Unknown,Transcriptomics,Genomics,Proteomics

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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds

ABSTRACT: Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. These data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Sequencing of 12 small RNA samples from whole seeds 6 days after pollination.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Mary Gehring

PROVIDER: E-GEOD-52807 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Seed development is dependent on a well-orchestrated interplay between 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, mutation of the cell cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) results in pollen that only successfully fertilizes the egg cell. Seeds generated from crosses with cdka;1 pollen develop endosperm with solely maternal and no paternal contribution. Here we have exploited cdka;1 fertilization as a novel tool for genomic dissection of parental effects during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds. By this approach, we identified 11 differentially expressed AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors. Here, AGL36 was chosen for an in-depth study. We show that AGL36 is imprinted and only expressed from the maternal genome. In addition, we demonstrate that AGL36 imprinting 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). These findings shed novel light on the interplay between maternal and paternal genomes in the seed and how imprinting is coordinated by different mechanisms. 3 biological replicates, each consisting of 35 siliques from 10 individual plants, were used. Arabidopsis thaliana wild type (ecotype Colombia-0 and Ler-0) and cdka;1 mutant (At3g48750 /SALK_109806) were sown out on soil and grown under the following conditions: 18oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 Î¼mol/m2/sek in light intensity. For each replica, 10 Ler plants were emasculated and pollinated after 48 hours, either with individual WT Col or with individual cdka;1 mutant pollen. Three days after pollination (3 DAP), the siliques of each biological replicate were dissected with hypodermic needles to remove carpel walls, the pistil with pollen attached to it and the pedicel with abcsission zone. The remaining seeds attached to the middle lamella were harvested in bulk in liquid nitrogen at the same time of the day. Biological replicas are dye-swapped between slides.

Dataset Information

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: small RNA-seq profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid seeds

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