REVIEW

MicroRNA-mediated DNA methylation in plants

  • Xiaoyun JIA 1,2 ,
  • Jun YAN 2 ,
  • Guiliang TANG , 2
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  • 1. College of Life Science, Shanxi Agricultural University, Taigu 030801, China
  • 2. Gene Suppression Laboratory, Department of Plant and Soil Sciences and KTRDC, University of Kentucky, Lexington, KY 40546, USA

Received date: 27 Dec 2010

Accepted date: 30 Jan 2011

Published date: 01 Apr 2011

Copyright

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg

Abstract

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.

Cite this article

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

DOI PMID

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

DOI PMID

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

DOI PMID

4
Bartel D P (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2): 281-297

DOI PMID

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

DOI PMID

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

DOI PMID

7
Carthew R W, Sontheimer E J (2009). Origins and mechanisms of miRNAs and siRNAs. Cell, 136(4): 642-655

DOI PMID

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

DOI PMID

9
Chapman E J, Carrington J C (2007). Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet, 8(11): 884-896

DOI PMID

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

DOI PMID

11
Chen X (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303(5666): 2022-2025

DOI PMID

12
Chinnusamy V, Zhu J K (2009). Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol, 12(2): 133-139

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

16
Ghildiyal M, Zamore P D (2009). Small silencing RNAs: an expanding universe. Nat Rev Genet, 10(2): 94-108

DOI PMID

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

DOI PMID

18
Henderson I R, Jacobsen S E (2007). Epigenetic inheritance in plants. Nature, 447(7143): 418-424

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

34
Ronemus M, Martienssen R (2005). RNA interference: methylation mystery. Nature, 433(7025): 472-473

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

40
Voinnet O (2009). Origin, biogenesis, and activity of plant microRNAs. Cell, 136(4): 669-687

DOI PMID

41
Wolffe A P, Matzke M A (1999). Epigenetics: regulation through repression. Science, 286(5439): 481-486

DOI PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

45
Xie Z, Qi X (2008). Diverse small RNA-directed silencing pathways in plants. Biochim Biophys Acta, 1779(11): 720-724

PMID

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

DOI PMID

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

DOI PMID

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

DOI PMID

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