Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 29, 2014, Pages 10642-10647

  Hu, Lanjuan ^a   Li, Ning ^a   Xu, Chunming ^a   Zhong, Silin ^a,b   Lin, Xiuyun ^c   Yang, Jingjing ^a   Zhou, Tianqi ^a   Yuliang, Anzhi ^a   Wu, Ying ^a   Chen, Yun Ru ^b   Cao, Xiaofeng ^d   Zemach, Assaf ^e   Rustgi, Sachin ^f   Von Wettstein, Diter ^f   Liu, Bao ^a  

^a NORTHEAST NORMAL UNIVERSITY   (China)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

^c JILIN ACADEMY OF AGRICULTURAL SCIENCES   (China)

^d INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 2; UNCLASSIFIED DRUG;

ARABIDOPSIS THALIANA; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; CROP IMPROVEMENT; DNA METHYLATION; DNA REPLICATION; ENZYME ACTIVITY; GENE EXPRESSION REGULATION; GENE MUTATION; GENE REPRESSION; HETEROZYGOTE; LETHALITY; LOSS OF FUNCTION MUTATION; MITOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PYROSEQUENCING; RICE; RNA SEQUENCE; SEED DEVELOPMENT; SEEDLING; TRANSCRIPTION REGULATION; TRANSPOSON; UPREGULATION; VEGETATIVE GROWTH;

MONOCOTYLEDONS; ORYZA SATIVA L.;

CYTOSINE; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; METHYLTRANSFERASES; MUTATION; OPEN READING FRAMES; ORYZA SATIVA; PLANT PROTEINS; RNA, PLANT; SEEDLING;

EID: 84904645254     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1410761111     Document Type: Article

References (37)

1. Feng S, et al. (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107(19):8689-8694.
2. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3):204-220.
3. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328(5980):916-919.
4. Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRMand CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99(Suppl 4):16491-16498. (Pubitemid 35470998)
5. Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152(1-2):352-364.
6. Zemach A, et al. (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153(1):193-205.
7. Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260(5116):1926-1928. (Pubitemid 23258270)
8. Genger RK, Kovac KA, Dennis ES, Peacock WJ, Finnegan EJ (1999) Multiple DNA methyltransferase genes in Arabidopsis thaliana. Plant Mol Biol 41(2):269-278.
9. Kankel MW, et al. (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163(3):1109-1122. (Pubitemid 36417951)
10. Saze H, Mittelsten Scheid O, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34(1):65-69. (Pubitemid 36548792)
11. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130(5):851-862. (Pubitemid 47334929)
12. Cokus SJ, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184):215-219. (Pubitemid 351380251)
13. Lister R, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523-536.
14. Chen T, et al. (2007) Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat Genet 39(3):391-396. (Pubitemid 46328497)
15. Kouzminova E, Selker EU (2001) dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20(15):4309-4323. (Pubitemid 32751846)
16. Pavlopoulou A, Kossida S (2007) Plant cytosine-5 DNA methyltransferases: Structure, function, and molecular evolution. Genomics 90(4):530-541. (Pubitemid 47407765)
17. Yamauchi T, et al. (2009) Homologous recombination-mediated knock-in targeting of the MET1a gene for a maintenance DNA methyltransferase reproducibly reveals dosage-dependent spatiotemporal gene expression in rice. Plant J 60(2):386-396.
18. Yamauchi T, Johzuka-Hisatomi Y, Terada R, Nakamura I, Iida S (2014) The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice. Plant Mol Biol 85(3):219-232.
19. Zemach A, et al. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci USA 107(43):18729-18734.
20. Wen S, et al. (2012) Structural genes of wheat and barley 5-methylcytosine DNA glycosylases and their potential applications for human health. Proc Natl Acad Sci USA 109(50):20543-20548.
21. Springer NM (2013) Epigenetics and crop improvement. Trends Genet 29(4):241-247.
22. La H, et al. (2011) A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proc Natl Acad Sci USA 108(37):15498-15503.
23. Li X, et al. (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics 13:300.
24. Feng S, Jacobsen SE, Reik W (2010) Epigenetic reprogramming in plant and animal development. Science 330(6004):622-627.
25. Rigal M, Kevei Z, Pélissier T, Mathieu O (2012) DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. EMBO J 31(13):2981-2993.
26. Lu F, et al. (2008) Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J Integr Plant Biol 50(7):886-896.
27. Trapnell C, et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31(1):46-53.
28. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: Where genetics meets genomics. Nat Rev Genet 3(5):329-341. (Pubitemid 34506715)
29. Chen X, Zhou DX (2013) Rice epigenomics and epigenetics: Challenges and opportunities. Curr Opin Plant Biol 16(2):164-169.
30. Zhang H, Zhu JK (2011) RNA-directed DNA methylation. Curr Opin Plant Biol 14(2):142-147.
31. Bond DM, Baulcombe DC (2014) Small RNAs and heritable epigenetic variation in plants. Trends Cell Biol 24(2):100-107.
32. Melnyk CW, Molnar A, Bassett A, Baulcombe DC (2011) Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr Biol 21(19):1678-1683.
33. Calarco JP, et al. (2012) Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151(1):194-205.
34. Cao X, et al. (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13(24):2212-2217. (Pubitemid 38024949)
35. Slotkin RK, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136(3):461-472.
36. Schmitz RJ, Zhang X (2011) High-throughput approaches for plant epigenomic studies. Curr Opin Plant Biol 14(2):130-136.
37. Zhang X (2008) The epigenetic landscape of plants. Science 320(5875):489-492.