A Genome-Wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm

PLoS Genetics

Volumn 7, Issue 6, 2011, Pages

  Luo, Ming ^a   Taylor, Jennifer M ^a   Spriggs, Andrew ^a   Zhang, Hongyu ^a,b   Wu, Xianjun ^b   Russell, Scott ^c   Singh, Mohan ^d   Koltunow, Anna ^a  

^a CSIRO   (Australia)

^b SICHUAN AGRICULTURAL UNIVERSITY   (China)

^c UNIVERSITY OF OKLAHOMA   (United States)

^d UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PLANT RNA;

ALLELE; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; ENDOSPERM; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENOME IMPRINTING; NONHUMAN; PLANT GENE; PLANT SEED; RICE; RNA EXTRACTION; SINGLE NUCLEOTIDE POLYMORPHISM; ALTERNATIVE RNA SPLICING; CHROMOSOME MAP; CROP; CROSS BREEDING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; PLANT GENOME; POLYADENYLATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY;

ARABIDOPSIS; JAPONICA; LILIOPSIDA; MAMMALIA;

ALTERNATIVE SPLICING; ARABIDOPSIS; CHROMOSOME MAPPING; CROPS, AGRICULTURAL; CROSSES, GENETIC; ENDOSPERM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENETIC LOCI; GENOME, PLANT; GENOMIC IMPRINTING; ORYZA SATIVA; POLYADENYLATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, PLANT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 79959818388     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002125     Document Type: Article

References (68)

1. Feil R, Berger F, (2007) Convergent evolution of genomic imprinting in plants and mammals. Trends Genet 23: 192-9.
2. Raissig MT, Baroux C, Grossniklaus U, (2011) Regulation and Flexibility of Genomic Imprinting during Seed Development. Plant Cell 10.1105/tpc.110.081018. [Epub ahead of print].
3. Köhler C, Weinhofer-Molisch I, (2010) Mechanisms and evolution of genomic imprinting in plants. Heredity 105: 57-63.
4. Ideraabdullah FY, Vigneau S, Bartolomei MS, (2008) Genomic imprinting mechanisms in mammals. Mutat Res 647: 77-85.
5. Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, et al. (2002) DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110: 33-42.
6. Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, et al. (2006) DEMETER DNA glycosylase establishes MEDEA Polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495-506.
7. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, et al. (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303: 521-523.
8. Jullien PE, Kinoshita T, Ohad N, Berger F, (2006) Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18: 1360-1372.
9. Jullien PE, Mosquna A, Ingouff M, Sakata T, Ohad N, et al. (2008) Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol 6: e194 doi:10.1371/journal.pbio.0060194.
10. Jullien PE, Katz A, Oliva M, Ohad N, Berger F, (2006) Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol 16: 486-492.
11. Köhler C, Page DR, Gagliardini V, Grossniklaus U, (2005) The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 37: 28-30.
12. Baroux C, Gagliardini V, Page DR, Grossniklaus U, (2006) Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev 20: 1081-1086.
13. Makarevich G, Villar CB, Erilova A, Köhler C, (2008) Mechanism of PHERES1 imprinting in Arabidopsis. J Cell Sci 121: 906-912.
14. Fitz Gerald JN, Hui PS, Berger F, (2009) Polycomb group-dependent imprinting of the actin regulator AtFH5 regulates morphogenesis in Arabidopsis thaliana. Development 136: 3399-3404.
15. Gutiérrez-Marcos JF, Costa LM, Dal Prà M, Scholten S, Kranz E, et al. (2006) Epigenetic asymmetry of imprinted genes in plant gametes. Nat Genet 38: 876-8.
16. Haun WJ, Springer NM, (2008) Maternal and paternal alleles exhibit differential histone methylation and acetylation at maize imprinted genes. Plant J 56: 903-12.
17. Babak T, Deveale B, Armour C, Raymond C, Cleary MA, et al. (2008) Global survey of genomic imprinting by transcriptome sequencing. Curr Biol 18: 1735-41.
18. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, et al. (2010) High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain. Science 329: 643-648.
19. Tycko B, Morison IM, (2002) Physiological functions of imprinted genes. Journal of Cellular Physiology 192: 245-58.
20. Wood AJ, Oakey RJ, (2006) Genomic Imprinting in Mammals: Emerging Themes and Established Theories. PLoS Genet 2: e147 doi:10.1371/journal.pgen.0020147.
21. Hirasawa R, Feil R, (2010) Genomic imprinting and human disease. Essays Biochem 48: 187-200.
22. Frost JM, Moore GE, (2010) The importance of imprinting in the human placenta. PLoS Genet 6: e1001015 doi:10.1371/journal.pgen.1001015.
23. Scott RJ, Spielman M, Bailey J, Dickinson HG, (1998) Parent-of-origin effects on seed development in Arabidopsis thaliana. Development 125: 3329-41.
24. Lin BY, (1984) Ploidy barrier to endosperm development in maize. Genetics 107: 103-115.
25. Birchler JA, (1993) Dosage analysis of maize endosperm development. Ann Rev Genet 27: 181-204.
26. Drews GN, Yadegari R, (2002) Development and function of the angiosperm female gametophyte. Annu Rev Genet 36: 99-124.
27. Jahnke S, Scholten S, (2009) Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 19: 1677-1681.
28. Hsieh TF, Shin J, Uzawa R, Silva P, Cohen S, et al. (2011) Inaugural Article: Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci U S A 108: 1755-1762.
29. Haig D, Westoby M, (1989) Parent specific gene expression and the triploid endosperm. Am Nature 134: 147-155.
30. Chaudhury AM, Ming L, Miller C, Craig S, Dennis ES, et al. (1997) Fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci USA 94: 4223-4228.
31. Grossniklaus U, Vielle-Calzada JP, Hoeppner MA, Gagliano WB, (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280: 446-450.
32. Dilkes B, Comai L, (2004) A Differential Dosage Hypothesis for Parental Effects in Seed Development. The Plant Cell 16: 3174-3180.
33. Josefsson C, Dilkes B, Comai L, (2006) Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16: 1322-1328.
34. Kinoshita T, (2007) Reproductive barrier and genomic imprinting in the endosperm of flowering plants. Genes Genet Syst 82: 177-86.
35. Gutierrez-Marcos JF, Pennington PD, Costa LM, Dickinson HG, (2003) Imprinting in the endosperm: a possible role in preventing wide hybridization. Philos Trans R Soc Lond B Biol Sci 358: 1105-11 Review.
36. Guo M, Rupe MA, Danilevskaya ON, Yang X, Hu Z, (2003) Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J 36: 30-44.
37. Stupar RM, Hermanson PJ, Springer NM, (2007) Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm. Plant Physiol 145: 411-25.
38. Danilevskaya ON, Hermon P, Hantke S, Muszynski MG, Kollipara K, et al. (2003) Duplicated fie genes in maize: expression pattern and imprinting suggest distinct functions. Plant Cell 15: 425-438.
39. Gutiérrez-Marcos JF, Costa LM, Biderre-Petit C, Khbaya B, O'Sullivan DM, et al. (2004) maternally expressed gene1 is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression. Plant Cell 16: 1288-1301.
40. Hermon P, Srilunchang KO, Zou J, Dresselhaus T, Danilevskaya ON, (2007) Activation of the imprinted Polycomb group Fie1 gene in maize endosperm requires demethylation of the maternal allele. Plant Mol Biol 64: 387-395.
41. Luo M, Platten D, Chaudhury A, Peacock WJ, Dennis ES, (2009) Expression, imprinting, and evolution of rice homologs of the polycomb group genes. Mol Plant 2: 711-23.
42. Ishikawa R, Ohnishi T, Kinoshita Y, Eiguchi M, Kurata N, et al. (2010) Rice interspecies hybrids show precocious or delayed developmental transitions in the endosperm without change to the rate of syncytial nuclear division. Plant J 65: 798-806.
43. Itoh J, Nonomura K, Ikeda K, Yamaki S, Inukai Y, et al. (2005) Rice plant development: from zygote to spikelet. Plant Cell Physiol 46: 23-47.
44. Wood AJ, Schulz R, Woodfine K, Koltowska K, Beechey CV, et al. (2008) Regulation of alternative polyadenylation by genomic imprinting. Genes Dev 22: 1141-6.
45. Thorvaldsen JL, Bartolomei MS, (2007) SnapShot: Imprinted gene clusters. Cell 130: 958.
46. de Dios Alché J, M'rani-Alaoui M, Castro AJ, Rodríguez-García MI, (2004) Ole e 1, the major allergen from olive (Olea europaea L.) pollen, increases its expression and is released to the culture medium during in vitro germination. Plant Cell Physiol 45: 1149-57.
47. Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, et al. (2009) Paternal control of embryonic patterning in Arabidopsis thaliana. Science 323: 1485-8.
48. Denis CL, Chen J, (2003) The CCR4-NOT complex plays diverse roles in mRNA metabolism. Prog Nucleic Acid Res Mol Biol 73: 221-50.
49. Spassov D, Jurecic R, (2003) The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function? IUBMB Life 55: 359-366.
50. Gonzalez D, Bowen AJ, Carroll TS, Conlan RS, (2007) The transcription corepressor LEUNIG interacts with the histone deacetylase HDA19 and mediator components MED14 (SWP) and CDK8 (HEN3) to repress transcription. Mol Cell Biol 27: 5306-5315.
51. Kato H, Tjernberg A, Zhang W, Krutchinsky AN, An W, et al. (2002) SYT associates with human SNF/SWI complexes and the C-terminal region of its fusion partner SSX1 targets histones. J Biol Chem 277: 5498-505.
52. Gehring M, Bubb KL, Henikoff S, (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451.
53. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, et al. (2004) Genetic and Functional Diversification of Small RNA Pathways in Plants. PLoS Biol 2: e104 doi:10.1371/journal.pbio.0020104.
54. Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, et al. (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma 112: 308-315.
55. Ogas J, Kaufmann S, Henderson J, Somerville C, (1999) PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc Natl Acad Sci U S A 96: 13839-44.
56. He G, Zhu X, Elling AA, Chen L, Wang X, et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. The Plant Cell 22: 17-33.
57. Renfree MB, Ager EI, Shaw G, Pask AJ, (2008) Genomic imprinting in marsupial placentation. Reproduction 136: 523-31.
58. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324: 1451-1454.
59. Kraft E, Bostick M, Jacobsen SE, Callis J, (2008) ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Plant J 56: 704-715.
60. Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, et al. (2010) Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107: 18729-34.
61. Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-4.
62. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
63. Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Sciense 296: 79-92.
64. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-10.
65. Gou XP, Wang SH, Chen F, (1999) Isolation and cytological observation of viable sperm cells of rice. Acta Botanica Sinica 41: 669-674.
66. Xu H, Theerakulpisut P, Goulding N, Suphioglu C, Singh MB, et al. (1995) Cloning, expression and immunological characterization of Ory s 1, the major allergen of rice pollen. Gene 164: 255-9.
67. von Besser K, Frank AC, Johnson MA, Preuss D, (2006) Arabidopsis HAP2 (GCS1) is a sperm-specific gene required for pollen tube guidance and fertilization. Development 133: 4761-9.
68. Li C, (2008) Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics 9: 231.