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MacroH2A deletion causes neuronal developmental deficits and autism-like behavior in mice

ABSTRACT: Purpose:To further understand how MacroH2A regulates the proliferation of neural progenitor cells, RNA-seq was used to analyze genome-wide changes in the cerebral cortex and littermate wild type of E13.5 MacroH2A knockout mice Methods: Total RNA was extracted from wild-type E13.5 brain tissue and knock-out E13.5 brain tissue. Specifically, the Agilent 2100 Bioanalyzer was used for quality control and quantification. Total RNA was then converted to cDNA and combined with the library. Illumina HiSeq 2500 platform in Annoroad Genomics uses RNA sequencing analysis Results: Approximately one thousand transcripts showed differential expression between the wild-type(WT) and knock-out mice brain cortex, with a fold change ≥1.5 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development and proliferation.The down-regulated genes exhibited enrichment of biological processes related to the negative regulation of cell proliferation and developmental process. These results reflected human MacroH2A plays a role in brain neuron development.

ORGANISM(S): Mus musculus

PROVIDER: GSE147064 | GEO | 2020/03/17

REPOSITORIES: GEO

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Deficiency of STING-signaling leads to neurogenic abnormalities and Autistic-Like Behaviors in the embryonic cortex [bulk RNA-seq]

Project description:Purpose: To gain futher insight into how STING regulates the proliferative of neural progenitors ,RNA-seq was used to analyze the genome-wide changes resulting from the cerebral cortices of E13 STING conditional knock out mice and littermate wild-type. Methods: Total RNA from E13 telencephalic tissue of wild-type(WT) and STINGf/f;Nestin-Cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, total RNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics Results: Approximately one thousand transcripts showed differential expression between the wild-type(WT) and STINGf/f;Nestin-Cre mice brain cortex, with a fold change ≥1.5 and p value <0.05.Geneontology analysis of the down or up-regulated genes showed obvious enrichment of biological processes related to brain development and cell fate commitment. These results reflected STING plays a role in cortex development. Conclusions: RNA-seq based transcriptome characterization would provide a overall understanding how STING gene contribute to brain cortical development.

2020-03-06 | GSE146455 | GEO

Endothelial UCP2 regulates the neurogenic-to-astrogenic fate switch during brain development

Project description:Purpose: To gain futher insight into how endothelial UCP2 regulates the neurogenic-to-astrogenic fate switch ,RNA-seq was used to analyze the genome-wide changes resulting from isolated endothelial cells of E14.5 and E17.5 UCP2 endothelial conditional knock out mice and littermate wild-type. Methods: mRNA from E15 and E18 isolated endothelial cells of wild-type(WT) and UCP2f/f;Tie2-cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics Results: Approximately one thousand transcripts showed differential expression between the wild-type(WT) and UCP2ECKO mice brain cortex, with a fold change ≥2 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development process and regulation of cell communication.The down-regulated genes exhibited enrichment of biological processes related to cell fate commitment. These results reflected endothelial UCP2 plays roles in cortex development. Conclusions: Endothelial UCP2 RNA-seq would provide a overall understanding how endothelial UCP2 regulates the neurogenic-to-astrogenic fate switch during brain development

2021-10-13 | GSE185656 | GEO

The human gene FOXM1 promotes cortical folding and improves learning and memory ability in mice [E15]

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2020-02-13 | GSE145169 | GEO

Gasdermin D deficiency affects mitochondrial dynamics and metabolic to orchestrates neurogenesis during embryonic development

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2023-11-13 | GSE247326 | GEO

macroH2A histone variants act as a barrier upon reprogramming towards pluripotency

Project description:Here we report that the histone variant macroH2A acts as a barrier to induced pluripotency. Using fibroblasts isolated from macroH2A double knockout mice, we observed enhanced reprogramming efficiency compared to fibroblasts from wild type animals. We further show that macroH2A isoforms act synergistically in this process. Genomic analysis in wild type fibroblasts reveals that macroH2A1 and H3K27me3 domains co-localize and occupy pluripotency genes. While the absence of macroH2A does not affect H3K27me3 in fibroblasts, macroH2A1 is highly enriched at a set of Utx target genes that are reactivated early during iPS reprogramming.

2013-03-01 | GSE40813 | GEO

macroH2A histone variants act as a barrier upon reprogramming towards pluripotency

2013-03-01 | E-GEOD-40813 | biostudies-arrayexpress

CCDC25 Regulates Neurogenesis During the Brain Devolopment

Project description:Purpose:T To investigate the role of CCDC25 in the development of cortical nerves Methods: mRNA from E13 neural steneural stem cell were obtained. Culture in vitro for 4 days, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately one thousand transcripts showed differential expression between the control and knock down brain cortex, with a fold change ≥2 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development process and regulation of cell communication.The down-regulated genes exhibited enrichment of biological processes related to cell movement. These results reflected ccdc25 plays a vital role in cortex development. Conclusions: Endothelial Arid1a RNA-seq would provide a overall understanding how endothelial Arid1a regulates the Balance among angiogenesis, neurogenesis, and astrogenesis in the developing Brain

2023-01-27 | GSE223764 | GEO

Microglial metabolism mediated by BACH1 orchestrates astrogenesis during brain development

Project description:Purpose: To gain futher insight into how microglia-derived BACH1 regulates microglial metabolism and astrogenesis, RNA-seq was used to analyze the genome-wide changes resulting from isolated microglia of E16 microglial BACH1 conditional knock out mice and littermate wild-type. Methods: mRNA from E16 isolated microglia of Bach1fl/fl and Bach1cKO-Cx3 mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately one thousand transcripts showed differential expression between the Bach1fl/fl and Bach1cKO-Cx3 mice brain microglia, with a fold change ≥3 and p value <0.05. Geneontology analysis of the downregulated genes were enriched in terms related to cell proliferation, glial cell differentiation and cell communication and upregulated genes were enriched in terms related to negative regulation of cell proliferation, negative regulation of astrocyte differentiation and glial cell fate commitment. These results reflected microglia BACH1 plays roles in cortex development. Conclusions: Microglia BACH1 RNA-seq would provide a overall understanding how microglia-derived BACH1regulates astrogenesis during brain development.

2023-03-25 | GSE227957 | GEO

Purification of macroH2A.1 and macroH2A.2 Nucleosomes from Fetal Mouse Liver

Project description:MacroH2As core histone variants have a unique structure that includes C-terminal nonhistone domain. MacroH2As are highly conserved in vertebrates, and are thought to regulate gene expression. However the nature of genes regulated by macroH2As and the biological significance of macroH2As for the organism remain unclear. Our gene expression studies indicate that macroH2A.1 and macroH2A.2 work together to regulate specific genes. In these studies we examine the distributions of macroH2A.1 and macroH2A.2 nucleosomes to determine if they are localized to the genes that show altered expression in macroH2A knockout mouse liver. MacroH2A.1 and macroH2A.2 nucleosomes prepared from ~ 50 fetal mouse livers were purified by thio-affinity chromatography. Five samples were sequenced: Thiopropyl Sepharose, Normal Liver - contains mononucleosomal DNA from macroH2A.1-containing nucleosomes; Activate Thiol Sepharose, Normal Liver - contains mononucleosomal DNA primarily from macroH2A.2-containing nucleosomes. Starting Material, Normal Liver - this is a reference samplefor the first two samples. It contains mononucleosomal DNA from bulk fetal liver chromatin. Activated Thiol Sepharose, Knockout Livers - this is a control sample that contains mononucleosomal DNA from non-macroH2A nucleosomes that contaminate the macroH2A.2 nucleosomes. This fraction was prepared from macroH2A1/2 double knockout fetal livers; Starting Material, Knockout Liver - this is a reference sample for the fourth sample. It contains mononucleosomal DNA from bulk chromatin prepared from macroH2A1/2 double knockout fetal livers.

2014-10-15 | E-GEOD-57796 | biostudies-arrayexpress

Composite macroH2A/NRF-1 Nucleosomes Suppress Noise and Generate Robustness in Gene Expression

Project description:The histone variant macroH2A has been implicated in transcriptional repression, but the molecular mechanisms that contribute to global macroH2A-dependent genome regulation remain elusive. Using ChIP-seq coupled with transcriptional profiling in macroH2A knock-down cells (GSE53103) we demonstrate that singular macroH2A nucleosomes occupy transcription start sites of subsets of both expressed and repressed genes with opposing regulatory consequences. Specifically macroH2A nucleosomes mask repressor binding sites in expressed genes, but activator binding sites in repressed genes thus generating distinct chromatin landscapes limiting genetic or extracellular inductive signals. We show that composite nucleosomes containing macroH2A and NRF-1 are stably positioned on gene regulatory regions and can buffer the transcriptional noise typifying antiviral responses. In contrast, macroH2A nucleosomes without NRF-1 bind promoters weakly and mark genes with noisier gene expression patterns. Thus, the strategic position and stabilization of macroH2A nucleosomes in human promoters defines robust gene expression patterns.

2015-05-06 | GSE53133 | GEO

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