Regulation of active DNA Demethylation by an α-crystallin domain protein in arabidopsis

Molecular Cell

Volumn 55, Issue 3, 2014, Pages 361-371

  Qian, Weiqiang ^a,b   Miki, Daisuke ^a   Lei, Mingguang ^b   Zhu, Xiaohong ^b   Zhang, Huiming ^b   Liu, Yunhua ^b   Li, Yan ^a   Lang, Zhaobo ^b   Wang, Jing ^a   Tang, Kai ^b   Liu, Renyi ^a   Zhu, Jian Kang ^a,b  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA CRYSTALLIN;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; GENE; GENE LOCUS; GENE MUTATION; GENE SILENCING; HEAT STRESS; IDM2 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROTEIN DOMAIN; REPORTER GENE;

ARABIDOPSIS;

ACETYLATION; ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA METHYLATION; DNA, PLANT; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; GENES, PLANT; HISTONE ACETYLTRANSFERASES; HISTONES; MUTATION; NUCLEAR PROTEINS; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, TERTIARY;

EID: 84906101577     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.06.008     Document Type: Article

References (49)

1. Agius F., Kapoor A., Zhu J.K. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc. Natl. Acad. Sci. USA 2006, 103:11796-11801.
2. Basha E., O'Neill H., Vierling E. Small heat shock proteins and α-crystallins: dynamic proteins with flexible functions. Trends Biochem. Sci. 2012, 37:106-117.
3. Bender J. DNA methylation and epigenetics. Annu. Rev. Plant Biol. 2004, 55:41-68.
4. Bengtsson, H., Simpson, K., Bullard, J., and Hansen, K. (2008). aroma.affymetrix: a generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Technical Report 745, Department of Statistics, University of California, Berkeley. http://statistics.berkeley.edu/sites/default/files/tech-reports/745.pdf.
5. Chen H., Zou Y., Shang Y., Lin H., Wang Y., Cai R., Tang X., Zhou J.M. Firefly luciferase complementation imaging assay for protein-protein interactions in plants. Plant Physiol. 2008, 146:368-376.
6. Edwards H.V., Cameron R.T., Baillie G.S. The emerging role of HSP20 as a multifunctional protective agent. Cell. Signal. 2011, 23:1447-1454.
7. Gao Z., Liu H.L., Daxinger L., Pontes O., He X., Qian W., Lin H., Xie M., Lorkovic Z.J., Zhang S., et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 2010, 465:106-109.
8. Gehring M., Huh J.H., Hsieh T.F., Penterman J., Choi Y., Harada J.J., Goldberg R.B., Fischer R.L. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 2006, 124:495-506.
9. Gehring M., Bubb K.L., Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009, 324:1447-1451.
10. Gong Z., Morales-Ruiz T., Ariza R.R., Roldán-Arjona T., David L., Zhu J.K. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 2002, 111:803-814.
11. Haag J.R., Pikaard C.S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 2011, 12:483-492.
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., Zhu J.K. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 2009, 137:498-508.
13. He X.J., Chen T., Zhu J.K. Regulation and function of DNA methylation in plants and animals. Cell Res. 2011, 21:442-465.
14. Hilton G.R., Lioe H., Stengel F., Baldwin A.J., Benesch J.L. Small heat-shock proteins: paramedics of the cell. Top. Curr. Chem. 2013, 328:69-98.
15. Hochberg Y., Benjamini Y. More powerful procedures for multiple significance testing. Stat. Med. 1990, 9:811-818.
16. Horwitz J. α-crystallin can function as a molecular chaperone. Proc. Natl. Acad. Sci. USA 1992, 89:10449-10453.
17. Hsieh T.F., Ibarra C.A., Silva P., Zemach A., Eshed-Williams L., Fischer R.L., Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science 2009, 324:1451-1454.
18. Huh J.H., Bauer M.J., Hsieh T.F., Fischer R.L. Cellular programming of plant gene imprinting. Cell 2008, 132:735-744.
19. Kim K.K., Kim R., Kim S.H. Crystal structure of a small heat-shock protein. Nature 1998, 394:595-599.
20. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11:204-220.
21. Lei M., Liu Y., Zhang B., Zhao Y., Wang X., Zhou Y., Raghothama K.G., Liu D. Genetic and genomic evidence that sucrose is a global regulator of plant responses to phosphate starvation in Arabidopsis. Plant Physiol. 2011, 156:1116-1130.
22. Li R., Yu C., Li Y., Lam T.W., Yiu S.M., Kristiansen K., Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25:1966-1967.
23. Li X., Qian W., Zhao Y., Wang C., Shen J., Zhu J.K., Gong Z. Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis. Proc. Natl. Acad. Sci. USA 2012, 109:11425-11430.
24. Lister R., O'Malley R.C., Tonti-Filippini J., Gregory B.D., Berry C.C., Millar A.H., Ecker J.R. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133:523-536.
25. MacRae T.H. Structure and function of small heat shock/α-crystallin proteins: established concepts and emerging ideas. Cell. Mol. Life Sci. 2000, 57:899-913.
26. Matzke M.A., Birchler J.A. RNAi-mediated pathways in the nucleus. Nat. Rev. Genet. 2005, 6:24-35.
27. Matzke M., Kanno T., Daxinger L., Huettel B., Matzke A.J. RNA-mediated chromatin-based silencing in plants. Curr. Opin. Cell Biol. 2009, 21:367-376.
28. Ortega-Galisteo A.P., Morales-Ruiz T., Ariza R.R., Roldán-Arjona T. Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. Plant Mol. Biol. 2008, 67:671-681.
29. Penterman J., Zilberman D., Huh J.H., Ballinger T., Henikoff S., Fischer R.L. DNA demethylation in the Arabidopsis genome. Proc. Natl. Acad. Sci. USA 2007, 104:6752-6757.
30. Pikaard C.S. Methylating the DNA of the most repressed: special access required. Mol. Cell 2013, 49:1021-1022.
31. Pontes O., Li C.F., Costa Nunes P., Haag J., Ream T., Vitins A., Jacobsen S.E., Pikaard C.S. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 2006, 126:79-92.
32. Qian W., Miki D., Zhang H., Liu Y., Zhang X., Tang K., Kan Y., La H., Li X., Li S., et al. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 2012, 336:1445-1448.
33. Saleh A., Alvarez-Venegas R., Avramova Z. An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in Arabidopsis plants. Nat. Protoc. 2008, 3:1018-1025.
34. Scharf K.D., Siddique M., Vierling E. The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing α-crystallin domains (Acd proteins). Cell Stress Chaperones 2001, 6:225-237.
35. Sun Y., MacRae T.H. The small heat shock proteins and their role in human disease. FEBS J. 2005, 272:2613-2627.
36. Tariq M., Paszkowski J. DNA and histone methylation in plants. Trends Genet. 2004, 20:244-251.
37. van Montfort R.L., Basha E., Friedrich K.L., Slingsby C., Vierling E. Crystal structure and assembly of a eukaryotic small heat shock protein. Nat. Struct. Biol. 2001, 8:1025-1030.
38. Wang X., Duan C.G., Tang K., Wang B., Zhang H., Lei M., Lu K., Mangrauthia S.K., Wang P., Zhu G., et al. RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc. Natl. Acad. Sci. USA 2013, 110:15467-15472.
39. Welsh M.J., Gaestel M. Small heat-shock protein family: function in health and disease. Ann. N Y Acad. Sci. 1998, 851:28-35.
40. Whitham S.A., Anderberg R.J., Chisholm S.T., Carrington J.C. Arabidopsis RTM2 gene is necessary for specific restriction of tobacco etch virus and encodes an unusual small heat shock-like protein. Plant Cell 2000, 12:569-582.
41. Wierzbicki A.T. The role of long non-coding RNA in transcriptional gene silencing. Curr. Opin. Plant Biol. 2012, 15:517-522.
42. Xia R., Wang J., Liu C., Wang Y., Wang Y., Zhai J., Liu J., Hong X., Cao X., Zhu J.K., Gong Z. ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell 2006, 18:85-103.
43. Zemach A., Kim M.Y., Hsieh P.H., Coleman-Derr D., Eshed-Williams L., Thao K., Harmer S.L., Zilberman D. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 2013, 153:193-205.
44. Zhang H., Zhu J.K. Active DNA demethylation in plants and animals. Cold Spring Harb. Symp. Quant. Biol. 2012, 77:161-173.
45. Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., Ecker J.R. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 2006, 126:1189-1201.
46. Zhang X., Bernatavichute Y.V., Cokus S., Pellegrini M., Jacobsen S.E. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009, 10:R62.
47. Zheng X., Pontes O., Zhu J., Miki D., Zhang F., Li W.X., Iida K., Kapoor A., Pikaard C.S., Zhu J.K. ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 2008, 455:1259-1262.
48. Zhu J.K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 2009, 43:143-166.
49. Zhu J., Kapoor A., Sridhar V.V., Agius F., Zhu J.K. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr. Biol. 2007, 17:54-59.