Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

Current Biology

Volumn 18, Issue 10, 2008, Pages 758-762

  Addo Quaye, Charles ^a   Eshoo, Tifani W ^b   Bartel, David P ^d,e   Axtell, Michael J ^b,c  

^a The Pennsylvania State University   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^e MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

PLANT; RNA

Indexed keywords

MESSENGER RNA; MICRORNA; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; GENETICS; METABOLISM; MULTIGENE FAMILY; SEQUENCE ANALYSIS;

ARABIDOPSIS; MICRORNAS; MULTIGENE FAMILY; RNA, MESSENGER; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA;

ANIMALIA; ARABIDOPSIS;

EID: 43449091567     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2008.04.042     Document Type: Article

References (36)

1. Bartel D.P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
2. 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
3. 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
4. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., and Bartel D.P. Prediction of plant microRNA targets. Cell 110 (2002) 513-520
5. 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
6. Vaucheret H. MicroRNA-dependent trans-acting siRNA production. Sci. STKE 2005 (2005) pe43
7. 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
8. Franco-Zorrilla J.M., Valli A., Todesco M., Mateos I., Puga M.I., Rubio-Somoza I., Leyva A., Weigel D., Garcia J.A., and Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39 (2007) 1033-1037
9. Kasschau K.D., Xie Z., Allen E., Llave C., Chapman E.J., Krizan K.A., and Carrington J.C. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell 4 (2003) 205-217
10. 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
11. Axtell M.J., and Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 17 (2005) 1658-1673
12. Schmid M., Davison T.S., Henz S.R., Pape U.J., Demar M., Vingron M., Scholkopf B., Weigel D., and Lohmann J.U. A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37 (2005) 501-506
13. Rajagopalan R., Vaucheret H., Trejo J., and Bartel D.P. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20 (2006) 3407-3425
14. Fahlgren N., Howell M.D., Kasschau K.D., Chapman E.J., Sullivan C.M., Cumbie J.S., Givan S.A., Law T.F., Grant S.R., Dangl J.L., et al. High-throughput sequencing of Arabidopsis microRNAs: Evidence for frequent birth and death of MIRNA genes. PLoS ONE 2 (2007) e219
15. 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
16. Kurihara Y., and Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. USA 101 (2004) 12753-12758
17. Talmor-Neiman M., Stav R., Frank W., Voss B., and Arazi T. Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss. Plant J. 47 (2006) 25-37
18. 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
19. Axtell M.J., and Bowman J. Evolution of plant microRNAs and their targets. Trends Plant Sci. (2008) in press
20. Palatnik J.F., Wollmann H., Schommer C., Schwab R., Boisbouvier J., Rodriguez R., Warthmann N., Allen E., Dezulian T., Huson D., et al. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 13 (2007) 115-125
21. Allen R.S., Li J., Stahle M.I., Dubroue A., Gubler F., and Millar A.A. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc. Natl. Acad. Sci. USA 104 (2007) 16371-16376
22. 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
23. Lu C., Tej S.S., Luo S., Haudenschild C.D., Meyers B.C., and Green P.J. Elucidation of the small RNA component of the transcriptome. Science 309 (2005) 1567-1569
24. 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
25. 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
26. Mourrain P., Beclin C., Elmayan T., Feuerbach F., Godon C., Morel J.B., Jouette D., Lacombe A.M., Nikic S., Picault N., et al. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101 (2000) 533-542
27. 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
28. 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
29. Montgomery T.A., Howell M.D., Cuperus J.T., Li D., Hansen J.E., Alexander A.L., Chapman E.J., Fahlgren N., Allen E., and Carrington J.C. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133 (2008) 128-141
30. 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
31. 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
32. 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
33. Gy I., Gasciolli V., Lauressergues D., Morel J.B., Gombert J., Proux F., Proux C., Vaucheret H., and Mallory A.C. Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 19 (2007) 3451-3461
34. Souret F.F., Kastenmayer J.P., and Green P.J. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell 15 (2004) 173-183
35. Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., and Enright A.J. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34 (2006) D140-D144
36. Farh K.K., Grimson A., Jan C., Lewis B.P., Johnston W.K., Lim L.P., Burge C.B., and Bartel D.P. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310 (2005) 1817-1821