Kasschau K.D., and Carrington J.C. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19 (2007) 926-942
21. Hunter C., Sun H., and Poethig R.S. The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member. Curr. Biol. 13 (2003) 1734-1739
22. Hunter C., Willmann M.R., Wu G., Yoshikawa M., de la Luz Gutierrez-Nava M., and Poethig S.R. Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 133 (2006) 2973-2981
23. Jones-Rhoades M.W., and Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 (2004) 787-799
24. Kasschau K.D., Fahlgren N., Chapman E.J., Sullivan C.M., Cumbie J.S., Givan S.A., and Carrington J.C. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5 (2007) e57
25. Kumagai M.H., Donson J., Della-Cioppa G., Harvey D., Hanley K., and Grill L.K. Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc. Natl. Acad. Sci. USA 92 (1995) 1679-1683
26. Li C.F., Pontes O., El-Shami M., Henderson I.R., Bernatavichute Y.V., Chan S.W., Lagrange T., Pikaard C.S., and Jacobsen S.E. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 126 (2006) 93-106
27. Liu J., Valencia-Sanchez M.A., Hannon G.J., and Parker R. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol. 7 (2005) 719-723
28. Llave C., Xie Z., Kasschau K.D., and Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297 (2002) 2053-2056
29. Lu C., Kulkarni K., Souret F.F., Muthuvalliappan R., Tej S.S., Poethig R.S., Henderson I.R., Jacobsen S.E., Wang W., Green P.J., and Meyers B.C. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 16 (2006) 1276-1288
30. Ma J.B., Yuan Y.R., Meister G., Pei Y., Tuschl T., and Patel D.J. Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434 (2005) 666-670
31. Parker J.S., Roe S.M., and Barford D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434 (2005) 663-666
32. Peragine A., Yoshikawa M., Wu G., Albrecht H.L., and Poethig R.S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 18 (2004) 2368-2379
33. Qi Y., Denli A.M., and Hannon G.J. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell 19 (2005) 421-428
34. Qi Y., He X., Wang X.J., Kohany O., Jurka J., and Hannon G.J. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443 (2006) 1008-1012
35. Rivas F.V., Tolia N.H., Song J.J., Aragon J.P., Liu J., Hannon G.J., and Joshua-Tor L. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Mol. Biol. 12 (2005) 340-349
36. Ronemus M., Vaughn M.W., and Martienssen R.A. MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell 18 (2006) 1559-1574
37. Ruby J.G., Jan C., Player C., Axtell M.J., Lee W., Nusbaum C., Ge H., and Bartel D.P. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127 (2006) 1193-1207
38. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., and Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8 (2005) 517-527
39. Steiner F.A., Hoogstrate S.W., Okihara K.L., Thijssen K.L., Ketting R.F., Plasterk R.H., and Sijen T. Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nat. Struct. Mol. Biol. 14 (2007) 927-933
40. Sunkar R., and Zhu J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16 (2004) 2001-2019
41. Talmor-Neiman M., Stav R., Klipcan L., Buxdorf K., Baulcombe D.C., and Arazi T. Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis. Plant J. 48 (2006) 511-521
42. Tolia N.H., and Joshua-Tor L. Slicer and the argonautes. Nat. Chem. Biol. 3 (2007) 36-43
43. Tomari Y., Du T., and Zamore P.D. Sorting of Drosophila small silencing RNAs. Cell 130 (2007) 299-308
44. Vazquez F., Vaucheret H., Rajagopalan R., Lepers C., Gasciolli V., Mallory A.C., Hilbert J.L., Bartel D.P., and Crete P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16 (2004) 69-79
45. Xie Z., Allen E., Wilken A., and Carrington J.C. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 102 (2005) 12984-12989
46. Yoshikawa M., Peragine A., Park M.Y., and Poethig R.S. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 19 (2005) 2164-2175
47. Zhang X., Yuan Y.R., Pei Y., Lin S.S., Tuschl T., Patel D.J., and Chua N.H. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 20 (2006) 3255-3268
48. Zilberman D., Cao X., and Jacobsen S.E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299 (2003) 716-719