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(ChIP-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

ABSTRACT: (ChIP-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

PROVIDER: PRJNA1097640 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28590300.fastq.gz	Fastqsanger.gz
	SRR28590301.fastq.gz	Fastqsanger.gz
	SRR28590302.fastq.gz	Fastqsanger.gz
	SRR28590303.fastq.gz	Fastqsanger.gz
	SRR28590304.fastq.gz	Fastqsanger.gz

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(ChIP-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

Project description:Pathogenic variants of ubiquitin-specific protease 7 (USP7) cause the neurodevelopmental disorder Hao-Fountain syndrome. However, which of its pleiotropic substrates are relevant for neurodevelopment has remained unclear. Here, we present a combination of quantitative proteomics, transcriptomics and epigenomics to define the core USP7 circuitry during neurodifferentiation. USP7 activity is required for the transcriptional programs that direct the differentiation of human ESCs to neural stem cells, and neuronal differentiation of SHSY5Y neuroblastoma cells. In addition to other substrates, including TRIM27, USP7 controls the dosage of the Polycomb H2AK119ub1 ubiquitin ligases ncPRC1.1 and ncPRC1.6. We found that BCOR-ncPRC1.1, but not ncPRC1.6 or TRIM27, is a key effector of USP7-dependent neuronal differentiation. Indeed, BCOR-ncPRC1.1 mediates the majority of USP7-dependent gene regulation during this process. Besides providing a detailed map of the USP7 regulome during neuronal differentiation, our results suggest that Hao-Fountain syndrome and ncPRC1.1-associated neurodevelopmental disorders involve dysregulation of a shared epigenetic network.

2025-03-12 | GSE263491 | GEO

(RNA-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

2025-03-12 | GSE263490 | GEO

(RNA-seq-H9) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

2025-03-12 | GSE263489 | GEO

(RNA-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

Project description:(RNA-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

| PRJNA1097633 | ENA

Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

Project description:Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

| PRJNA1097638 | ENA

(RNA-seq-H9) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

Project description:(RNA-seq-H9) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

| PRJNA1097634 | ENA

Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-03-12 | GSE263492 | GEO

The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

Project description:Precise control of protein ubiquitination is essential for brain development, and hence, disruption of ubiquitin signaling networks can lead to neurological disorders. Mutations of the deubiquitinase USP7 cause the Hao-Fountain syndrome (HAFOUS), characterized by developmental delay, intellectual disability, autism, and aggressive behavior. These neurological and behavioral manifestations indicate important unknown roles of USP7 specificially in the nervous system. Here, we report that conditional deletion of USP7 in excitatory neurons in the mouse forebrain triggers diverse phenotypes including growth delay, sensorimotor deficits, learning and memory impairment, and aggressive behavior, resembling clinical features of HAFOUS. USP7 deletion induces neuronal apoptosis in a manner dependent of the tumor suppressor p53. However, most behavioral abnormalities in USP7 conditional mice persist despite p53 loss. Strikingly, USP7 deletion in the brain perturbs the synaptic proteome and dendritic spine morphogenesis independently of p53. Integrated proteomics and subsequent ubiquitin biochemical analysis identify the RNA splicing factor Ppil4 as a novel neuronal substrate of USP7. Consistent with the role of Ppil4 in RNA splicing, loss of USP7 disrupts splicing program of synaptic genes in the cerebral cortex. Improtantly, knockdown of Ppil4 in cortical neurons impairs dendritic spine morphogenesis, phenocopying the effect of USP7 loss on dendritic spines. These findings reveal a novel USP7-Ppil4 ubiquitin signaling link that regulates neuronal connectivity in the developing brain, with implications for our understanding of the pathogenesis of HAFOUS and other neurodevelopmental disorders.

2025-02-25 | GSE280944 | GEO

DNA Fountain

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Chromatin contacts within a fountain-like structure

Project description:Hundreds of DNA replication forks functioning simultaneously are essential for timely DNA duplication, but the organization of replication forks are poorly understood in mammalian cells. Here, we developed a replication-enriched in situ HiC (Repli-HiC) method to capture chromatin contacts located adjacent to replication forks and found two types of fountain-like chromatin contacts at thousands of loci. Interactions within fountain-spanning regions are confirmed by q3C-seq analysis of different stages of S phase cells.

2024-03-04 | GSE230613 | GEO

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