Cop1 wildtype and knock out ChIP-seq for CEBPb, H3K4me3 and H3K27ac in primary microglia
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA637393 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11928486.fastq.gz | Fastqsanger.gz | |||
| SRR11928487.fastq.gz | Fastqsanger.gz | |||
| SRR11928488.fastq.gz | Fastqsanger.gz | |||
| SRR11928489.fastq.gz | Fastqsanger.gz | |||
| SRR11928490.fastq.gz | Fastqsanger.gz |
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Project description:Cop1 wildtype and knock out ChIP-seq for CEBPb, H3K4me3 and H3K27ac in BMDMs
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Project description:The realization in the last decade that dysregulated microglia are intimately involved in Alzheimer’s disease (AD) pathogenesis has been a major advance. The precise mechanisms controlling pathogenic programs of microglia gene expression, however, remain poorly understood. The transcription factor (TF) c/EBPß is highly expressed in microglia and is known to regulate expression of pro-inflammatory genes. Notably, c/EBPß is upregulated in AD. Despite mounting evidence that the levels of this pivotal pro-inflammatory TF are tightly regulated, how this is achieved is unclear as alterations in its amounts are not reflected in transcript levels. Remarkably, we find that this TF is primarily regulated post-translationally. Here we show that the ubiquitin ligase Cop1 functions as a “brake” on microglial activation by targeting c/EBPß for ubiquitination and subsequent proteasomal mediated degradation. In the absence of Cop1, c/EBPß protein rapidly and dramatically accumulates leading to engagement of a potent pro-inflammatory and ApoE gene-expression program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies revealed that the neurotoxicity was almost entirely attributable to complement. Unexpectedly, loss of a single allele of c/EBPß, rescued the pro-inflammatory phenotype underscoring a significant gene dosage effect. We also found that Cop1 deletion accelerated disease progression in a mouse model of tau-mediated neurodegeneration where elevated ApoE plays a deleterious role. Taken together these results point to c/EBPß as a potential therapeutic target for inflammation-driven neurodegeneration as the heterozygote animal is otherwise normal.
2020-08-14 | GSE147558 | GEO
Project description:The realization in the last decade that dysregulated microglia are intimately involved in Alzheimer’s disease (AD) pathogenesis has been a major advance. The precise mechanisms controlling pathogenic programs of microglia gene expression, however, remain poorly understood. The transcription factor (TF) c/EBPß is highly expressed in microglia and is known to regulate expression of pro-inflammatory genes. Notably, c/EBPß is upregulated in AD. Despite mounting evidence that the levels of this pivotal pro-inflammatory TF are tightly regulated, how this is achieved is unclear as alterations in its amounts are not reflected in transcript levels. Remarkably, we find that this TF is primarily regulated post-translationally. Here we show that the ubiquitin ligase Cop1 functions as a “brake” on microglial activation by targeting c/EBPß for ubiquitination and subsequent proteasomal mediated degradation. In the absence of Cop1, c/EBPß protein rapidly and dramatically accumulates leading to engagement of a potent pro-inflammatory and ApoE gene-expression program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies revealed that the neurotoxicity was almost entirely attributable to complement. Unexpectedly, loss of a single allele of c/EBPß, rescued the pro-inflammatory phenotype underscoring a significant gene dosage effect. We also found that Cop1 deletion accelerated disease progression in a mouse model of tau-mediated neurodegeneration where elevated ApoE plays a deleterious role. Taken together these results point to c/EBPß as a potential therapeutic target for inflammation-driven neurodegeneration as the heterozygote animal is otherwise normal.
2020-08-14 | GSE151845 | GEO
Project description:ChIP-seq of K562 cells: H3K4me3, H3K27ac, EZH2
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Project description:Dysregulated microglia are intimately involved in neurodegeneration including Alzheimer’s disease (AD) pathogenesis, but the mechanisms controlling pathogenic microglial gene expression remain poorly understood. The transcription factor CCAAT/enhancer binding protein beta (c/EBPß) regulates pro-inflammatory genes in microglia and is upregulated in AD. We show expression of c/EBPß in microglia is regulated post-translationally by the ubiquitin ligase COP1 (also called RFWD2). Ubiquitination of c/EBPß by COP1 targets it for proteasomal degradation. In the absence of COP1, c/EBPß accumulates rapidly and drives a potent pro-inflammatory and ApoE gene-expression program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies reveal that neurotoxicity is almost entirely attributable to complement. Remarkably, loss of a single allele of Cebpb prevented the pro-inflammatory phenotype. COP1-deficient microglia markedly accelerated tau-mediated neurodegeneration in a mouse model where elevated ApoE plays a deleterious role. Collectively, these results identify c/EBPß as a potential therapeutic target for inflammation-driven neurodegeneration.
2020-08-14 | GSE145454 | GEO
Project description:In order to assess the physiological role of Cop1 in vivo we generated mice that do no longer express the protein. Cop1KO mice die at around E10.5 of embryonic development. In order to gain insights into the molecular mechanisms that cause the embryonic death we compared the genome-wide gene expression profile of E9.5 wild-tytpe and Cop1-null embryos. The data do not support a role for Cop1 in the regulation of the p53 pathway in vivo and highlight a role for Cop1 in cardiovascular development and/or angiogenesis. The abstract of the associated publication is as follows:Biochemical data have suggested conflicting roles for the E3 ubiquitin ligase Cop1 in tumourigenesis. Here we present the first in vivo investigation of the role of Cop1 in cancer aetiology. We used an innovative genetic approach to generate an allelic series of Cop1 and show that Cop1 hypomorphic mice spontaneously develop malignancy at a high frequency in their first year of life and are highly susceptible to radiation-induced lymphomagenesis. Biochemically, we show that Cop1 regulates c-Jun oncoprotein stability and modulates c-Jun/AP1 transcriptional activity in vivo. Cop1-deficiency stimulates cell proliferation in a c-Jun-dependent manner. We conclude that Cop1 is a tumour suppressor that antagonizes c-Jun oncogenic activity in vivo. RNA from 6 different control embryos (+/+ or +/-) were mixed and subdivided into control pool 1 and pool 2. RNA from 6 different Cop-null embryos were mixed and subdivided into KO pool 1 and pool 2.
2011-01-13 | E-GEOD-18636 | biostudies-arrayexpress
Project description:The realization in the last decade that dysregulated microglia are intimately involved in Alzheimer’s disease (AD) pathogenesis has been a major advance. The precise mechanisms controlling pathogenic programs of microglia gene expression, however, remain poorly understood. The transcription factor (TF) c/EBPß is highly expressed in microglia and is known to regulate expression of pro-inflammatory genes. Notably, c/EBPß is upregulated in AD. Despite mounting evidence that the levels of this pivotal pro-inflammatory TF are tightly regulated, how this is achieved is unclear as alterations in its amounts are not reflected in transcript levels. Remarkably, we find that this TF is primarily regulated post-translationally. Here we show that the ubiquitin ligase Cop1 functions as a “brake” on microglial activation by targeting c/EBPß for ubiquitination and subsequent proteasomal mediated degradation. In the absence of Cop1, c/EBPß protein rapidly and dramatically accumulates leading to engagement of a potent pro-inflammatory and ApoE gene-expression program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies revealed that the neurotoxicity was almost entirely attributable to complement. Unexpectedly, loss of a single allele of c/EBPß, rescued the pro-inflammatory phenotype underscoring a significant gene dosage effect. We also found that Cop1 deletion accelerated disease progression in a mouse model of tau-mediated neurodegeneration where elevated ApoE plays a deleterious role. Taken together these results point to c/EBPß as a potential therapeutic target for inflammation-driven neurodegeneration as the heterozygote animal is otherwise normal.
2020-08-14 | GSE147557 | GEO
Project description:ChIP-seq of H3K4me3 and H3K27ac of dermal fibroblasts
| PRJEB22016 | ENA
Project description:Considered as fundamental epigenetic regulators controlling many key cellular processes, histone modifications are a well-conserved and widely studied class of epigenetic modifications. Genome-wide studies have identified enhancers as DNA sequences that bind to H3K4me1 and H3K27ac and promoters as DNA sequences that bind to H3K4me3. To explore how the Twist1 complex (Twist1/YY1/p300) regulates miR-9 expression, we performed ChIP-seq in PLC-PRF-5 cells, providing a panorama of p300, H3K4me3, H3K4me1, and H3K27ac.
2022-07-21 | GSE208334 | GEO