Regulation of imprinted gene expression in Arabidopsis endosperm.
Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
Tzung-Fu
TF
Hsieh
Juhyun
J
Shin
Rie
R
Uzawa
Pedro
P
Silva
Stephanie
S
Cohen
Matthew J
MJ
Bauer
Meryl
M
Hashimoto
Ryan C
RC
Kirkbride
John J
JJ
Harada
Daniel
D
Zilberman
Robert L
RL
Fischer
D017360:Arabidopsis / Q000196:embryology / Q000235:genetics*; D019175:DNA Methylation; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018392:Genomic Imprinting; D009154:Mutation; D056771:Ovule; D011058:Pollen; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000378:metabolism
Trends Genet. 2007 Apr;23(4):192-9
17316885
Nat Genet. 2005 Jan;37(1):28-30
15619622
Genes Dev. 2008 Jun 15;22(12):1597-606
18559476
Trends Genet. 1991 Feb;7(2):45-9
2035190
Mol Plant. 2009 Jul;2(4):654-660
19825646
PLoS Genet. 2008 Aug 15;4(8):e1000156
18704160
Cell. 2008 Mar 7;132(5):735-44
18329361
Genes Dev. 2003 Jun 15;17(12):1540-53
12815071
Science. 2009 Jun 12;324(5933):1447-51
19520961
Curr Biol. 2009 Oct 13;19(19):1677-81
19781944
PLoS Genet. 2010 Oct 07;6(10):
20949070
Nature. 2008 Oct 9;455(7214):826-9
18772888
Annu Rev Cell Dev Biol. 2009;25:21-44
19575669
Science. 2004 Jan 23;303(5657):521-3
14631047
Plant J. 2008 Dec;56(5):704-15
18643997
Plant Cell. 2010 Jan;22(1):17-33
20086188
Nucleic Acids Res. 2001 Nov 1;29(21):4319-33
11691919
Plant Physiol. 2005 Oct;139(2):701-12
16169962
Curr Biol. 2007 Feb 20;17(4):379-84
17239600
PLoS Biol. 2008 Aug 12;6(8):e194
18700816
Plant Mol Biol. 2010 Nov;74(4-5):479-91
20852917
Trends Genet. 2009 Sep;25(9):414-23
19716619
Trends Plant Sci. 2009 Oct;14(10):550-6
19748816
Nature. 2010 Mar 25;464(7288):628-32
20208518
Science. 2010 Aug 6;329(5992):643-8
20616232
Nature. 2004 Nov 4;432(7013):53-7
15525980
Cell. 2006 Feb 10;124(3):495-506
16469697
Curr Opin Plant Biol. 2009 Oct;12(5):548-55
19709924
Biochem Biophys Res Commun. 2008 Nov 21;376(3):553-7
18805399
Curr Biol. 2007 Jan 9;17(1):54-9
17208187
Protoplasma. 2010 Dec;247(3-4):195-214
20661606
Plant Mol Biol. 1999 Sep;41(2):269-78
10579493
Development. 2009 Oct;136(20):3399-404
19783734
Plant Cell. 1999 Oct;11(10):1945-52
10521524
Plant Physiol. 2007 Feb;143(2):812-24
17172287
Plant Cell. 2006 Jun;18(6):1360-72
16648367
Plant Cell. 2005 May;17(5):1424-33
15805477
J Exp Bot. 2008;59(1):85-92
17905731
Science. 2001 Jan 12;291(5502):306-9
11209081
Nat Rev Mol Cell Biol. 2009 Jun;10(6):385-97
19424292
Curr Opin Cell Biol. 2008 Jun;20(3):266-73
18439810
Plant Cell. 2008 Sep;20(9):2387-98
18796636
Science. 2009 Jun 12;324(5933):1451-4
19520962
EMBO Rep. 2010 Dec;11(12):950-5
21052090
J Cell Sci. 2008 Mar 15;121(Pt 6):906-12
18303047
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13244-9
16924116
Plant Mol Biol. 1995 Nov;29(4):869-73
8541512