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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

ABSTRACT: Imprinted gene expression occurs during seed development in plants and is closely tied to differential DNA methylation of maternal and paternal alleles, particularly at proximal transposable elements (TEs). Since the epigenetic modification of TEs can vary within species, we investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three strains of Arabidopsis that display diverse seed size phenotypes. Unexpectedly we found that one strain, Cvi, is globally CG hypomethylated. We discovered three examples of strain-specific imprinting caused by epigenetic variation at a TE. Our data allowed us to predict and experimentally validate an instances of allele-specific imprinting in additional strains based only on methylation patterns. We conclude that numerous differences in imprinting can evolve in highly similar, recently diverged genotypes due to epiallelic variation present within the species. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE52806 | GEO | 2014/07/08

SECONDARY ACCESSION(S): PRJNA230119

REPOSITORIES: GEO

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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: BS-seq of Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

Project description: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.

2014-07-08 | GSE52805 | GEO

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

2014-07-08 | GSE52807 | GEO

2014-07-08 | E-GEOD-52805 | biostudies-arrayexpress

2014-07-08 | E-GEOD-52807 | biostudies-arrayexpress

Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and reciprocal F1 hybrid embryo and endosperm

Project description:Imprinted gene expression occurs during seed development in plants and is closely tied to differential DNA methylation of maternal and paternal alleles, particularly at proximal transposable elements (TEs). Since the epigenetic modification of TEs can vary within species, we investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three strains of Arabidopsis that display diverse seed size phenotypes. Unexpectedly we found that one strain, Cvi, is globally CG hypomethylated. We discovered three examples of strain-specific imprinting caused by epigenetic variation at a TE. Our data allowed us to predict and experimentally validate an instances of allele-specific imprinting in additional strains based only on methylation patterns. We conclude that numerous differences in imprinting can evolve in highly similar, recently diverged genotypes due to epiallelic variation present within the species. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds. Examination of parent-of-origin specific and total gene expression in embryo, endosperm, and whole seeds. Samples with the same heading are biological replicates (e.g. CVN1, CVN2, and CVN3). High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col, Ler and Cvi reciprocal F1 hybrid embryo and endosperm tissue isolated at 6 days after pollination to identify imprinted genes.

2014-07-08 | E-GEOD-52806 | biostudies-arrayexpress

A variably imprinted epiallele impacts seed development

Project description:The contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in endosperm seed tissue. Proper endosperm development is essential for the production of viable seeds. We previously showed that in Arabidopsis thaliana intraspecific imprinting variation is correlated with naturally occurring DNA methylation polymorphisms. Here, we investigated the mechanisms and function of allele-specific imprinting of the class IV homeodomain-Leucine zipper (HD-ZIP) transcription factor HDG3. In imprinted strains, HDG3 is expressed primarily from the methylated paternally inherited allele. We manipulated the methylation state of endogenous HDG3 in a non-imprinted strain and demonstrated that methylation of a proximal transposable element is sufficient to promote HDG3 expression and imprinting. Gain of HDG3 imprinting was associated with earlier endosperm cellularization. These results indicate that epigenetic variation alone is sufficient to explain imprinting variation and show that epialleles can underlie variation in seed development phenotypes.

2018-10-29 | GSE118371 | GEO

Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus

Project description:In plants, imprinted gene expression occurs in endosperm seed tissue and can be associated with differential DNA methylation between maternal and paternal alleles. Imprinting is theorized to have been selected for because of conflict between parental genomes in offspring, but most studies of imprinting have been conducted in Arabidopsis thaliana, an inbred primarily self-fertilizing species that should have limited parental conflict. We examined embryo and endosperm allele-specific expression and DNA methylation genome-wide in the wild outcrossing species Arabidopsis lyrata. Here we show that the majority of A. lyrata imprinted genes exhibit parentally-biased expression in A. thaliana, suggesting that there is evolutionary conservation in gene imprinting. Surprisingly, we discovered substantial interspecies differences in methylation features associated with paternally expressed imprinted genes (PEGs). Unlike A. thaliana, the maternal allele of many A. lyrata PEGs was hypermethylated in the CHG context. Increased maternal allele CHG methylation was associated with increased expression bias in favor of the paternal allele. We propose that CHG methylation maintains or reinforces repression of maternal alleles of PEGs. These data suggest that while the genes subject to imprinting are largely conserved, there is flexibility in the epigenetic mechanisms employed between closely related species to maintain monoallelic expression. This supports the idea that imprinting of specific genes is a functional phenomenon, and not simply a byproduct of seed epigenomic reprogramming.

2016-09-01 | GSE76076 | GEO

Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

Project description:Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in a sequence specific manner. What factors regulate DNA methylation at a given site in the genome largely remains elusive. Here by generating single nucleotide resolution maps of DNA methylation we have surveyed the effect of mutations in a comprehensive list of genes involved in gene silencing in Arabidopsis. We find that DNA methylation is site-specifically regulated by different factors. Furthermore, we have identified novel regulators of DNA methylation. We have generated a comprehensive resource to further understanding the control of DNA methylation patterning. Whole genome methylation maps of 86 silencing mutants involved in gene silencing and chromatin modifications were generated using BS-seq (Cokus et al., Nature 2008 ).

2013-01-11 | E-GEOD-39901 | biostudies-arrayexpress

Transcription profiling of Arabidopsis Ler/Cvi recombinant inbred line popultion to assess natural variation in gene expression

Project description:To assess natural variation in gene expression in Arabidopsis thaliana, genome wide gene expression variation was analyzed in a Ler/Cvi recombinant inbred line (RIL) population.The variation in expression could be explained for many genes by expression quantitative trait loci (eQTLs). These eQTLs are combined with regulator candidate gene selection to generate genetic regulatory networks.

2008-01-24 | E-TABM-214 | biostudies-arrayexpress

High-throughput pyrosequencing of endogenous small RNAs from Arabidopsis thaliana wild-type and ddm1 mutant.

Project description:DNA methylation is essential for silencing transposable elements and some genes in higher eukaryotes, implying that this modification must be tightly controlled. However, accidental changes in DNA methylation can be transmitted through mitosis, as in cancer, or meiosis, leading to epiallelic variation. Here, we demonstrate the existence of an efficient and faithful mechanism that protects against transgenerational loss of DNA methylation in the plant Arabidopsis. This process is specific to the subset of heavily methylated genomic repeats that are targeted by the RNAi machinery, and does not spread into flanking regions. Remethylation is often progressive over two to four sexual generations. This differential and incremental correction of epigenetic defects may preserve genome stability while increasing adaptive opportunities.

2009-02-02 | GSE13419 | GEO

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