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Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36.

Shirzadi R, Andersen ED, Bjerkan KN, Gloeckle BM, Heese M, Ungru A, Winge P, Koncz C, Aalen RB, Schnittger A, Grini PE - PLoS Genet. (2011)

Bottom Line: In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed.Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented.Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences (IMBV), University of Oslo, Oslo, Norway.

ABSTRACT
Seed development in angiosperms is dependent on the interplay among different transcriptional programs operating in the embryo, the endosperm, and the maternally-derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed. Here we have exploited cdka;1 fertilization as a novel tool for the identification of seed regulators and factors involved in parent-of-origin-specific regulation during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds and identified approximately 600 genes that are downregulated in the absence of a paternal genome. Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented. Here, AGL36 was chosen for an in-depth study and shown to be imprinted. We demonstrate that AGL36 parent-of-origin-dependent expression is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds.

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The effect of DNA methylation on parental AGL36 expression.(A,B) SNP analyses of 3 DAP seeds from crosses with DNA methylation mutants. The amplified SNP containing regions of AGL36 and FWA cDNA were digested with AlwNI and NheI, respectively, and analyzed in a Bioanalyzer. (A) Homozygous cmt3-7, kyp-2, and ago4-1 mutants in the Ler ecotype were used as pollen donors to pollinate Col plants, while homozygous drm1;drm2 and heterozygous ddm1-2 mutants in the Ws-2 and Col ecotype respectively, were used as male to fertilize Ler ovules. No paternal AGL36 expression could be detected in these crosses. (B) Upper panel: Hemizygous met1-4+/− in the Col ecotype reciprocally crossed with Ler wild-type plants show that the paternal allele of AGL36 is expressed when met1-4 is crossed as male. No paternal bands are observed when met1-4 is used as the maternal cross partner. Using pollen from first generation met1-4−/− homozygous plants in a Ler x met1-4−/− cross gives rise to prominent bands of the digested paternal Col expression product. In the reciprocal met1-4−/− x Ler cross no paternal expression can be detected. Lower panel: FWA control using the same tissue as above showing imprinted expression of FWA in dependence of MET1. Paternal FWA expression was observed when plants hemizygous and homozygous for met1-4 were crossed as male to Ler wild-type.
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pgen-1001303-g005: The effect of DNA methylation on parental AGL36 expression.(A,B) SNP analyses of 3 DAP seeds from crosses with DNA methylation mutants. The amplified SNP containing regions of AGL36 and FWA cDNA were digested with AlwNI and NheI, respectively, and analyzed in a Bioanalyzer. (A) Homozygous cmt3-7, kyp-2, and ago4-1 mutants in the Ler ecotype were used as pollen donors to pollinate Col plants, while homozygous drm1;drm2 and heterozygous ddm1-2 mutants in the Ws-2 and Col ecotype respectively, were used as male to fertilize Ler ovules. No paternal AGL36 expression could be detected in these crosses. (B) Upper panel: Hemizygous met1-4+/− in the Col ecotype reciprocally crossed with Ler wild-type plants show that the paternal allele of AGL36 is expressed when met1-4 is crossed as male. No paternal bands are observed when met1-4 is used as the maternal cross partner. Using pollen from first generation met1-4−/− homozygous plants in a Ler x met1-4−/− cross gives rise to prominent bands of the digested paternal Col expression product. In the reciprocal met1-4−/− x Ler cross no paternal expression can be detected. Lower panel: FWA control using the same tissue as above showing imprinted expression of FWA in dependence of MET1. Paternal FWA expression was observed when plants hemizygous and homozygous for met1-4 were crossed as male to Ler wild-type.

Mentions: CMT3 DNA methylation has been reported to be guided to specific sites by KRYPTONITE (KYP) H3K9 methylation [51]. When mutant cmt3-7 and kyp-2 pollen were crossed to Col wild-type plants, no difference in AGL36 expression was observed (Figure 5A). In the reciprocal cross with cmt3-7 also no difference could be detected compared to wild-type expression (Figure S6).


Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36.

Shirzadi R, Andersen ED, Bjerkan KN, Gloeckle BM, Heese M, Ungru A, Winge P, Koncz C, Aalen RB, Schnittger A, Grini PE - PLoS Genet. (2011)

The effect of DNA methylation on parental AGL36 expression.(A,B) SNP analyses of 3 DAP seeds from crosses with DNA methylation mutants. The amplified SNP containing regions of AGL36 and FWA cDNA were digested with AlwNI and NheI, respectively, and analyzed in a Bioanalyzer. (A) Homozygous cmt3-7, kyp-2, and ago4-1 mutants in the Ler ecotype were used as pollen donors to pollinate Col plants, while homozygous drm1;drm2 and heterozygous ddm1-2 mutants in the Ws-2 and Col ecotype respectively, were used as male to fertilize Ler ovules. No paternal AGL36 expression could be detected in these crosses. (B) Upper panel: Hemizygous met1-4+/− in the Col ecotype reciprocally crossed with Ler wild-type plants show that the paternal allele of AGL36 is expressed when met1-4 is crossed as male. No paternal bands are observed when met1-4 is used as the maternal cross partner. Using pollen from first generation met1-4−/− homozygous plants in a Ler x met1-4−/− cross gives rise to prominent bands of the digested paternal Col expression product. In the reciprocal met1-4−/− x Ler cross no paternal expression can be detected. Lower panel: FWA control using the same tissue as above showing imprinted expression of FWA in dependence of MET1. Paternal FWA expression was observed when plants hemizygous and homozygous for met1-4 were crossed as male to Ler wild-type.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3040660&req=5

pgen-1001303-g005: The effect of DNA methylation on parental AGL36 expression.(A,B) SNP analyses of 3 DAP seeds from crosses with DNA methylation mutants. The amplified SNP containing regions of AGL36 and FWA cDNA were digested with AlwNI and NheI, respectively, and analyzed in a Bioanalyzer. (A) Homozygous cmt3-7, kyp-2, and ago4-1 mutants in the Ler ecotype were used as pollen donors to pollinate Col plants, while homozygous drm1;drm2 and heterozygous ddm1-2 mutants in the Ws-2 and Col ecotype respectively, were used as male to fertilize Ler ovules. No paternal AGL36 expression could be detected in these crosses. (B) Upper panel: Hemizygous met1-4+/− in the Col ecotype reciprocally crossed with Ler wild-type plants show that the paternal allele of AGL36 is expressed when met1-4 is crossed as male. No paternal bands are observed when met1-4 is used as the maternal cross partner. Using pollen from first generation met1-4−/− homozygous plants in a Ler x met1-4−/− cross gives rise to prominent bands of the digested paternal Col expression product. In the reciprocal met1-4−/− x Ler cross no paternal expression can be detected. Lower panel: FWA control using the same tissue as above showing imprinted expression of FWA in dependence of MET1. Paternal FWA expression was observed when plants hemizygous and homozygous for met1-4 were crossed as male to Ler wild-type.
Mentions: CMT3 DNA methylation has been reported to be guided to specific sites by KRYPTONITE (KYP) H3K9 methylation [51]. When mutant cmt3-7 and kyp-2 pollen were crossed to Col wild-type plants, no difference in AGL36 expression was observed (Figure 5A). In the reciprocal cross with cmt3-7 also no difference could be detected compared to wild-type expression (Figure S6).

Bottom Line: In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed.Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented.Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biosciences (IMBV), University of Oslo, Oslo, Norway.

ABSTRACT
Seed development in angiosperms is dependent on the interplay among different transcriptional programs operating in the embryo, the endosperm, and the maternally-derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed. Here we have exploited cdka;1 fertilization as a novel tool for the identification of seed regulators and factors involved in parent-of-origin-specific regulation during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds and identified approximately 600 genes that are downregulated in the absence of a paternal genome. Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented. Here, AGL36 was chosen for an in-depth study and shown to be imprinted. We demonstrate that AGL36 parent-of-origin-dependent expression is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds.

Show MeSH
Related in: MedlinePlus