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Whole-transcriptome analysis using RNA sequencing in OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells

ABSTRACT: Whole-transcriptome analysis using RNA sequencing in OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells

PROVIDER: PRJNA557353 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9860300_1.fastq.gz	Fastqsanger.gz
	SRR9860300_2.fastq.gz	Fastqsanger.gz
	SRR9860295_1.fastq.gz	Fastqsanger.gz
	SRR9860295_2.fastq.gz	Fastqsanger.gz
	SRR9860296_1.fastq.gz	Fastqsanger.gz

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Whole-transcriptome analysis using RNA sequencing in OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells

Project description:Whole-transcriptome analysis was performed on RNA from OTUD5-wild type, OTUD5-null, and GDC0349-treated HEK293 cells to identify the cellular processes regulated by OTUD5 and mTOR simultaneously.

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OTUD5 complex mass spectrometry

Project description:DUBs are involved in various pathways and signalling networks by pairing with E3 ubiquitin ligases in protein complexes. In order to test whether OTUD5 associates with an E3 ubiquitin ligase to regulate cell proliferation, the stable Flag-OTUD5/Hep3B cell line was established by transfecting Hep3B cells with plasmids expressing pCIN4-Flag-OTUD5. The cellular factors interacting with OTUD5 were purified by anti-Flag antibody-conjugated M2 beads.

2020-09-11 | PXD019907 | Pride

Autophagy of OTUD5 Destabilizes GPX4 to Confer Ferroptosis-Dependent Kidney Injury

Project description:Ferroptosis is an iron-dependent programmed cell death associated with severe kidney diseases, linked to decreased glutathione peroxidase 4 (GPX4). However, the spatial distribution of renal GPX4-mediated ferroptosis and the molecular events causing GPX4 reduction during ischemia-reperfusion (I/R) remain largely unknown. Using spatial transcriptomics, we identify that GPX4 is situated at the interface of the inner cortex and outer medulla, a hyperactive ferroptosis site post-I/R injury. We show that OTU deubiquitinase 5 (OTUD5) is a GPX4-binding protein that confers ferroptosis resistance by stabilizing GPX4. During I/R, ferroptosis is induced by mTORC1-mediated autophagy, causing OTUD5 degradation and subsequent GPX4 decay. Functionally, OTUD5 deletion intensifies renal tubular cell ferroptosis and exacerbates acute kidney injury, while AAV-mediated OTUD5 delivery mitigates ferroptosis and promotes renal function recovery from I/R injury. In this work, our study highlights a new autophagy-dependent ferroptosis module: hypoxia/ischemia-induced OTUD5 autophagy triggers GPX4 degradation, offering a potential therapeutic avenue for I/R-related kidney diseases.

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Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation [RNA-Seq]

Project description:Reversible modification of proteins with linkage-specific ubiquitin chains is critical for intracellular signaling. Yet, information on physiological roles and underlying signaling mechanisms of particular ubiquitin linkages during human development are limited. Here, relying on genomic constraint scores, we identify 10 patients with a novel multiple congenital anomaly disorder caused by hemizygous variants in OTUD5, encoding a K48-/K63-linkage-specific deubiquitylase. By studying these mutations, we find that OTUD5 controls neuroectodermal differentiation through cleaving K48-linked ubiquitin chains to counteract degradation of a select group of chromatin regulators. These include ARID1A/B, HDAC2, and HCF1, mutation of which underlie different developmental disorders that exhibit phenotypic overlap with OTUD5 patients. Consequently, loss of OTUD5 during early differentiation leads to less accessible chromatin at neuroectodermal enhancers and thus aberrant rewiring of gene expression networks. Our study describes a novel developmental disorder we name LINKED (LINKage-specific-deubiquitylation-deficiency-induced Embryonic Defects) syndrome, provides a previously unrecognized mechanistic link between phenotypically related diseases, and reveals linkage-specific ubiquitin cleavage from substrate groups (i.e. chromatin remodelers) as an essential mode of signaling required to coordinate embryonic differentiation pathways.

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Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation [ATAC-Seq]

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whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

Project description:Comparison of methylome of HEK293-CT cells and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1) We used BS-seq to identify genomic regions differentially methylated upon overexpression of the chromatin repressor BAHD1 in HEK293 cells.

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Project description:RNA-seq analysis of wild-type HEK293, HEK293 treated with DMSO, ML216 or NSC617145, wild-type mESCs and dhx9KO mESCs

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whole-genome bisulfite sequencing (BS-seq) of HEK293 cells (HEK293-CT) and HEK293 cells stably over-expressing the BAHD1 gene (HEK-BAHD1)

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Project description:Next Generation Sequencing of wild-type HEK293 cells compared to STAT5b knock-out HEK293 cells using Crispr/Cas9

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LFQP of lysates from wild-type, RAB18-, TBC1D20-, RAB3GAP1- and RAB3GAP2-null RPE1 cells

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2024-01-26 | PXD016326 | Pride

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