Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

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

Volumn 110, Issue 19, 2013, Pages 7934-7939

  Rodrigues, Jessica A ^a   Ruan, Randy ^b,c   Nishimura, Toshiro ^a   Sharma, Manoj K ^b,c   Sharma, Rita ^b,c   Ronald, Pamela C ^b,c   Fischer, Robert L ^a   Zilberman, Daniel ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c JOINT BIOENERGY INSTITUTE   (United States)

Author keywords

Chromatin; DNA methylation; Gene imprinting; RNA interference

Indexed keywords

PLANT DNA; PLANT RNA;

ANGIOSPERM; ARTICLE; CHROMATIN; CONTROLLED STUDY; CULTIVAR; DNA METHYLATION; ENDOSPERM; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; GENOME IMPRINTING; MONOCOT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PRIORITY JOURNAL; PROMOTER REGION; RICE; RNA METHYLATION; TRANSCRIPTION TERMINATION; TRANSPOSON;

CHROMATIN; DNA METHYLATION; GENE IMPRINTING; RNA INTERFERENCE;

ALLELES; CHROMATIN; DNA METHYLATION; ENDOSPERM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; GENOME, PLANT; GENOMIC IMPRINTING; ORYZA SATIVA; RNA INTERFERENCE; RNA, PLANT; RNA, SMALL INTERFERING; SEEDS;

EID: 84877350957     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1306164110     Document Type: Article

References (32)

1. Zemach A, Zilberman D (2010) Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Curr Biol 20(17):R780-R785.
2. He XJ, Chen T, Zhu JK (2011) Regulation and function of DNA methylation in plants and animals. Cell Res 21(3): 442-465.
3. Zhang H, Zhu JK (2011) RNA-directed DNA methylation. Curr Opin Plant Biol 14(2): 142-147.
4. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3): 204-220.
5. Morales-Ruiz T, et al. (2006) DEMETER and REPRESSOR OF SILENCING 1 encode 5- methylcytosine DNA glycosylases. Proc Natl Acad Sci USA 103(18): 6853-6858.
6. Penterman J, et al. (2007) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104(16): 6752-6757.
7. Ibarra CA, et al. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337(6100): 1360-1364.
8. Zhu JK (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43: 143-166.
9. Choi Y, et al. (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110(1): 33-42.
10. Schoft VK, et al. (2011) Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proc Natl Acad Sci USA 108(19): 8042-8047.
11. Bauer MJ, Fischer RL (2011) Genome demethylation and imprinting in the endosperm. Curr Opin Plant Biol 14(2): 162-167.
12. Mosher RA, et al. (2009) Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460(7252): 283-286.
13. Lu J, Zhang C, Baulcombe DC, Chen ZJ (2012) Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc Natl Acad Sci USA 109(14): 5529-5534.
14. Mosher RA, et al. (2011) An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs. PLoS ONE 6(10):e25756.
15. Chaw SM, Chang CC, Chen HL, Li WH (2004) Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 58(4): 424-441.
16. Zemach A, et al. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci USA 107(43): 18729-18734.
17. Nasu S, et al. (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res 9(5): 163-171.
18. Ouyang S, et al. (2007) The TIGR Rice Genome Annotation Resource: Improvements and new features. Nucleic Acids Res 35(Database issue):D883-D887.
19. Project IRGS; International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052): 793-800.
20. Zhang W, et al. (2012) High-resolution mapping of open chromatin in the rice genome. Genome Res 22(1): 151-162.
21. Luo M, et al. (2011) A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. PLoS Genet 7(6):e1002125.
22. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328(5980): 916-919.
23. Lu C, et al. (2012) Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol 29(3): 1005-1017.
24. Ono A, et al. (2012) A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny. Plant J 71(4): 564-574.
25. Gutiérrez-Marcos JF, et al. (2006) Epigenetic asymmetry of imprinted genes in plant gametes. Nat Genet 38(8): 876-878.
26. Waters AJ, et al. (2011) Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 23(12): 4221-4233.
27. Zhang M, et al. (2011) Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm. Proc Natl Acad Sci USA 108(50): 20042-20047.
28. Hsieh T-F, et al. (2011) Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci USA 108(5): 1755-1762.
29. Gutierrez-Marcos JF, Dickinson HG (2012) Epigenetic reprogramming in plant reproductive lineages. Plant Cell Physiol 53(5): 817-823.
30. Slotkin RK, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136(3): 461-472.
31. Hsieh T-F, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324(5933): 1451-1454.
32. Couvillion MT, et al. (2009) Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes Dev 23(17): 2016-2032.