A non-canonical plant microRNA target site

Nucleic Acids Research

Volumn 42, Issue 8, 2014, Pages 5270-5279

  Brousse, Cécile ^a   Liu, Qikun ^b   Beauclair, Linda ^a   Deremetz, Aurélie ^a   Axtell, Michael J ^b   Bouché, Nicolas ^a  

^a INSTITUT JEAN PIERRE BOURGIN   (France)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGONAUTE 1 PROTEIN; BLUE COPPER BINDING PROTEIN; MICRORNA; MICRORNA 398; NUCLEOTIDE; PLANT RNA; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; BASE PAIRING; BIOINFORMATICS; BLUE COPPER BINDING PROTEIN GENE; CONTROLLED STUDY; GENE ISOLATION; NICOTIANA BENTHAMIANA; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT LEAF; PREDICTION; PRIORITY JOURNAL; PROTEIN RNA BINDING; TRANSGENIC PLANT;

5' UNTRANSLATED REGIONS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE PAIRING; CARRIER PROTEINS; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; RNA, MESSENGER; RNA, PLANT;

EID: 84899865836     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku157     Document Type: Article

References (36)

1. Axtell, M.J. (2013) Classification and comparison of small RNAs from plants. Ann. Rev. Plant Biol., 64, 137-159.
2. Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
3. Chi, S.W., Hannon, G.J. and Darnell, R.B. (2012) An alternative mode of microRNA target recognition. Nat. Struct. Mol. Biol., 19, 321-327.
4. Shin, C., Nam, J.W., Farh, K.K., Chiang, H.R., Shkumatava, A. and Bartel, D.P. (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell, 38, 789-802.
5. Loeb, G.B., Khan, A.A., Canner, D., Hiatt, J.B., Shendure, J., Darnell, R.B., Leslie, C.S. and Rudensky, A.Y. (2012) Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol. Cell, 48, 760-770.
6. Beauclair, L., Yu, A. and Bouche, N. (2010) microRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. Plant J., 62, 454-462.
7. Bonnet, E., Wuyts, J., Rouze, P. and Van de Peer, Y. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl Acad. Sci. USA, 101, 11511-11516.
8. Jones-Rhoades, M.W. and Bartel, D.P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14, 787-799.
9. Sunkar, R. and Zhu, J.K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16, 2001-2019.
10. Sunkar, R., Li, Y.F. and Jagadeeswaran, G. (2012) Functions of microRNAs in plant stress responses. Trends Plant Sc., 17, 196-203.
11. Dugas, D.V. and Bartel, B. (2008) Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Mol. Biol., 67, 403-417.
12. Sunkar, R., Kapoor, A. and Zhu, J.K. (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell, 18, 2051-2065.
13. Yamasaki, H., Hayashi, M., Fukazawa, M., Kobayashi, Y. and Shikanai, T. (2009) SQUAMOSA promoter binding protein-like7 is a central regulator for copper homeostasis in Arabidopsis. Plant Cell, 21, 347-361.
14. Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y.Y., Sieburth, L. and Voinnet, O. (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science, 320, 1185-1190.
15. Vaucheret, H. (2008) Plant ARGONAUTES. Trends Plant Sci., 13, 350-358.
16. Nakagawa, T., Suzuki, T., Murata, S., Nakamura, S., Hino, T., Maeo, K., Tabata, R., Kawai, T., Tanaka, K., Niwa, Y. et al. (2007) Improved Gateway binary vectors: high-performance vectors for creation of fusion constructs in transgenic analysis of plants. Biosci. Biotechnol. Biochem., 71, 2095-2100.
17. Liu, Q., Wang, F. and Axtell, M.J. (2014) Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. Plant Cell, doi:10.1105/tpc.113.120972.
18. Llave, C., Kasschau, K.D. and Carrington, J.C. (2000) Virus-encoded suppressor of posttranscriptional gene silencing targets a maintenance step in the silencing pathway. Proc. Natl Acad. Sci. USA, 97, 13401-13406.
19. Bouche, N., Lauressergues, D., Gasciolli, V. and Vaucheret, H. (2006) An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J., 25, 3347-3356.
20. Llave, C., Xie, Z., Kasschau, K.D. and Carrington, J.C. (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297, 2053-2056.
21. Kruger, J. and Rehmsmeier, M. (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res., 34, W451-W454.
22. Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10, 1507-1517.
23. Khan, J.A., Wang, Q., Sjolund, R.D., Schulz, A. and Thompson, G.A. (2007) An early nodulin-like protein accumulates in the sieve element plasma membrane of Arabidopsis. Plant Physiol., 143, 1576-1589.
24. German, M.A., Pillay, M., Jeong, D.H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L.A., Nobuta, K., German, R. et al. (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol., 26, 941-946.
25. Souret, F.F., Kastenmayer, J.P. and Green, P.J. (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell, 15, 173-183.
26. Bernal, M., Casero, D., Singh, V., Wilson, G.T., Grande, A., Yang, H., Dodani, S.C., Pellegrini, M., Huijser, P., Connolly, E.L. et al. (2012) Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. Plant Cell, 24, 738-761.
27. Li, J.F., Chung, H.S., Niu, Y., Bush, J., McCormack, M. and Sheen, J. (2013) Comprehensive protein-based artificial microRNA screens for effective gene silencing in plants. Plant Cell, 25, 1507-1522.
28. Iwakawa, H.O. and Tomari, Y. (2013) Molecular insights into microRNA-mediated translational repression in plants. Mol. Cell, 52, 591-601.
29. Tafer, H. and Hofacker, I.L. (2008) RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics, 24, 2657-2663.
30. Addo-Quaye, C., Miller, W. and Axtell, M.J. (2009) CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics, 25, 130-131.
31. Holmes-Davis, R., Tanaka, C.K., Vensel, W.H., Hurkman, W.J. and McCormick, S. (2005) Proteome mapping of mature pollen of Arabidopsis thaliana. Proteomics, 5, 4864-4884.
32. Wei, L.Q., Yan, L.F. and Wang, T. (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol., 12, R53.
33. Elbashir, S.M., Martinez, J., Patkaniowska, A., Lendeckel, W. and Tuschl, T. (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J., 20, 6877-6888.
34. Nakanishi, K., Weinberg, D.E., Bartel, D.P. and Patel, D.J. (2012) Structure of yeast Argonaute with guide RNA. Nature, 486, 368-374.
35. Nikovics, K., Blein, T., Peaucelle, A., Ishida, T., Morin, H., Aida, M. and Laufs, P. (2006) The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell, 18, 2929-2945.
36. Fabian, M.R., Sonenberg, N. and Filipowicz, W. (2010) Regulation of mRNA translation and stability by microRNAs. Annu. Rev. Biochem., 79, 351-379.