The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation

Plant Journal

Volumn 72, Issue 3, 2012, Pages 491-500

  Xie, Meng ^a   Ren, Guodong ^a   Zhang, Chi ^a   Yu, Bin ^a  

^a UNIVERSITY OF NEBRASKA   (United States)

Author keywords

Arabidopsis; epigenetics; RNA directed DNA methylation; SGS3 LIKE proteins; small RNAs

Indexed keywords

ARABIDOPSIS; COILED-COIL DOMAINS; COMPLEX FORMATIONS; DNA METHYLATION; EPIGENETICS; GEL FILTRATION; HETEROTETRAMERS; HOMODIMERS; IN-VIVO; RNA-BINDING PROTEIN; SMALL RNA;

DNA; PROTEINS;

RNA;

ARABIDOPSIS PROTEIN; DNA BINDING PROTEIN; DOUBLE STRANDED RNA; FDM1 PROTEIN, ARABIDOPSIS; IDN2 PROTEIN, ARABIDOPSIS; MULTIPROTEIN COMPLEX; PLANT DNA; PLANT RNA; RNA BINDING PROTEIN;

ARABIDOPSIS; ARTICLE; DIMERIZATION; DNA METHYLATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MUTATION; PROTEIN TERTIARY STRUCTURE; TWO HYBRID SYSTEM;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DIMERIZATION; DNA METHYLATION; DNA, PLANT; DNA-BINDING PROTEINS; GENE EXPRESSION; GENE EXPRESSION REGULATION, PLANT; MULTIPROTEIN COMPLEXES; MUTATION; PROTEIN STRUCTURE, TERTIARY; RNA, DOUBLE-STRANDED; RNA, PLANT; RNA-BINDING PROTEINS; TWO-HYBRID SYSTEM TECHNIQUES;

ARABIDOPSIS;

EID: 84868202138     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2012.05092.x     Document Type: Article

References (39)

1. Ausin, I., Mockler, T.C., Chory, J., and, Jacobsen, S.E., (2009) IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat. Struct. Mol. Biol. 16, 1325-1327.
2. Ausin, I., Greenberg, M.V., Simanshu, D.K., et al. (2012) INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc. Natl Acad. Sci. USA, 109, 8374-8381.
3. Bateman, A., (2002) The SGS3 protein involved in PTGS finds a family. BMC Bioinformatics, 3, 21.
4. Bies-Etheve, N., Pontier, D., Lahmy, S., Picart, C., Vega, D., Cooke, R., and, Lagrange, T., (2009) RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep. 10, 649-654.
5. Cao, X., and, Jacobsen, S.E., (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc. Natl Acad. Sci. USA, 99, 16491-16498.
6. Cao, X., Aufsatz, W., Zilberman, D., Mette, M.F., Huang, M.S., Matzke, M., and, Jacobsen, S.E., (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr. Biol. 13, 2212-2217.
7. Curtis, M.D., and, Grossniklaus, U., (2003) A GATEWAY cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133, 462-469.
8. El-Shami, M., Pontier, D., Lahmy, S., Braun, L., Picart, C., Vega, D., Hakimi, M.A., Jacobsen, S.E., Cooke, R., and, Lagrange, T., (2007) Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539-2544.
9. Feng, S., Jacobsen, S.E., and, Reik, W., (2010) Epigenetic reprogramming in plant and animal development. Science, 330, 622-627.
10. Gao, Z., Liu, H.L., Daxinger, L., et al. (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature, 465, 106-109.
11. Havecker, E.R., Wallbridge, L.M., Hardcastle, T.J., Bush, M.S., Kelly, K.A., Dunn, R.M., Schwach, F., Doonan, J.H., and, Baulcombe, D.C., (2010) The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell, 22, 321-334.
12. He, X.J., Hsu, Y.F., Zhu, S., Wierzbicki, A.T., Pontes, O., Pikaard, C.S., Liu, H.L., Wang, C.S., Jin, H., and, Zhu, J.K., (2009) An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell, 137, 498-508.
13. Herr, A.J., Jensen, M.B., Dalmay, T., and, Baulcombe, D.C., (2005) RNA polymerase IV directs silencing of endogenous DNA. Science, 308, 118-120.
14. Ito, M., Koike, A., Koizumi, N., and, Sano, H., (2003) Methylated DNA-binding proteins from Arabidopsis. Plant Physiol. 133, 1747-1754.
15. Jiao, X., Trifillis, P., and, Kiledjian, M., (2002) Identification of target messenger RNA substrates for the murine deleted in azoospermia-like RNA-binding protein. Biol. Reprod. 66, 475-485.
16. Kanno, T., Mette, M.F., Kreil, D.P., Aufsatz, W., Matzke, M., and, Matzke, A.J., (2004) Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 14, 801-805.
17. Kanno, T., Huettel, B., Mette, M.F., Aufsatz, W., Jaligot, E., Daxinger, L., Kreil, D.P., Matzke, M., and, Matzke, A.J., (2005) Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat. Genet. 37, 761-765.
18. Kanno, T., Bucher, E., Daxinger, L., Huettel, B., Bohmdorfer, G., Gregor, W., Kreil, D.P., Matzke, M., and, Matzke, A.J., (2008) A structural- maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat. Genet. 40, 670-675.
19. Law, J.A., Ausin, I., Johnson, L.M., Vashisht, A.A., Zhu, J.K., Wohlschlegel, J.A., and, Jacobsen, S.E., (2010) A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in Arabidopsis. Curr. Biol. 20, 951-956.
20. Law, J.A., Vashisht, A.A., Wohlschlegel, J.A., and, Jacobsen, S.E., (2011) SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 7, e1002195.
21. Liu, J., Bai, G., Zhang, C., Chen, W., Zhou, J., Zhang, S., Chen, Q., Deng, X., He, X.J., and, Zhu, J.K., (2011) An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing. Cell Res. 21, 1691-1700.
22. Moazed, D., (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature, 457, 413-420.
23. Mourrain, P., Beclin, C., Elmayan, T., et al. (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 101, 533-542.
24. Onodera, Y., Haag, J.R., Ream, T., Costa Nunes, P., Pontes, O., and, Pikaard, C.S., (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell, 120, 613-622.
25. Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L., and, Poethig, R.S., (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 18, 2368-2379.
26. Pontier, D., Yahubyan, G., Vega, D., Bulski, A., Saez-Vasquez, J., Hakimi, M.A., Lerbs-Mache, S., Colot, V., and, Lagrange, T., (2005) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 19, 2030-2040.
27. Rowley, M.J., Avrutsky, M.I., Sifuentes, C.J., Pereira, L., and, Wierzbicki, A.T., (2011) Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet. 7, e1002120.
28. Smith, L.M., Pontes, O., Searle, I., Yelina, N., Yousafzai, F.K., Herr, A.J., Pikaard, C.S., and, Baulcombe, D.C., (2007) An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell, 19, 1507-1521.
29. Wierzbicki, A.T., Haag, J.R., and, Pikaard, C.S., (2008) Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell, 135, 635-648.
30. Wierzbicki, A.T., Ream, T.S., Haag, J.R., and, Pikaard, C.S., (2009) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat. Genet. 41, 630-634.
31. Xie, Z., Johansen, L.K., Gustafson, A.M., Kasschau, K.D., Lellis, A.D., Zilberman, D., Jacobsen, S.E., and, Carrington, J.C., (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104.
32. Xie, M., Ren, G., Costa-Nunes, P., Pontes, O., and, Yu, B., (2012) A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation. Nucleic Acids Res. 40, 4422-4431.
33. Yu, B., Bi, L., Zheng, B., et al. (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl Acad. Sci. USA, 105, 10073-10078.
34. Zhang, H., and, Zhu, J.K., (2011) RNA-directed DNA methylation. Curr. Opin. Plant Biol. 14, 142-147.
35. Zhang, C.J., Ning, Y.Q., Zhang, S.W., Chen, Q., Shao, C.R., Guo, Y.W., Zhou, J.X., Li, L., Chen, S., and, He, X.J., (2012) IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet. 8, e1002693.
36. Zheng, X., Zhu, J., Kapoor, A., and, Zhu, J.K., (2007) Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J. 26, 1691-1701.
37. Zheng, B., Wang, Z., Li, S., Yu, B., Liu, J.Y., and, 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, 2850-2860.
38. Zheng, Z., Xing, Y., He, X.J., Li, W., Hu, Y., Yadav, S.K., Oh, J., and, Zhu, J.K., (2010) An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant J. 62, 92-99.
39. Zilberman, D., Cao, X., and, Jacobsen, S.E., (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299, 716-719.