Epigenetic signatures associated with paternally-expressed imprinted genes in the endosperm
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ABSTRACT:
PROVIDER: PRJNA490691 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7825980_1.fastq.gz | Fastqsanger.gz | |||
| SRR7825980_2.fastq.gz | Fastqsanger.gz | |||
| SRR7825981_1.fastq.gz | Fastqsanger.gz | |||
| SRR7825981_2.fastq.gz | Fastqsanger.gz | |||
| SRR7825982_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomic imprinting is an epigenetic phenomenon causing parental alleles to be active depending on their parent-of-origin. In plants, imprinted genes are mainly confined to the endosperm, an ephemeral tissue supporting embryo development. Differential methylation of histone H3 on lysine 27 (H3K27me3) established by the Polycomb Repressive Complex 2 (PRC2) is a major regulatory mechanism determining activity of paternally expressed imprinted genes (PEGs) in animals and plants. Here, we show that the coding region of many PEGs is marked by an epigenetic signature of H3K27me3, H3K9me2 and CHG methylation and that the combination of these three modifications correlates with paternally-biased gene expression in the endosperm. The maternal alleles of PEGs are marked by CHG methylation in the central cell, indicating that the repressive epigenetic signature of PEGs is established before fertilization. We use the presence of the three modifications to predict novel PEGs and propose that genomic imprinting is substantially more common than previously estimated based on expression data.
2019-02-07 | GSE119915 | GEO
Project description:Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. 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 (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. Epigenetics Examination of genomic imprinting in Arabidopsis endosperm
2011-03-10 | E-GEOD-24644 | biostudies-arrayexpress
Project description:Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana
2015-09-28 | GSE62401 | GEO
Project description:Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. 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 (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. Epigenetics
2011-03-10 | GSE24644 | GEO
Project description:Genetic imprinting is an epigenetic phenomenon that describes unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms including mammals and flowering plants. The function of imprinted genes was rarely reported. We report genome-wide analysis of gene expression, DNA methylation, and small RNAs in the rice endosperm and functional tests of five imprinted genes in seed development using CRISPR/Cas9 editing technology. We identified 162 maternally expressed genes(MEGs) and 95 paternally expressed genes (PEGs) in the rice endosperm, which were associated with miniature inverted-repeat transposable elements, imprinted differentially methylated loci, and some 21-22-siRNAs and lncRNAs. Remarkably, one-third of MEGs and nearly half of PEGs were associated with grain-yield quantitative trait loci and enriched in the endosperm-expressed genes. Disrupting two MEGs increased the amount of small starch granules and reduced grain size, weight, and embryo size, while mutating three PEGs reduced starch content and seed fertility. Our data support both MEGs and PEGs in rice are required for starch and nutrient accumulation, mediating offspring fitness and optimal seed size. This imprinting strategy provides potential means for improving grain yield of rice and other cereal crops.
2017-02-04 | GSE77710 | GEO
Project description:We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small Class II (cut and paste) transposable elements, those in endosperm are much more uniformly derived, including sequences from other TE classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that demethylation of maternal endosperm DNA is conserved in flowering plants.
2013-05-01 | GSE44898 | GEO
Project description:BACKGROUND:Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression. RESULTS:In this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles, we are able to predict known PEGs at high accuracy and identify several new PEGs that we confirm using INTACT-based transcriptomes generated in this study. CONCLUSIONS:The presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows prediction of genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.
| S-EPMC6385439 | biostudies-literature
Project description:We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small Class II (cut and paste) transposable elements, those in endosperm are much more uniformly derived, including sequences from other TE classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that demethylation of maternal endosperm DNA is conserved in flowering plants. Examination of DNA methylation and small RNA expression in the seeds of two cultivars from the japonica subspecies of Oryza sativa L.
2013-05-01 | E-GEOD-44898 | biostudies-arrayexpress
Project description:Following publication of the original article [1], the authors reported that Additional file 4, "Table S5. Parent-of-origin RNAseq dataset of 4 DAP INTACT-purified endosperm of Col × Ler reciprocal crosses" had the following error.
| S-EPMC6717997 | biostudies-literature
Project description:Imprinted genes with parental-biased allelic expression are enriched in pathways regulating energy homeostasis. Here, we functionally characterize a large cluster of maternally-expressed microRNAs (miRNAs) to explore the molecular and cellular consequences of imprinted miRNA activity in neurons. Using an induced neuron (iN) culture system, we show maternally-expressed miRNAs from the miR-379/410 cluster direct the RNA induced silencing complex (RISC) to transcriptional and developmental regulators, including paternally-expressed transcripts. Maternal deletion of this imprinted miRNA cluster results in increased protein levels of several targets and up-regulation of a broader gene program regulating synaptic transmission and neuronal function. A subset of these transcriptional changes can be attributed to de-repression of Plagl1, a paternally-expressed transcriptional activator that regulates Igf2, a major factor in energy homeostasis. These data suggest non-coding RNAs actively engage as maternally-expressed miRNAs antagonize paternally-driven gene programs in neurons.
2019-11-23 | GSE140838 | GEO