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Transcriptome profiling in USP7 inhibitor (P22077)-treated H1299 and HeLa cells

ABSTRACT: To investigate the molecular pathway signature responsive to pharmacological inhibition of USP7, we analyzed transcriptome in P22077 (a USP7 selective inhibitor)-treated H1299 and HeLa cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213931 | GEO | 2023/09/30

REPOSITORIES: GEO

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Genome-wide maps of acetylated lysine 27 of Histone 3 (ChIP-seq) and gene expression profiling (RNA-seq) in wildtype and USP7-KO H1299 lung cancer lines

Project description:Ubiquitin Specific Protease 7 (USP7), also named as herpesvirus-associated ubiquitin-specific protease (HAUSP), is one of the most abundant deubiquitinase and plays multifaceted roles in many cellular functions, including the protein homeostasis, DNA repair, gene transcription, and oncogenic pathways. To investigate the role of USP7 in p53-deficient lung cancer cells, the CRISPR/Cas9-mediated gene editing was employed to inactivate the USP7 locus in H1299 cells. The alterations of transcriptional enhancers and gene expression were analyzed by H3K27ac ChIP-seq and RNA-seq, respectively, in wildtype and USP7-KO H1299 lung cancer cells.

2021-09-16 | GSE172506 | GEO

Reduced representative bisulfite sequencing (RRBS) analysis for a genome-wide comparison of DNA methylation in wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO HeLa cell lines.

Project description:To better characterize the effects of USP7 on DNA methylation, we performed reduced representative bisulfite sequencing (RRBS) analysis for a genome-wide comparison of DNA methylation in wild-type, USP7-KO-1, DNMT3A/3B-DKO and DNMT3A/DNMT3B/USP7-TKO HeLa cell lines. RRBS analysis showed increased DNA methylation in USK7-KO cells and loss of USP7 elevates DNA methylation on pre-existing sites and de novo methylation.

2020-09-07 | GSE136159 | GEO

Microarry from Treg with conditional knockout of Usp7

Project description:Microarry from Treg with conditional knockout of Usp7 RNA from three independent samples from FACS sorted CD4+YFP+ Treg of fl-Usp7/Foxp3cre mice, compared to Foxp3cre control (C57BL/6 background).

2015-09-15 | E-GEOD-72988 | biostudies-arrayexpress

YG001: A Usp7-Tip60 pathway regulates early adipogenesis

Project description:USP7, a dominant DUB activity in 3T3-L1 adipocytes and in mouse adipose tissue, increases Tip60 protein levels, and deubiquitinates Tip60 both in intact cells and in vitro. Treatment with a pan deubiquitinase (DUB) inhibitor, or knockdown of USP7, decreases adipogenesis. Transcriptome analysis reveals a common set of cell cycle genes to be co-regulated by both Tip60 and USP7. Knock down of either factor results in impaired mitotic clonal expansion, an early step in adipogenesis. These results therefore reveal deubiquitination of a transcriptional coregulator to be a key mechanism in the regulation of early adipogenesis Mature 3T3-L1 adipocytes were subjected to RNAi-mediated knock down with control(C), USP7(U)- or Tip60(T)-specific oligonucleotides. For this, 4 replicates of differentiated 3T3-L1 cells were transfected with Amaxa technology. Two days after transfection cells were washed twice with PBS twice and lysed in 0.5ml Trizol (Invitrogen). mRNA expression of Tip60 and USP7 was assessed by qRT-PCR. Amplified cRNA samples were labeled with either cy3 or cy5 and put on microarray together with and oppositely labeled common reference sample consisting of cRNA derived from undifferentiated 3T3-L1 cells.

2013-08-28 | E-GEOD-28587 | biostudies-arrayexpress

USP7 cooperates with SCML2 to regulate the activity of PRC1

Project description:In this experiment, we sought to identify the distribution of USP7 on chromatin relative to other PRC1 components ChIP-seq for USP7 in 293T-REx cells

2015-06-10 | E-GEOD-61048 | biostudies-arrayexpress

Chromatin organization in T-ALL cells upon USP7 inhibitor with or without dexamethasone (Hi-C)

Project description:We report chromatin organization changes in DND41 cells upon USP7 inhibitor with or without dexamethasone. DND41 cells were treated with USP7 inhibitor with or without dexamethasone. ATAC-seq were performed to detect chromatin organization change

2022-12-13 | GSE182682 | GEO

Chromatin accessibility in T-ALL cells upon USP7 inhibitor with or without dexamethasone (ATAC-Seq)

Project description:We report chromatin accessibility changes in DND41 cells upon USP7 inhibitor with or without dexamethasone. DND41 cells were treated with USP7 inhibitor with or without dexamethasone. ATAC-seq were performed to detect chromatin accessibility change

2022-12-13 | GSE182681 | GEO

Chromatin accessibility in T-ALL cells upon USP7 inhibitor with or without dexamethasone (RNA-Seq)

2022-12-13 | GSE182680 | GEO

USP7: combing tools towards selectivity

Project description:Active-site probes based on the ubiquitin scaffold have been successfully applied as tools to determine the levels of active deubiquitinating enzymes (DUBs). Here, we show the development of a Ub-based reagent selective for the DUB USP7. This concept can be applied for the generation of other new selective reagents.

2019-03-13 | PXD012535 | Pride

Effect of the USP7 inhibitor HBX41,108 on lipopolysaccharide induced gene expression in mouse bone marrow derived macrophages.

Project description:USP7 is a deubiquitinase enzyme that removes polyubiquitin chains form a number of substrates including MDM2, p53 and NF-κB. In this study we assessed the impact of the USP7 inhibitor HBX41,108 on lipopolysaccharide (LPS) induded transcriptional responses in murine bone marrow derived macrophages.

2020-06-15 | GSE149478 | GEO

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