Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin–Dependent Regulation of

1. NowackMK

UngruA

BjerkanKN

GriniPE

SchnittgerA

2010 Reproductive cross-talk: seed development in flowering plants. Biochem Soc Trans 38 604 612

2. FeilR

BergerF

2007 Convergent evolution of genomic imprinting in plants and mammals. Trends Genet 23 192 199

3. JullienPE

BergerF

2009 Gamete-specific epigenetic mechanisms shape genomic imprinting. Curr Opin Plant Biol 12 637 642

4. LinBY

1984 Ploidy Barrier to Endosperm Development in Maize. Genetics 107 103 115

5. ScottRJ

SpielmanM

BaileyJ

DickinsonHG

1998 Parent-of-origin effects on seed development in Arabidopsis thaliana. Development 125 3329 3341

6. HaigD

WestobyM

1991 Genomic Imprinting in Endosperm: Its Effect on Seed Development in Crosses between Species, and between Different Ploidies of the Same Species, and Its Implications for the Evolution of Apomixis. Philosophical Transactions: Biological Sciences 333 1 13

7. DeChiaraTM

EfstratiadisA

RobertsonEJ

1990 A growth-deficiency phenotype in heterozygous mice carrying an insulin-like growth factor II gene disrupted by targeting. Nature 345 78 80

8. FilsonAJ

LouviA

EfstratiadisA

RobertsonEJ

1993 Rescue of the T-associated maternal effect in mice carrying null mutations in Igf-2 and Igf2r, two reciprocally imprinted genes. Development 118 731 736

9. LauMM

StewartCE

LiuZ

BhattH

RotweinP

1994 Loss of the imprinted IGF2/cation-independent mannose 6-phosphate receptor results in fetal overgrowth and perinatal lethality. Genes Dev 8 2953 2963

10. LeightonPA

IngramRS

EggenschwilerJ

EfstratiadisA

TilghmanSM

1995 Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375 34 39

11. KinoshitaT

MiuraA

ChoiY

KinoshitaY

CaoX

2004 One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303 521 523

12. LawrenceRJ

EarleyK

PontesO

SilvaM

ChenZJ

2004 A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell 13 599 609

13. GrossniklausU

Vielle-CalzadaJP

HoeppnerMA

GaglianoWB

1998 Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280 446 450

14. ChaudhuryAM

MingL

MillerC

CraigS

DennisES

1997 Fertilization-independent seed development in Arabidopsis thaliana. Proc Natl Acad Sci U S A 94 4223 4228

15. OhadN

MargossianL

HsuYC

WilliamsC

RepettiP

1996 A mutation that allows endosperm development without fertilization. Proc Natl Acad Sci U S A 93 5319 5324

16. KohlerC

HennigL

BouveretR

GheyselinckJ

GrossniklausU

2003 Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development. Embo J 22 4804 4814

17. GuittonAE

PageDR

ChambrierP

LionnetC

FaureJE

2004 Identification of new members of Fertilisation Independent Seed Polycomb Group pathway involved in the control of seed development in Arabidopsis thaliana. Development 131 2971 2981

18. TiwariS

SchulzR

IkedaY

DythamL

BravoJ

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

19. JullienPE

KinoshitaT

OhadN

BergerF

2006 Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18 1360 1372

20. AdamsS

VinkenoogR

SpielmanM

DickinsonHG

ScottRJ

2000 Parent-of-origin effects on seed development in Arabidopsis thaliana require DNA methylation. Development 127 2493 2502

21. JohnstonAJ

MatveevaE

KirioukhovaO

GrossniklausU

GruissemW

2008 A Dynamic Reciprocal RBR-PRC2 Regulatory Circuit Controls Arabidopsis Gametophyte Development. Curr Biol 18 1680 1686

22. JullienP

MosqunaA

IngouffM

SakataT

OhadN

2008 Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol 6 e194 doi:10.1371/journal.pbio.0060194

23. GehringM

ReikW

HenikoffS

2009 DNA demethylation by DNA repair. Trends Genet 25 82 90

24. ChoiY

GehringM

JohnsonL

HannonM

HaradaJJ

2002 DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110 33 42

25. BarouxC

GagliardiniV

PageDR

GrossniklausU

2006 Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev 20 1081 1086

26. Fitz GeraldJN

HuiPS

BergerF

2009 Polycomb group-dependent imprinting of the actin regulator AtFH5 regulates morphogenesis in Arabidopsis thaliana. Development 136 3399 3404

27. JullienPE

KatzA

OlivaM

OhadN

BergerF

2006 Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol 16 486 492

28. KinoshitaT

YadegariR

HaradaJJ

GoldbergRB

FischerRL

1999 Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11 1945 1952

29. KohlerC

HennigL

SpillaneC

PienS

GruissemW

2003 The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev 17 1540 1553

30. MakarevichG

LeroyO

AkinciU

SchubertD

ClarenzO

2006 Different Polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep 7 947 952

31. ScottRJ

SpielmanM

2006 Genomic imprinting in plants and mammals: how life history constrains convergence. Cytogenet Genome Res 113 53 67

32. KinoshitaY

SazeH

KinoshitaT

MiuraA

SoppeWJ

2007 Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 49 38 45

33. LuoM

BilodeauP

DennisES

PeacockWJ

ChaudhuryA

2000 Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc Natl Acad Sci U S A 97 10637 10642

34. TiwariS

SpielmanM

DayRC

ScottRJ

2006 Proliferative phase endosperm promoters from Arabidopsis thaliana. Plant Biotechnol J 4 393 407

35. GehringM

BubbKL

HenikoffS

2009 Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324 1447 1451

36. IslesAR

HollandAJ

2005 Imprinted genes and mother-offspring interactions. Early Hum Dev 81 73 77

37. MorisonIM

RamsayJP

SpencerHG

2005 A census of mammalian imprinting. Trends Genet 21 457 465

38. ReikW

LewisA

2005 Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat Rev Genet 6 403 410

39. WoodAJ

OakeyRJ

2006 Genomic imprinting in mammals: emerging themes and established theories. PLoS Genet 2 e147 doi:10.1371/journal.pgen.0020147

40. NowackMK

GriniPE

JakobyMJ

LafosM

KonczC

2006 A positive signal from the fertilization of the egg cell sets off endosperm proliferation in angiosperm embryogenesis. Nat Genet 38 63 67

41. IwakawaH

ShinmyoA

SekineM

2006 Arabidopsis CDKA;1, a cdc2 homologue, controls proliferation of generative cells in male gametogenesis. Plant J 45 819 831

42. AwSJ

HamamuraY

ChenZ

SchnittgerA

BergerF

2010 Sperm entry is sufficient to trigger division of the central cell but the paternal genome is required for endosperm development in Arabidopsis. Development 137 2683 2690

43. NowackMK

ShirzadiR

DissmeyerN

DolfA

EndlE

2007 Bypassing genomic imprinting allows seed development. Nature 447 312 315

44. LeBH

ChengC

BuiAQ

WagmaisterJA

HenryKF

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

45. de FolterS

ImminkRG

KiefferM

ParenicovaL

HenzSR

2005 Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. Plant Cell 17 1424 1433

46. KangIH

SteffenJG

PortereikoMF

LloydA

DrewsGN

2008 The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis. Plant Cell 20 635 647

47. ParenicovaL

de FolterS

KiefferM

HornerDS

FavalliC

2003 Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15 1538 1551

48. RiosG

LossowA

HertelB

BreuerF

SchaeferS

2002 Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes. Plant J 32 243 253

49. GriniPE

SchnittgerA

SchwarzH

ZimmermannI

SchwabB

1999 Isolation of ethyl methanesulfonate-induced gametophytic mutants in Arabidopsis thaliana by a segregation distortion assay using the multimarker chromosome 1. Genetics 151 849 863

50. CaoX

JacobsenSE

2002 Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A 99 Suppl 4 16491 16498

51. JacksonJP

LindrothAM

CaoX

JacobsenSE

2002 Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416 556 560

52. ChanSW

ZilbermanD

XieZ

JohansenLK

CarringtonJC

2004 RNA silencing genes control de novo DNA methylation. Science 303 1336

53. JeddelohJA

StokesTL

RichardsEJ

1999 Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22 94 97

54. DayRC

HerridgeRP

AmbroseBA

MacknightRC

2008 Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiol 148 1964 1984

55. JullienPE

BergerF

2010 Parental genome dosage imbalance deregulates imprinting in Arabidopsis. PLoS Genet 6 e1000885 doi:10.1371/journal.pgen.1000885

56. KohlerC

PageDR

GagliardiniV

GrossniklausU

2005 The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 37 28 30

57. BeckerA

TheissenG

2003 The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29 464 489

58. KofujiR

SumikawaN

YamasakiM

KondoK

UedaK

2003 Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses. Mol Biol Evol 20 1963 1977

59. BemerM

Wolters-ArtsM

GrossniklausU

AngenentGC

2008 The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules. Plant Cell 20 2088 2101

60. PortereikoMF

LloydA

SteffenJG

PunwaniJA

OtsugaD

2006 AGL80 is required for central cell and endosperm development in Arabidopsis. Plant Cell 18 1862 1872

61. ColomboM

MasieroS

VanzulliS

LardelliP

KaterMM

2008 AGL23, a type I MADS-box gene that controls female gametophyte and embryo development in Arabidopsis. Plant J 54 1037 1048

62. SteffenJG

KangIH

PortereikoMF

LloydA

DrewsGN

2008 AGL61 interacts with AGL80 and is required for central cell development in Arabidopsis. Plant Physiol 148 259 268

63. De BodtS

RaesJ

FlorquinK

RombautsS

RouzeP

2003 Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants. J Mol Evol 56 573 586

64. JosefssonC

DilkesB

ComaiL

2006 Parent-dependent loss of gene silencing during interspecies hybridization. Curr Biol 16 1322 1328

65. WaliaH

JosefssonC

DilkesB

KirkbrideR

HaradaJ

2009 Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr Biol 19 1128 1132

66. ErilovaA

BrownfieldL

ExnerV

RosaM

TwellD

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

67. ZhangX

YazakiJ

SundaresanA

CokusS

ChanSW

2006 Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis. Cell 126 1189 1201

68. YadegariR

KinoshitaT

LotanO

CohenG

KatzA

2000 Mutations in the FIE and MEA genes that encode interacting polycomb proteins cause parent-of-origin effects on seed development by distinct mechanisms. Plant Cell 12 2367 2382

69. HsiehTF

IbarraCA

SilvaP

ZemachA

Eshed-WilliamsL

2009 Genome-wide demethylation of Arabidopsis endosperm. Science 1451 1454

70. BarlowDP

1993 Methylation and imprinting: from host defense to gene regulation? Science 260 309 310

71. ChanSW

ZhangX

BernatavichuteYV

JacobsenSE

2006 Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol 4 e363 doi:10.1371/journal.pbio.0040363

72. MosherRA

MelnykCW

KellyKA

DunnRM

StudholmeDJ

2009 Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460 283 286

73. ZhangX

ClarenzO

CokusS

BernatavichuteYV

PellegriniM

2007 Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5 e129 doi:10.1371/journal.pbio.0050129

74. MakarevichG

VillarC

ErilovaA

KohlerC

2008 Mechanism of PHERES1 imprinting in Arabidopsis. Journal of Cell Science 121 906 912

75. NgoQA

MooreJM

BaskarR

GrossniklausU

SundaresanV

2007 Arabidopsis GLAUCE promotes fertilization-independent endosperm development and expression of paternally inherited alleles. Development 134 4107 4117

76. SazeH

Mittelsten ScheidO

PaszkowskiJ

2003 Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34 65 69

77. WangD

TysonMD

JacksonSS

YadegariR

2006 Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis. Proc Natl Acad Sci U S A 103 13244 13249

78. ZilbermanD

CaoX

JacobsenSE

2003 ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299 716 719

79. GoodrichJ

PuangsomleeP

MartinM

LongD

MeyerowitzEM

1997 A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386 44 51

80. LindrothAM

CaoX

JacksonJP

ZilbermanD

McCallumCM

2001 Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292 2077 2080

81. CaoX

JacobsenSE

2002 Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12 1138 1144

82. MurashigeT

SkoogF

1962 A rewised medium for rapid growth and bioassays with tobacco tissue cultures. Physiologia Plantarum 15 473 497

83. YangYH

DudoitS

LuuP

LinDM

PengV

2002 Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30 e15

84. SmythGK

2004 Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3 1 25

85. StoreyJD

2002 A direct approach to false discovery rates. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64 479 498

86. HulsenT

de VliegJ

AlkemaW

2008 BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics 9 488

87. CurtisMD

GrossniklausU

2003 A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133 462 469

88. BentA

2006 Arabidopsis thaliana floral dip transformation method. Methods Mol Biol 343 87 103

89. HuangS

AnYQ

McDowellJM

McKinneyEC

MeagherRB

1997 The Arabidopsis thaliana ACT11 actin gene is strongly expressed in tissues of the emerging inflorescence, pollen, and developing ovules. Plant Mol Biol 33 125 139

90. PfafflMW

2001 A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29 e45