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High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

ABSTRACT: Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex.

ORGANISM(S): Mus musculus

PROVIDER: GSE22131 | GEO | 2010/07/08

SECONDARY ACCESSION(S): PRJNA127583

REPOSITORIES: GEO

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High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

Project description:Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Examination of allele specific expression in the brains of reciprocal crosses of F1 hybrid mice from CASTEiJ and C57BL/6J crosses. Processed data files (GenomicAligned, SNP_calls, TranscriptomeAligned, fRNAdbAligned) and README file linked below as supplementary files.

2010-07-08 | E-GEOD-22131 | biostudies-arrayexpress

Noncanonical Genomic Imprinting Effects In Offspring

Project description:We report genomic imprinting effects in the arcuate nucleus, dorsal raphe nucleus, liver and muscle of adult female mice Examination of allele-specific gene expression hybrid mice generated from reciprocal crosses of CastEiJ x C57BL/6J mice

2015-08-01 | E-GEOD-70484 | biostudies-arrayexpress

Mouse preimplantation imprinting

Project description:Mouse preimplantation imprinting

| PRJNA638349 | ENA

Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain (IMPLICON-Seq)

Project description:DNA methylation is a common mechanism regulating monoallelic expression of different genes, including imprinted genes. How age-induced alterations of methylation levels vary across alleles and impact on monoallelic expression is unknown. In the brain, this phenomenon may contribute mechanistically to neuronal dysfunction and disease. In order to investigate the allele-specific transcriptional and epigenetic signatures of aging, we used key brain areas, hippocampus and cerebellum, of juvenile and old hybrid mice obtained from BL6×CAST reciprocal crosses. We set out to explore whether epigenetic drift affects global DNA methylation machinery by investigating 5- methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels. Mass spectrometry analysis showed a significant increase of 5hmC levels in hippocampus of old mice, but this was not accompanied by measurable differences in methylating or demethylating enzymes. The expression of several repetitive elements (LINEs, SINEs, IAP) was also analysed with a reduction of the intracisternal A-particle (IAP) retrotransposons seen in HCP of old mice. We uncovered the allelic-specific DNA methylation profile of aging using genomic imprinting as a read-out by IMPLICON and allelic-expression by RNA sequencing. Here, imprinting is not substantially changed during aging, not affecting their normal monoallelic expression. This work provides the first epigenetic and transcriptional landscape of aging with allelic resolution and confirms that genomic imprinting is a stable epigenetic phenomenon across the whole lifespan.

2024-07-15 | GSE232547 | GEO

Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain (RNA-Seq)

Project description:DNA methylation is a common mechanism regulating monoallelic expression of different genes, including imprinted genes. How age-induced alterations of methylation levels vary across alleles and impact on monoallelic expression is unknown. In the brain, this phenomenon may contribute mechanistically to neuronal dysfunction and disease. In order to investigate the allele specific transcriptional and epigenetic signatures of aging, we used key brain areas, hippocampus and cerebellum, of juvenile and old hybrid mice obtained from BL6×CAST/EiJ (CAST) reciprocal crosses. We set out to explore whether epigenetic drift affects global DNA methylation machinery by investigating 5- methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels. Mass spectrometry analysis showed a significant increase of 5hmC levels in hippocampus of old mice, but this was not accompanied by measurable differences in methylating and demethylating enzymes. The expression of several repetitive elements (LINEs, SINEs, IAP) was also analysed, strictly dependent on 5mC and 5hmC levels, and reporting a reduction of the intracisternal A-particle (IAP) retrotransposons in HCP of old mice. We uncovered the allelic-specific DNA methylation profile of aging using genomic imprinting as a read-out by IMPLICON and allelic expression by RNA sequencing. Here, imprinting is not substantially changed during aging, not affecting their normal monoallelic expression. This work provides the first epigenetic and transcriptional landscape of aging with allelic resolution and confirms that genomic imprinting is a stable epigenetic phenomenon across the whole lifespan.

2024-07-15 | GSE232546 | GEO

Mouse preimplantation imprinting [WGBS]

Project description:Mouse preimplantation imprinting [WGBS]

| PRJNA638354 | ENA

Transcriptome analysis of wild-type and mir-125b-2 maternal knock-out mice whole brain by Next Generation Sequencing

Project description:Genomic imprinting, a special case of epigenetic mechanisms, predominantly occurs in placenta and brain. Few imprinted microRNAs were identified in brain and their functional roles in brain were not well-investigated. Here we identified Mir125b-2 was maternally, but not paternally, expressed in mouse brain in a brain-region-specific manner. Mir125b-2 is predominantly expressed in mouse brain during neonatal stage and Mir125b-2 homozygous knockout (KO) mice displayed decreased brain weight.

2023-03-20 | GSE211881 | GEO

Lineage-specific genomic imprinting in the ZNF791 locus [BiSulfite-seq]

Project description:To identify genomic imprinting in pigs, we generated parthenogenetic porcine embryos alongside biparental normal embryos, and then performed whole-genome bisulfite sequencing and RNA sequencing on these samples. In our analyses, we discovered a maternally methylated differentially methylated region within the orthologous ZNF791 locus in pigs, while identifying both a major imprinted isoform of the ZNF791-like gene and an imprinted antisense transcript that has not been previously annotated. Importantly, our comparative analyses of the orthologous ZNF791 gene in various eutherian mammals, including humans, non-human primates, rodents, artiodactyls, and dogs, revealed that this gene is subjected to genomic imprinting exclusively in domesticated animals, thereby highlighting lineage-specific imprinting.

2024-10-16 | GSE263495 | GEO

Lineage-specific genomic imprinting in the ZNF791 locus [RNA-seq]

2024-10-16 | GSE263494 | GEO

Sequential gene activation and extensive gene imprinting during early embryo development in maize

Project description:The embryo is responsible for transmitting genetic information to the next generation. However, the underlying gene expression and gene imprinting during early embryo development remain largely elusive in maize. Using high-throughput RNA sequencing, we analyzed the allelic gene expression patterns of maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3 to 13 days after pollination). A total of 9532 genes were found to be differentially expressed in developmental stage, 3512 of 9532 genes were affected by cross direction. Co-expression analysis uncovered the sequential gene activations during maize embryo development. Further, we found 64 embryo strongly imprinted genes, including 57 maternally expressed imprinted genes (MEG) and 7 paternally expressed imprinted genes (PEG) in the maize embryo. Among them, 20 genes were continuously imprinted and 36 imprinted genes were newly identified. By applying In situ hybridization, we verified that six of the differentially expressed genes showed enriched transcription in the embryo. In addition, mutant analyses indicated that three of the imprinted genes displayed reduced embryo size. Therefore, our data shed new light on our understanding of the gene expression and gene imprinting in early maize embryo development, and suggested that imprinted genes are important for proper embryo development.

2017-12-05 | GSE95399 | GEO

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