title: Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana.
abstract: BACKGROUND
  Crossing plants of the same species but different ploidies can have dramatic effects on seed growth, but little is known about the alterations to transcriptional programmes responsible for this. Parental genomic imbalance particularly affects proliferation of the endosperm, with an increased ratio of paternally to maternally contributed genomes ('paternal excess') associated with overproliferation, while maternal excess inhibits endosperm growth. One interpretation is that interploidy crosses disrupt the balance in the seed of active copies of parentally imprinted genes. This is supported by the observation that mutations in imprinted FIS-class genes of Arabidopsis thaliana share many features of the paternal excess phenotype. Here we investigated gene expression underlying parent-of-origin effects in Arabidopsis through transcriptional profiling of siliques generated by interploidy crosses and FIS-class mutants.
  
  
  RESULTS
  We found that fertilized fis1 mutant seeds have similar profiles to seeds with paternal excess, showing that the shared phenotypes are underpinned by similar patterns of gene expression. We identified genes strongly associated with enhanced or inhibited seed growth; this provided many candidates for further investigation including MADS-box transcription factors, cell cycle genes, and genes involved in hormone pathways.
  
  
  CONCLUSIONS
  The work presented here is a step towards understanding the effects on seed development of the related phenomena of parental genome balance and imprinting.
authors.affiliation: Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.
authors.forename: Sushma
authors.initials: S
authors.lastname: Tiwari
authors.forename: Melissa
authors.initials: M
authors.lastname: Spielman
authors.forename: Reiner
authors.initials: R
authors.lastname: Schulz
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Oakey
authors.forename: Gavin
authors.initials: G
authors.lastname: Kelsey
authors.forename: Andres
authors.initials: A
authors.lastname: Salazar
authors.forename: Ke
authors.initials: K
authors.lastname: Zhang
authors.forename: Roger
authors.initials: R
authors.lastname: Pennell
authors.forename: Rod J
authors.initials: RJ
authors.lastname: Scott
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D049109:Cell Proliferation; D002843:Chromatin / Q000235:genetics; D016000:Cluster Analysis; D015536:Down-Regulation / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D010937:Plant Growth Regulators / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics* / Q000254:growth & development; D014158:Transcription, Genetic; D015854:Up-Regulation / Q000235:genetics
chemical_list: D002843:Chromatin; D010937:Plant Growth Regulators; D012333:RNA, Messenger
references.citation: Bioinformatics. 2005 May 15;21(10):2568-9
references.pmid: 15731212
references.citation: Curr Biol. 2005 Apr 26;15(8):750-4
references.pmid: 15854908
references.citation: Nat Genet. 2006 Aug;38(8):876-8
references.pmid: 16823380
references.citation: Plant Physiol. 2004 Jun;135(2):745-55
references.pmid: 15173566
references.citation: Biotech Histochem. 1996 Mar;71(2):84-7
references.pmid: 9138536
references.citation: Curr Biol. 2009 Oct 13;19(19):1677-81
references.pmid: 19781944
references.citation: Plant Cell Rep. 2006 Jun;25(6):540-5
references.pmid: 16408177
references.citation: Science. 2004 Jan 23;303(5657):521-3
references.pmid: 14631047
references.citation: Plant Physiol. 2008 Sep;148(1):259-68
references.pmid: 18599653
references.citation: Bioinformatics. 2004 Jun 12;20(9):1464-5
references.pmid: 14962934
references.citation: Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17531-6
references.pmid: 16293693
references.citation: Nat Genet. 2005 Jan;37(1):28-30
references.pmid: 15619622
references.citation: Curr Biol. 2002 Jan 22;12(2):153-8
references.pmid: 11818068
references.citation: J Cell Biol. 1997 Dec 15;139(6):1485-93
references.pmid: 9396754
references.citation: Development. 2004 Nov;131(21):5263-76
references.pmid: 15456723
references.citation: Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):472-6
references.pmid: 16387852
references.citation: Nucleic Acids Res. 2001 Nov 1;29(21):4319-33
references.pmid: 11691919
references.citation: Nucleic Acids Res. 2006 Jul 19;34(12):e88
references.pmid: 16855283
references.citation: Curr Biol. 2009 Jul 14;19(13):1128-32
references.pmid: 19559614
references.citation: Curr Biol. 2006 Jul 11;16(13):1322-8
references.pmid: 16824920
references.citation: Curr Biol. 2006 Mar 7;16(5):486-92
references.pmid: 16527743
references.citation: Plant J. 2002 Dec;32(6):1057-66
references.pmid: 12492846
references.citation: Plant Physiol. 2007 Oct;145(2):317-29
references.pmid: 17675552
references.citation: Curr Biol. 2006 Mar 21;16(6):553-63
references.pmid: 16546078
references.citation: Plant J. 2006 Mar;45(5):804-18
references.pmid: 16460513
references.citation: Trends Plant Sci. 2005 Mar;10(3):123-9
references.pmid: 15749470
references.citation: Planta. 2004 Nov;220(1):38-46
references.pmid: 15248065
references.citation: Plant Cell. 2004 May;16(5):1288-301
references.pmid: 15105441
references.citation: Genes Dev. 2004 Feb 15;18(4):448-60
references.pmid: 14977918
references.citation: Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):4186-91
references.pmid: 10097185
references.citation: Curr Biol. 2001 Feb 20;11(4):277-81
references.pmid: 11250158
references.citation: Plant Mol Biol. 2005 Jul;58(5):609-24
references.pmid: 16158238
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D1009-14
references.pmid: 17986450
references.citation: Biotechniques. 2003 Feb;34(2):374-8
references.pmid: 12613259
references.citation: Proc Natl Acad Sci U S A. 1996 May 28;93(11):5319-24
references.pmid: 11607683
references.citation: Plant Cell. 2004 Apr;16(4):1035-46
references.pmid: 15020747
references.citation: Plant Cell. 2004;16 Suppl:S203-13
references.pmid: 15010515
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15694-9
references.pmid: 16227434
references.citation: EMBO Rep. 2006 Sep;7(9):947-52
references.pmid: 16878125
references.citation: Plant Cell. 2001 Mar;13(3):495-509
references.pmid: 11251092
references.citation: Plant J. 2005 Feb;41(4):546-66
references.pmid: 15686519
references.citation: Development. 1998 Sep;125(17):3329-41
references.pmid: 9693137
references.citation: Nature. 2009 Jul 9;460(7252):283-6
references.pmid: 19494814
references.citation: Genes Dev. 2003 Jun 15;17(12):1540-53
references.pmid: 12815071
references.citation: Plant Cell. 1998 Feb;10(2):231-43
references.pmid: 9490746
references.citation: Plant Cell. 2004;16 Suppl:S214-27
references.pmid: 15010513
references.citation: Science. 1998 Apr 17;280(5362):446-50
references.pmid: 9545225
references.citation: Science. 2009 Jun 12;324(5933):1447-51
references.pmid: 19520961
references.citation: Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):4223-8
references.pmid: 9108133
references.citation: Development. 2004 Mar;131(5):1089-100
references.pmid: 14973283
references.citation: Nucleic Acids Res. 2001 May 1;29(9):e45
references.pmid: 11328886
references.citation: Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
references.pmid: 9843981
references.citation: Plant Mol Biol. 1992 Jul;19(4):611-22
references.pmid: 1627774
references.citation: J Biol Chem. 2002 May 10;277(19):16553-8
references.pmid: 11867638
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: J Biol Chem. 2002 Mar 22;277(12):9911-9
references.pmid: 11786543
references.citation: Plant Cell. 1999 Oct;11(10):1945-52
references.pmid: 10521524
references.citation: Philos Trans R Soc Lond B Biol Sci. 2002 Jun 29;357(1422):749-60
references.pmid: 12079670
references.citation: Bioinformatics. 2006 Aug 1;22(15):1863-70
references.pmid: 16731695
references.citation: EMBO J. 2003 Sep 15;22(18):4804-14
references.pmid: 12970192
references.citation: Plant Physiol. 2003 Jan;131(1):287-97
references.pmid: 12529536
references.citation: Int J Dev Biol. 2005;49(5-6):707-16
references.pmid: 16096976
references.citation: Trends Plant Sci. 2006 Apr;11(4):167-75
references.pmid: 16530461
references.citation: Plant Cell. 2006 Jun;18(6):1360-72
references.pmid: 16648367
references.citation: PLoS Genet. 2009 Sep;5(9):e1000663
references.pmid: 19779546
references.citation: Plant Biotechnol J. 2006 Jul;4(4):393-407
references.pmid: 17177805
references.citation: Plant Cell. 2005 May;17(5):1424-33
references.pmid: 15805477
references.citation: Development. 2004 Jun;131(12):2971-81
references.pmid: 15151989
references.citation: Plant Physiol. 2008 Dec;148(4):1964-84
references.pmid: 18923020
references.citation: Philos Trans R Soc Lond B Biol Sci. 2003 Jun 29;358(1434):1105-11
references.pmid: 12831476
references.citation: Plant Biol (Stuttg). 2006 May;8(3):371-81
references.pmid: 16807830
references.citation: Trends Genet. 2001 Dec;17(12):705-11
references.pmid: 11718924
references.citation: Mol Cell. 2000 Oct;6(4):791-802
references.pmid: 11090618
references.citation: Plant Cell. 2008 Sep;20(9):2387-98
references.pmid: 18796636
references.citation: Plant J. 2003 Oct;36(1):30-44
references.pmid: 12974809
references.citation: Nucleic Acids Res. 2005 Sep 22;33(17):5404-14
references.pmid: 16179646
references.citation: Genes Dev. 1999 Nov 15;13(22):2971-82
references.pmid: 10580004
references.citation: Plant Cell. 2000 Nov;12(11):2271-82
references.pmid: 11090224
references.citation: Science. 2009 Jun 12;324(5933):1451-4
references.pmid: 19520962
references.citation: Pac Symp Biocomput. 2000;:455-66
references.pmid: 10902193
references.citation: J Biol Chem. 2006 Apr 7;281(14):9560-8
references.pmid: 16452472
references.citation: Plant Cell. 2008 Mar;20(3):635-47
references.pmid: 18334668
references.citation: Mol Phylogenet Evol. 2003 Dec;29(3):464-89
references.pmid: 14615187