Prediction of plant microRNA targets

Cell

Volumn 110, Issue 4, 2002, Pages 513-520

  Rhoades, Matthew W ^a,b   Reinhart, Brenda J ^a   Lim, Lee P ^a,b   Burge, Christopher B ^b   Bartel, Bonnie ^c   Bartel, David P ^a,b  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; CELL DIFFERENTIATION; CELL LINEAGE; CONTROLLED STUDY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RICE;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0037162702     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(02)00863-2     Document Type: Article

References (49)

1. Aida M., Ishida T., Fukaki H., Fujisawa H., Tasaka M. Genes involved in organ separation in Arabidopsis. an analysis of the cup-shaped cotyledon mutant Plant Cell. 9:1997;841-857.
2. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408:2000;796-815.
3. Bernstein E., Denli A.M., Hannon G.J. The rest is silence. RNA. 7:2001;1509-1521.
4. Bohmert K., Camus I., Bellini C., Bouchez D., Caboche M., Benning C. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 17:1998;170-180.
5. Bolle C., Koncz C., Chua N.H. PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction. Genes Dev. 14:2000;1269-1278.
6. Cui Y., Brugière N., Jackman L., Bi Y.-M., Rothstein S. Structural and transcriptional comparative analysis of the S locus regions in two self-incompatible Brassica napus lines. Plant Cell. 11:1999;2217-2231.
7. Di Laurenzio L., Wysocka-Diller J., Malamy J.E., Pysh L., Helariutta Y., Freshour G., Hahn M.G., Feldmann K.A., Benfey P.N. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell. 86:1996;423-433.
8. Dsouza M., Larsen N., Overbeek R. Searching for patterns in genomic data. Trends Genet. 13:1997;497-498.
9. Elbashir S.M., Martinez J., Patkaniowska A., Lendeckel W., Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20:2001;6877-6888.
10. Gocal G.F., Sheldon C.C., Gubler F., Moritz T., Bagnall D.J., MacMillan C.P., Li S.F., Parish R.W., Dennis E.S., Weigel D., King R.W. GAMYB-like genes, flowering, and gibberellin signalling in Arabidopsis. Plant Physiol. 127:2001;1682-1693.
11. Grishok A., Pasquinelli A.E., Conte D., Li N., Parrish S., Ha I., Baillie D.L., Fire A., Ruvkun G., Mello C.C. 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.
12. Ha I., Wightman B., Ruvkun G. A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev. 10:1996;3041-3050.
13. Hamilton A.J., Baulcombe D.C. A novel species of small antisense RNA in posttranscriptional gene silencing. Science. 286:1999;950-952.
14. Helariutta Y., Fukaki H., Wysocka-Diller J., Nakajima K., Jung J., Sena G., Hauser M.T., Benfey P.N. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell. 101:2000;555-567.
15. Hutvágner G., Zamore P.D. Rnai. nature abhors a double-strand Curr. Opin. Genet. Dev. 12:2002;225-232.
16. Hutvágner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 293:2001;834-838.
17. Jacobsen S.E., Running M.P., Meyerowitz E.M. Disruption of an RNA helicase/RNAseIII gene in Arabidopsis causes unregulated cell division in floral meristems. Development. 126:1999;5231-5243.
18. Ketting R.F., Fischer S.E.J., Bernstein E., Sijen T., Hannon G.J., Plasterk R.H.A. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15:2001;2654-2659.
19. Kiss T. Small nucleolar RNAs. an abundant group of noncoding RNAs with diverse cellular functions Cell. 109:2002;145-148.
20. Klein J., Saedler H., Huijser P. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 250:1996;7-16.
21. Knight S.W., Bass B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science. 293:2001;2269-2271.
22. Lagos-Quintana M., Rauhut R., Lendeckel W., Tuschl T. Identification of novel genes coding for small expressed RNAs. Science. 294:2001;853-858.
23. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12:2002;735-739.
24. Lai E.C. MicroRNAs are complementary to 3′UTR motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30:2002;363-364.
25. Lau N.C., Lim L.P., Weinstein E.G., Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science. 294:2001;858-862.
26. Lee R.C., Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science. 294:2001;862-864.
27. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 75:1993;843-854.
28. Liscum E., Reed J.W. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol. Biol. 49:2002;387-400.
29. Llave C., Kasschau K.D., Rector M.A., Carrington J.C. Endogenous and silencing-associated small RNAs in plants. Plant Cell. 14:2002;1605-1619.
30. Matzke M.A., Matzke A.J., Pruss G.J., Vance V.B. RNA-based silencing strategies in plants. Curr. Opin. Genet. Dev. 11:2001;221-227.
31. McConnell J.R., Emery J., Eshed Y., Bao N., Bowman J., Barton M.K. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature. 411:2001;709-713.
32. McManus M.T., Petersen C.P., Haines B.B., Chen J., Sharp P.A. Gene silencing using micro-RNA designed hairpins. RNA. 8:2002;842-850.
33. Moss E.G., Lee R.C., Ambros V. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell. 88:1997;637-646.
34. Mourelatos Z., Dostie J., Paushkin S., Sharma A., Charroux B., Abel L., Rappsilber J., Mann M., Dreyfuss G. miRNPs. a novel class of ribonucleoproteins containing numerous microRNAs Genes Dev. 16:2002;720-728.
35. Olsen P.H., Ambros V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216:1999;671-680.
36. Peng J., Carol P., Richards D.E., King K.E., Cowling R.J., Murphy G.P., Harberd N.P. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 11:1997;3194-3205.
37. Ray A., Lang J.D., Golden T., Ray S. SHORT INTEGUMENT (SIN1), a gene required for ovule development in Arabidopsis, also controls flowering time. Development. 122:1996;2631-2638. a.
38. Ray S., Golden T., Ray A. Maternal effects of the short integument mutation on embryo development. Dev. Biol. 180:1996;365-369. b.
39. Reinhart B.J., Slack F.J., Basson M., Bettinger J.C., Pasquinelli A.E., Rougvie A.E., Horvitz H.R., Ruvkun G. The 21 nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 403:2000;901-906.
40. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 16:2002;1616-1626.
41. Riechmann J.L., Heard J., Martin G., Reuber L., Jiang C.-Z., Keddie J., Adam L., Pineda O., Ratcliffe O.J., Samaha R.R.et al. Arabidopsis transcription factors. genome-wide comparative analysis among eukaryotes Science. 290:2000;2105-2110.
42. Robinson-Beers K., Pruitt R.E., Gasser C.S. Ovule development in wild-type Arabidopsis and two female-sterile mutants. Plant Cell. 4:1992;1237-1249.
43. Rogg L.E., Bartel B. Auxin signaling. derepression through regulated proteolysis Dev. Cell. 1:2001;595-604.
44. Silverstone A.L., Ciampaglio C.N., Sun T. The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway. Plant Cell. 10:1998;155-169.
45. Slack F.J., Basson M., Liu Z., Ambros V., Horvitz H.R., Ruvkun G. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell. 5:2000;659-669.
46. Ulmasov T., Hagen G., Guilfoyle T.J. Dimerization and DNA binding of auxin response factors. Plant J. 19:1999;309-319.
47. Wightman B., Ha I., Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell. 75:1993;855-862.
48. Yeh R.F., Lim L.P., Burge C.B. Computational inference of homologous gene structures in the human genome. Genome Res. 11:2001;803-816.
49. Yu J., Hu S., Wang J., Wong G.K., Li S., Liu B., Deng Y., Dai L., Zhou Y., Zhang X.et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. 296:2002;79-92.