Received date: 27 Dec 2010
Accepted date: 30 Jan 2011
Published date: 01 Apr 2011
Copyright
DNA methylation, a major event in epigenetics, plays an essential role in the control of gene expression. Increasing evidence suggests that long and short non-coding RNAs are involved extensively in plants to direct the establishment, spread, and removal of DNA cytosine methylation throughout their genomes. Yet, little has been known about the role of microRNAs (miRNAs) in DNA methylation although the role of small interfering RNAs (siRNAs) in DNA methylation has been well established. Several recent studies, however, provided the evidence for miRNA-directed DNA methylation in plants, and the working mechanisms still need to be fully explored. In this review, we highlight the key features of miRNA-directed DNA methylation in plants and provide insight into the complexities of such an event in plants. The interaction between miRNAs and the epigenetic machinery and the future potential research questions are briefly discussed.
Xiaoyun JIA , Jun YAN , Guiliang TANG . MicroRNA-mediated DNA methylation in plants[J]. Frontiers in Biology, 2011 , 6(2) : 133 -139 . DOI: 10.1007/s11515-011-1136-4
| 1 |
Ahmad A, Zhang Y, Cao X F (2010). Decoding the epigenetic language of plant development. Mol Plant, 3(4): 719-728
|
| 2 |
Axtell M J, Snyder J A, Bartel D P (2007). Common functions for diverse small RNAs of land plants. Plant Cell, 19(6): 1750-1769
|
| 3 |
Bao N, Lye K W, Barton M K (2004). MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev Cell, 7(5): 653-662
|
| 4 |
Bartel D P (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2): 281-297
|
| 5 |
Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto Y Y, Sieburth L, Voinnet O (2008). Widespread translational inhibition by plant miRNAs and siRNAs. Science, 320(5880): 1185-1190
|
| 6 |
Cao X, Jacobsen S E (2002). Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol, 12(13): 1138-1144
|
| 7 |
Carthew R W, Sontheimer E J (2009). Origins and mechanisms of miRNAs and siRNAs. Cell, 136(4): 642-655
|
| 8 |
Chan S W, Henderson I R, Jacobsen S E (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet, 6(5): 351-360
|
| 9 |
Chapman E J, Carrington J C (2007). Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet, 8(11): 884-896
|
| 10 |
Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H (2010). siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res, 38(20): 6883-6894
|
| 11 |
Chen X (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303(5666): 2022-2025
|
| 12 |
Chinnusamy V, Zhu J K (2009). Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol, 12(2): 133-139
|
| 13 |
Cokus S J, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild C D, Pradhan S, Nelson S F, Pellegrini M, Jacobsen S E (2008). Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452(7184): 215-219
|
| 14 |
Das S, Foley N, Bryan K, Watters K M, Bray I, Murphy D M, Buckley P G, Stallings R L (2010). MicroRNA mediates DNA demethylation events triggered by retinoic acid during neuroblastoma cell differentiation. Cancer Res, 70(20): 7874-7881
|
| 15 |
Fattash I, Voss B, Reski R, Hess W R, Frank W (2007). Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol, 7(1): 13
|
| 16 |
Ghildiyal M, Zamore P D (2009). Small silencing RNAs: an expanding universe. Nat Rev Genet, 10(2): 94-108
|
| 17 |
Gonzalez S, Pisano D G, Serrano M (2008). Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs. Cell Cycle, 7(16): 2601-2608
|
| 18 |
Henderson I R, Jacobsen S E (2007). Epigenetic inheritance in plants. Nature, 447(7143): 418-424
|
| 19 |
Herr A J, Jensen M B, Dalmay T, Baulcombe D C (2005). RNA polymerase IV directs silencing of endogenous DNA. Science, 308(5718): 118-120
|
| 20 |
Kanno T, Huettel B, Mette M F, Aufsatz W, Jaligot E, Daxinger L, Kreil D P, Matzke M, Matzke A J (2005). Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet, 37(7): 761-765
|
| 21 |
Khraiwesh B, Arif M A, Seumel G I, Ossowski S, Weigel D, Reski R, Frank W (2010). Transcriptional control of gene expression by microRNAs. Cell, 140(1): 111-122
|
| 22 |
Kim D H, Saetrom P, Snøve O Jr, Rossi J J (2008). MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci USA, 105(42): 16230-16235
|
| 23 |
Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, Crété P, Voinnet O, Robaglia C (2009). Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell, 21(6): 1762-1768
|
| 24 |
Lee Y, Jeon K, Lee J T, Kim S, Kim V N (2002). MicroRNA maturation: stepwise processing and subcellular localization. EMBO J, 21(17): 4663-4670
|
| 25 |
Lelandais-Briere C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M (2009). Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell, 21(9): 2780-2796
|
| 26 |
Li C F, Pontes O, El-Shami M, Henderson I R, Bernatavichute Y V, Chan S W, Lagrange T, Pikaard C S, Jacobsen S E (2006). An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell, 126(1): 93-106
|
| 27 |
Liu B, Li P, Li X, Liu C, Cao S, Chu C, Cao X (2005). Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol, 139(1): 296-305
|
| 28 |
Llave C, Xie Z, Kasschau K D, Carrington J C (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297(5589): 2053-2056
|
| 29 |
Matzke M, Kanno T, Daxinger L, Huettel B, Matzke A J (2009). RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol, 21(3): 367-376
|
| 30 |
Onodera Y, Haag J R, Ream T, Nunes P C, Pontes O, Pikaard C S (2005). Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell, 120(5): 613-622
|
| 31 |
Park W, Li J, Song R, Messing J, Chen X (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol, 12(17): 1484-1495
|
| 32 |
Pontes O, Costa-Nunes P, Vithayathil P, Pikaard C S (2009). RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway. Mol Plant, 2(4): 700-710
|
| 33 |
Qi Y, He X, Wang X J, Kohany O, Jurka J, Hannon G J (2006). Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature, 443(7114): 1008-1012
|
| 34 |
Ronemus M, Martienssen R (2005). RNA interference: methylation mystery. Nature, 433(7025): 472-473
|
| 35 |
Sunkar R, Girke T, Jain P K, Zhu J K (2005a). Cloning and characterization of microRNAs from rice. Plant Cell, 17(5): 1397-1411
|
| 36 |
Sunkar R, Girke T, Zhu J K (2005b). Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res, 33(14): 4443-4454
|
| 37 |
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J K (2008). Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol, 8(1): 25
|
| 38 |
Tang G, Reinhart B J, Bartel D P, Zamore P D (2003). A biochemical framework for RNA silencing in plants. Genes Dev, 17(1): 49-63
|
| 39 |
Vazquez F, Blevins T, Ailhas J, Boller T, Meins F Jr (2008). Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res, 36(20): 6429-6438
|
| 40 |
Voinnet O (2009). Origin, biogenesis, and activity of plant microRNAs. Cell, 136(4): 669-687
|
| 41 |
Wolffe A P, Matzke M A (1999). Epigenetics: regulation through repression. Science, 286(5439): 481-486
|
| 42 |
Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y (2009). Rice microRNA effector complexes and targets. Plant Cell, 21(11): 3421-3435
|
| 43 |
Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010). DNA methylation mediated by a microRNA pathway. Mol Cell, 38(3): 465-475
|
| 44 |
Xie Z, Johansen L K, Gustafson A M, Kasschau K D, Lellis A D, Zilberman D, Jacobsen S E, Carrington J C (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biol, 2(5): E104
|
| 45 |
Xie Z, Qi X (2008). Diverse small RNA-directed silencing pathways in plants. Biochim Biophys Acta, 1779(11): 720-724
|
| 46 |
Zheng B, Wang Z, Li S, Yu B, Liu J Y, Chen X (2009). Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev, 23(24): 2850-2860
|
| 47 |
Zhu Q H, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C (2008). A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res, 18(9): 1456-1465
|
| 48 |
Zilberman D, Cao X, Jacobsen S E (2003). ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299(5607): 716-719
|
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