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Expression analysis of knockdown of USP7 in HEK293T cells.

ABSTRACT: Ubiquitin Specific Peptidase 7 (USP7) is a deubiquitinase of several important regulatory proteins, and important regulator of TGFb pathway. To investigate their role in cell signaling, we analyzed global mRNA levels in HEK293T cells that were knocked down with shRNAs against USP7 and non-targeting control (CTRL).

ORGANISM(S): Homo sapiens

PROVIDER: GSE139094 | GEO | 2020/10/18

REPOSITORIES: GEO

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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

Expression analysis of single and double knockdown of UBE4B and LSD1 in HEK293T cells.

Project description:Ubiquitin Ligase (UBE4B) and Lysine-Specific Demethylase (LSD1) are post-translational modifying enzymes affecting lysine ubiquitination and methylation of several important regulatory proteins, and are synergisticaly important for protein quality control. To inwestigate their role in cell signaling, we analyzed global mRNA levels in HEK293T cells that were knocked down with shRNAs against UBE4B, LSD1, both UBE4B and LSD1, and non-targeting control (CTRL).

2017-02-09 | GSE58026 | GEO

USP7 shRNA knock-down in T-ALL cells [Jurkat_HSB2_shRNA_RNA-seq]

Project description:RNAseq analysis of USP7 shRNA KD in T-ALL cell lines. USP7 shRNAs lentivirus was generated by co-transfecting 293T cells with shRNA vectors (OriGene or Sigma). T-ALL cells were transduced with USP7 shRNA lentivirus and sorted for GFP positive cells five days after transduction or selected by puromycin.

2021-03-09 | GSE148522 | GEO

Expression analysis of knockdown of USP7 in HEK293T cells.

Project description:Expression analysis of knockdown of USP7 in HEK293T cells.

| PRJNA578370 | ENA

YG001: A Usp7-Tip60 pathway regulates early adipogenesis

2013-08-28 | GSE28587 | GEO

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

USP7 represses lineage differentiation genes of mouse embryonic stem cells through both catalytic and non-catalytic activity

Project description:USP7, a ubiquitin-specific peptidase (USP), plays an important role in many cellular processes through its catalytic deubiquitination of various substrates. However, its nuclear function to regulate gene expression in mouse embryonic stem cells (mESCs) remains largely unknown. Here, we report that USP7 maintains mESCs identity through both catalytic activity-dependent and -independent repression of lineage differentiation genes. Usp7 depletion attenuates SOX2 level and derepresses lineage differentiation genes thereby compromising mESCs identity. Mechanistically, USP7 deubiquitinates and stabilizes SOX2 to repress mesoendodermal (ME) lineage genes. Moreover, USP7 assembles into RYBP-variant polycomb repressive complex 1 (vPRC1) and contributes to Polycomb chromatin domain-mediated repression of ME lineage genes in a catalytic activity-dependent manner. However, USP7 deficient in its deubiquitination function is able to maintain RYBP binding on chromatin to represses primitive endoderm-associated genes in mESCs. Overall, our study demonstrates that USP7 harbors both catalytic and non-catalytic scaffold activity to repress lineage differentiation genes thereby revealing a previously unrecognized role in controlling gene expression and maintaining mESCs identity.

2023-08-08 | GSE197427 | GEO

USP7 represses lineage differentiation genes of mouse embryonic stem cells through both catalytic and non-catalytic activity [CUT&Tag]

2023-08-08 | GSE197157 | GEO

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

DICER regulation by an USP7-MDM2 axis in cancer cells

Project description:DICER is an RNase III enzyme which plays a critical role in the microRNA mature process in the cytoplasm, but also is involved in other functions such as chromatin remodeling, epigenetic modification and DNA damage repair in the nucleus. The expression of DICER is almost decreased across the board in human cancers, which highlights that its expression is strictly controlled, however the underlying mechanisms still remain unknown. In this study, we find that deubiquitinase USP7 suppresses the expression of DICER at the protein level, which impacts DNA damage response (DDR) and cancer progression. MDM2, which is a well-known oncoprotein and also a substrate of USP7, is identified as a novel DICER ubiquitin E3 ligase, thus forming a new regulatory axis of USP7-MDM2-DICER. These findings may provide a new approach to the diagnosis, treatment and prognosis of malignant tumors.

2024-01-10 | GSE225307 | GEO

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