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Expression profiling of microRNAs in mouse livers with deletion of paternally-expressed, imprinted Mir483 [miRNA-seq]

ABSTRACT: Expression profiling of microRNAs in mouse livers with deletion of paternally-expressed, imprinted Mir483 [miRNA-seq]

PROVIDER: PRJNA1078899 | ENA |

REPOSITORIES: ENA

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Expression profiling of microRNAs in mouse livers with deletion of paternally-expressed, imprinted Mir483 [miRNA-seq]

Project description:In this study we generated mice with constitutive deletion of microRNA Mir483, which is imprinted and expressed from the paternal allele only. Global analysis of microRNA expression was performed by miRNA-seq in livers collected from E18.5 fetuses (mutants with deletion of paternal allele - Mir483Pat-KO - and wild-type controls).

2024-02-26 | GSE256305 | GEO

Expression profiling of mouse livers with deletion of paternally-expressed, imprinted Mir483 [RNA-seq]

Project description:Expression profiling of mouse livers with deletion of paternally-expressed, imprinted Mir483 [RNA-seq]

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Expression profiling of mouse livers with deletion of paternally-expressed, imprinted Mir483 [RNA-seq]

Project description:In this study we generated mice with constitutive deletion of microRNA Mir483, which is imprinted and expressed from the paternal allele only. Whole transcriptome analysis was performed by RNA-seq in livers collected from E18.5 fetuses (mutants with deletion of paternal allele - Mir483Pat-KO - and wild-type controls).

2024-02-26 | GSE256302 | GEO

Imprinted maternally-expressed microRNAs in induced neurons

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.

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Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

Project description:Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

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Epigenetic signatures associated with paternally-expressed imprinted genes in the endosperm

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.

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Imprinted maternally-expressed microRNAs in induced neurons

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Epigenetic signatures associated with paternally-expressed imprinted genes in the endosperm

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Imprinted Maternally Expressed microRNAs Antagonize Paternally Driven Gene Programs in Neurons.

Project description:Imprinted genes with parental-biased allelic expression are frequently co-regulated and enriched in common biological pathways. Here, we functionally characterize a large cluster of microRNAs (miRNAs) expressed from the maternally inherited allele ("maternally expressed") to explore the molecular and cellular consequences of imprinted miRNA activity. Using an induced neuron (iN) culture system, we show that 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 like Plagl1. Maternal deletion of this imprinted miRNA cluster resulted in increased protein levels of several targets and upregulation of a broader transcriptional program regulating synaptic transmission and neuronal function. A subset of the transcriptional changes resulting from miR-379/410 deletion can be attributed to de-repression of Plagl1. These data suggest maternally expressed miRNAs antagonize paternally driven gene programs in neurons.

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Both maternally and paternally imprinted genes regulate seed development in rice

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

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