miSSING LINKS: miRNAs and plant development

Current Opinion in Genetics and Development

Volumn 13, Issue 4, 2003, Pages 372-378

  Hunter, Christine ^a   Poethig, R Scott ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; MICRORNA; PLANT RNA; POST TRANSCRIPTIONAL GENE SILENCING PROTEIN; PROTEIN AGO 1; PROTEIN AGO 4; PROTEIN PNH; PROTEIN SDE 1; PROTEIN SDE 3; PROTEIN SGS 2; PROTEIN SGS 3; RIBONUCLEASE III; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ARABIDOPSIS; EMBRYOLOGY; GENE CONTROL; GENE IDENTIFICATION; GENE MUTATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC CODE; GENETICS; GENOME; MOLECULE; MUTATION; NONHUMAN; NULL ALLELE; PHENOTYPE; PLANT; PLANT DEVELOPMENT; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; REVIEW; RNA PROCESSING; SIGNAL TRANSDUCTION;

ARABIDOPSIS;

EID: 0042346346     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(03)00081-9     Document Type: Review

References (53)

1. Couzin J. Breakthrough of the year. Small RNAs make big splash. Science. 298:2002;2296-2297.
2. Hutvagner G., Zamore P.D. RNAi: nature abhors a double-strand. Curr Opin Genet Dev. 12:2002;225-232.
3. Carmell M.A., Xuan Z., Zhang M.Q., Hannon G.J. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16:2002;2733-2742.
4. Hamilton A., Voinnet O., Chappell L., Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J. 21:2002;4671-4679.
5. Voinnet O. RNA silencing: small RNAs as ubiquitous regulators of gene expression. Curr Opin Plant Biol. 5:2002;444-451.
6. Timmons L. The long and short of siRNAs. Mol Cell. 10:2002;435-437.
7. 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.
8. 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.
9. 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.
10. 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.
11. Seggerson K., Tang L., Moss E.G. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev Biol. 243:2002;215-225.
12. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., 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.
13. 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.
14. 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.
15. Martinez J., Patkaniowska A., Urlaub H., Luhrmann R., Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell. 110:2002;563-574.
16. Hutvagner G., Zamore P.D. A microRNA in a multiple-turnover RNAi enzyme complex. Science. 297:2002;2056-2060.
17. Doench J.G., Petersen C.P., Sharp P.A. siRNAs can function as miRNAs. Genes Dev. 17:2003;438-442.
18. 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 Identification of a large group of Arabidopsis siRNAs and miRNAs.
19. Park W., Li J., Song R., Messing J., Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol. 12:2002;1484-1495 Isolation of developmentally regulated miRNAs, along with the cloning of HEN1 and the demonstration that HEN1 and DCL1 are required for miRNA processing.
20. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 16:2002;1616-1626 Isolation of Arabidopsis miRNAs, and an analysis of their expression, predicted precursors and conservation in rice. This paper also shows that miRNA production requires DCL1.
21. Tang G., Reinhart B.J., Bartel D.P., Zamore P.D. A biochemical framework for RNA silencing in plants. Genes Dev. 17:2003;49-63 In this outstanding paper, the authors use a wheat-germ extract system to characterize both siRNAs and miRNAs and their activity. They demonstrate that plant miRNAs can act via RISC-mediated target cleavage, and show that a dominant mutation in the PHV gene blocks cleavage of its mRNA, providing a link between biochemical analysis and developmental phenotype.
22. Finnegan E.J., Margis R., Waterhouse P.M. Posttranscriptional gene silencing is not compromised in the Arabidopsis CARPEL FACTORY (DICER-LIKE1) mutant, a homolog of Dicer-1 from Drosophila. Curr Biol. 13:2003;236-240 The first demonstration that DCL1 does not affect siRNA processing, and an insightful discussion of the separation of the miRNA and siRNA pathways in Arabidopsis.
23. Kasschau K.D., Xie Z., Allen E., Llave C., Chapman E.J., Krizan K.A., 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 Exciting work showing that the viral protein HC-Pro increases miRNA levels but blocks miRNA function. In addition, the authors show that DCL1 differentially affects miRNA processing and that many predicted miRNA targets are, in fact, cleaved by their cognate miRNAs.
24. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. Prediction of plant microRNA targets. Cell. 110:2002;513-520 The prediction of Arabidopsis miRNA targets, which calls attention to the large number of developmentally important targets and the likelihood that the targets will be cleaved, rather than translationally repressed.
25. Llave C., Xie Z., Kasschau K.D., Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science. 297:2002;2053-2056 Prior to this work, it was thought that siRNAs directed target cleavage, whereas miRNAs regulated translation. This paper was the first to demonstrate that an endogenously encoded miRNA could bring about 'siRNA-like' cleavage of an mRNA target.
26. 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 Dominant alleles of these polarity genes represent mutations in the miRNA target sites, providing the first indication of a possible function for miRNAs in plants.
27. Schauer S.E., Jacobsen S.E., Meinke D.W., Ray A. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 7:2002;487-491.
28. Schwartz B.W., Meinke D.W. Disruption of morphogenesis and the transformation of the suspensor in abnormal suspensor mutants of Arabidopsis. Development. 120:1994;3235-3245.
29. Jacobsen S.E., Running M.P., Meyerowitz E.M. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development. 126:1999;5231-5243.
30. 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.
31. 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.
32. Golden T.A., Schauer S.E., Lang J.D., Pien S., Mushegian A.R., Grossniklaus U., Meinke D.W., Ray A. SHORT INTEGUMENTS1/SUSPENSOR1/CARPEL FACTORY, a Dicer homolog, is a maternal effect gene required for embryo development in Arabidopsis. Plant Physiol. 130:2002;808-822.
33. Ray S., Golden T., Ray A. Maternal effects of the short integument mutation on embryo development in Arabidopsis. Dev Biol. 180:1996;365-369.
34. Chen X., Liu J., Cheng Y., Jia D. HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower. Development. 129:2002;1085-1094.
35. 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.
36. Morel J.B., Godon C., Mourrain P., Beclin C., Boutet S., Feuerbach F., Proux F., Vaucheret H. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell. 14:2002;629-639 AGO1 and PNH are related genes, known to have overlapping roles in development. This paper demonstrates that although AGO1 has an additional role in PTGS, PNH is not required for this process.
37. Lynn K., Fernandez A., Aida M., Sedbrook J., Tasaka M., Masson P., Barton M.K. The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development. 126:1999;469-481.
38. McConnell J.R., Barton M.K. Effect of mutations in the PINHEAD gene of Arabidopsis on the formation of the shoot apical meristems. Dev Genet. 16:1995;358-366.
39. Moussian B., Schoof H., Haecker A., Jurgens G., Laux T. Role of the ZWILLE gene in the regulation of central shoot meristem cell fate during Arabidopsis embryogenesis. EMBO J. 17:1998;1799-1809.
40. Nishimura A., Ito M., Kamiya N., Sato Y., Matsuoka M. OsPNH1 regulates leaf development and maintenance of the shoot apical meristem in rice. Plant J. 30:2002;189-201.
41. Newman K.L., Fernandez A.G., Barton M.K. Regulation of axis determinacy by the Arabidopsis PINHEAD gene. Plant Cell. 14:2002;3029-3042.
42. Fagard M., Boutet S., Morel J.B., Bellini C., 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.
43. Beclin C., Boutet S., Waterhouse P., Vaucheret H. A branched pathway for transgene-induced RNA silencing in plants. Curr Biol. 12:2002;684-688.
44. Zilberman D., Cao X., Jacobsen S.E. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 299:2003;716-719.
45. 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.
46. Dalmay T., Hamilton A., Rudd S., Angell S., Baulcombe D.C. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell. 101:2000;543-553.
47. Dalmay T., Horsefield R., Braunstein T.H., Baulcombe D.C. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J. 20:2001;2069-2078.
48. Bateman A. The SGS3 protein involved in PTGS finds a family. BMC Bioinformatics. 3:2002;21. [ http://www.biomedcentral.com/1471-2105/3/21 ].
49. Jorgensen R.A. RNA traffics information systemically in plants. Proc Natl Acad Sci USA. 99:2002;11561-11563.
50. McConnell J.R., Barton M.K. Leaf polarity and meristem formation in Arabidopsis. Development. 125:1998;2935-2942.
51. Gwizdek C., Ossareh-Nazari B., Brownawell A.M., Doglio A., Bertrand E., Macara I.G., Dargemont C. Exportin-5 mediates nuclear export of minihelix-containing RNAs. J Biol Chem. 278:2003;5505-5508.
52. Bollman K., Aukerman M., Park M., Hunter C., Berardini T., Poethig R.S. Developmental functions of HASTY, the Arabidopsis orthologue of Exportin-5. Development. 130:2003;1493-1504.
53. Mallory A.C., Reinhart B.J., Bartel D., Vance V.B., Bowman L.H. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco. Proc Natl Acad Sci USA. 99:2002;15228-15233.