High-Resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm

PLoS Genetics

Volumn 7, Issue 6, 2011, Pages

  Wolff, Philip ^a,b   Weinhofer, Isabelle ^a   Seguin, Jonathan ^a   Roszak, Pawel ^a   Beisel, Christian ^c   Donoghue, Mark T A ^d   Spillane, Charles ^d   Nordborg, Magnus ^e   Rehmsmeier, Marc ^e   Köhler, Claudia ^a,b  

^a ETH ZURICH   (Switzerland)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c SWISS FEDERAL INSTITUTE OF TECHNOLOGY   (Switzerland)

^d NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^e GREGOR MENDEL INSTITUTE OF MOLECULAR PLANT BIOLOGY   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

FACTOR FOR INVERSION STIMULATION; POLYCOMB GROUP PROTEIN; REPRESSOR PROTEIN;

ALLELE; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; CROSS BREEDING; DNA METHYLATION; ENDOSPERM; EPIGENETICS; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE REPRESSION; GENE TARGETING; GENETIC ASSOCIATION; GENOME IMPRINTING; MOLECULAR EVOLUTION; NONHUMAN; PLANT GENE; PLANT GENOME; PLANT SEED; RNA SEQUENCE; SEQUENCE ANALYSIS; TRANSPOSON; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; MULTIGENE FAMILY;

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAMMALIA;

ALLELES; ANIMALS; ARABIDOPSIS; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; ENDOSPERM; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; GENOMIC IMPRINTING; MULTIGENE FAMILY; REPRESSOR PROTEINS; SEEDS;

EID: 79959848590     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002126     Document Type: Article

References (68)

1. Köhler C, Weinhofer-Molisch I, (2010) Mechanisms and evolution of genomic imprinting in plants. Heredity 105: 57-63.
2. Jullien PE, Berger F, (2009) Gamete-specific epigenetic mechanisms shape genomic imprinting. Curr Opin Plant Biol 12: 637-642.
3. Jahnke S, Scholten S, (2009) Epigenetic resetting of a gene imprinted in plant embryos. Curr Biol 19: 1677-1681.
4. Berger F, (2003) Endosperm: the crossroad of seed development. Curr Opin Plant Biol 6: 42-50.
5. Drews GN, Yadegari R, (2002) Development and function of the angiosperm female gametophyte. Annu Rev Genet 36: 99-124.
6. Gehring M, Bubb KL, Henikoff S, (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447-1451.
7. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, et al. (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324: 1451-1454.
8. 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.
9. Teixeira FK, Colot V, (2010) Repeat elements and the Arabidopsis DNA methylation landscape. Heredity 105: 14-23.
10. 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.
11. 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.
12. 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.
13. 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.
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. Hennig L, Derkacheva M, (2009) Diversity of Polycomb group complexes in plants: same rules, different players? Trends Genet 25: 414-423.
16. 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.
17. Xiao W, Gehring M, Choi Y, Margossian L, Pu H, et al. (2003) Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell 5: 891-901.
18. Makarevich G, Villar CB, Erilova A, Köhler C, (2008) Mechanism of PHERES1 imprinting in Arabidopsis. J Cell Sci 121: 906-912.
19. Villar CB, Erilova A, Makarevich G, Trösch R, Köhler C, (2009) Control of PHERES1 imprinting in Arabidopsis by direct tandem repeats. Mol Plant 2: 654-660.
20. Barlow DP, (1993) Methylation and imprinting: from host defense to gene regulation? Science 260: 309-310.
21. Haig D, Westoby M, (1989) Parent specific gene expression and the triploid endosperm. Am Nature 134: 147-155.
22. Trivers R, Burt A, (1999) Kinship and genomic imprinting. Results Probl Cell Differ 25: 1-21.
23. Reik W, Constancia M, Fowden A, Anderson N, Dean W, et al. (2003) Regulation of supply and demand for maternal nutrients in mammals by imprinted genes. J Physiol 547: 35-44.
24. 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.
25. Kiyosue T, Ohad N, Yadegari R, Hannon M, Dinneny J, et al. (1999) Control of fertilization-independent endosperm development by the MEDEA Polycomb gene in Arabidopsis. Proc Natl Acad Sci U S A 96: 4186-4191.
26. Tiwari S, Schulz R, Ikeda Y, Dytham L, Bravo J, et al. (2008) MATERNALLY EXPRESSED PAB C-TERMINAL, a Novel Imprinted Gene in Arabidopsis, Encodes the Conserved C-Terminal Domain of Polyadenylate Binding Proteins. Plant Cell 20: 2387-2398.
27. Spillane C, Schmid KJ, Laoueille-Duprat S, Pien S, Escobar-Restrepo JM, et al. (2007) Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448: 349-352.
28. Miyake T, Takebayashi N, Wolf DE, (2009) Possible diversifying selection in the imprinted gene, MEDEA, in Arabidopsis. Mol Biol Evol 26: 843-857.
29. O'Connell MJ, Loughran NB, Walsh TA, Donoghue MT, Schmid KJ, et al. (2010) A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals. Mamm Genome 21: 486-498.
30. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18: 2024-2033.
31. 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.
32. Kermicle J, (1970) Dependence of the R-mottled aleurone phenotype in maize on the mode of sexual transmission. Genetics 66: 69-85.
33. Chaudhuri S, Messing J, (1994) Allele-specific parental imprinting of dzr1, a posttranscriptional regulator of zein accumulation. Proc Natl Acad Sci U S A 91: 4867-4871.
34. Christensen C, King E, Jordan J, Drews GN, (1997) Megagametogenesis in Arabidopsis wild type and the Gf mutant. Sexual Plant Reproduction 10: 49-64.
35. Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, et al. (2009) Paternal control of embryonic patterning in Arabidopsis thaliana. Science 323: 1485-1488.
36. Colombo M, Masiero S, Vanzulli S, Lardelli P, Kater MM, et al. (2008) AGL23, a type I MADS-box gene that controls female gametophyte and embryo development in Arabidopsis. Plant J 54: 1037-1048.
37. de Folter S, Immink RG, Kieffer M, Parenicova L, Henz SR, et al. (2005) Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell 17: 1424-1433.
38. Kang IH, Steffen JG, Portereiko MF, Lloyd A, Drews GN, (2008) The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis. Plant Cell 20: 635-647.
39. Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, et al. (2008) DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135: 1201-1212.
40. Popp C, Dean W, Feng S, Cokus SJ, Andrews S, et al. (2010) Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463: 1101-1105.
41. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S, (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: 61-69.
42. Bourc'his D, Voinnet O, (2010) A small-RNA perspective on gametogenesis, fertilization, and early zygotic development. Science 330: 617-622.
43. Feng S, Jacobsen SE, Reik W, (2010) Epigenetic reprogramming in plant and animal development. Science 330: 622-627.
44. 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.
45. 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.
46. Erilova A, Brownfield L, Exner V, Rosa M, Twell D, et al. (2009) Imprinting of the Polycomb group gene MEDEA serves as a ploidy sensor in Arabidopsis. PLoS Genet 5: e1000663 doi:10.1371/journal.pgen.1000663.
47. Tiwari S, Spielman M, Schulz R, Oakey RJ, Kelsey G, et al. (2010) Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana. BMC Plant Biol 10: 72.
48. Jullien PE, Berger F, (2010) Parental genome dosage imbalance deregulates imprinting in Arabidopsis. PLoS Genet 6: e1000885 doi:10.1371/journal.pgen.1000885.
49. Spillane C, Baroux C, Escobar-Restrepo JM, Page DR, Laoueille S, et al. (2004) Transposons and tandem repeats are not involved in the control of genomic imprinting at the MEDEA locus in Arabidopsis. Cold Spring Harb Symp Quant Biol 69: 465-475.
50. Wan LB, Bartolomei MS, (2008) Regulation of imprinting in clusters: noncoding RNAs versus insulators. Adv Genet 61: 207-223.
51. Dilkes BP, Spielman M, Weizbauer R, Watson B, Burkart-Waco D, et al. (2008) The maternally expressed WRKY transcription factor TTG2 controls lethality in interploidy crosses of Arabidopsis. PLoS Biol 6: e308 doi:10.1371/journal.pbio.0060308.
52. Weinhofer I, Hehenberger E, Roszak P, Hennig L, Köhler C, (2010) H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet 6: e1001152 doi:10.1371/journal.pgen.1001152.
53. Chan SW, Henderson IR, Zhang X, Shah G, Chien JS, et al. (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet 2: e83 doi:10.1371/journal.pgen.0020083.
54. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
55. Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472.
56. Kapitonov VV, Jurka J, (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23: 521-529.
57. Hollister JD, Gaut BS, (2007) Population and evolutionary dynamics of Helitron transposable elements in Arabidopsis thaliana. Mol Biol Evol 24: 2515-2524.
58. Sweredoski M, DeRose-Wilson L, Gaut BS, (2008) A comparative computational analysis of nonautonomous helitron elements between maize and rice. BMC Genomics 9: 467.
59. Saze H, Scheid OM, Paszkowski J, (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34: 65-69.
60. Abouelhoda M, Kurtz S, Ohlebusch E, (2004) Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms 2: 53-86.
61. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B 57: 289-300.
62. Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, et al. (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci U S A 107: 8063-8070.
63. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
64. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, et al. (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129 doi:10.1371/journal.pbio.0050129.
65. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378.
66. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
67. Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
68. Yang Z, (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.