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USP22 controls type III interferon signaling and SARS-CoV-2 infection through activation of STING

ABSTRACT: Within the context of the DUB module in the SAGA complex, USP22 is involved in transcriptional elongation through the regulation of H2AK119ub1 and H2BK120ub1. However, up till now, the spectrum of USP22-regulated target genes largely remains unclear, partially due to organism-, cell- and context-dependent redundancy in alternative DUBs that might compensate for loss of USP22. To understand which genes are regulated by USP22, we profiled USP22-dependent changes in gene expression in the human intestinal epithelial cell (hIEC) line HT-29.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190036 | GEO | 2022/08/22

REPOSITORIES: GEO

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The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22

Project description:SAGA is a modular cofactor complex that is essential for eukaryotic transcription. SAGA’s complement of ~20 proteins exist within four structurally and functionally distinct modules, two of which are catalytic. Within the KAT module, GCN5 acetylates histone tails, leading to increased chromatin accessibility and bromodomain protein recruitment. The DUB module contains the ubiquitin hydrolase USP22. In yeast, the USP22 ortholog deubiquitylates H2B, resulting in Pol II S2 phosphorylation and subsequent transcriptional elongation. We report here that metazoan SAGA, and USP22 specifically, are required at a more proximal stage in activator-driven transcription, i.e. pre-initiation complex (PIC) assembly. A combination of genome-wide and proteomic analyses revealed that H2B deubiquitylation is not linked to USP22-dependent transcription. Instead, USP22 controls Mediator tail subunit ubiquitylation. Mechanistically, USP22 controls loading of Mediator tail and GTFs onto promoters, with Mediator core recruitment being USP22-independent. These findings place human SAGA function at the earliest steps in activator-driven transcription.

2021-04-12 | GSE158108 | GEO

The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22

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USP22 functions as an oncogenic driver in prostate cancer by regulating cell proliferation and DNA repair

Project description:The deubiquitinase USP22 is a member of the SAGA transcriptional activation complex. This study used models of USP22 overexpression and depletion to identify differentially expressed gene networks.

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Investigating the role of USP22 in reprogramming

Project description:Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by overexpressing OCT4, SOX2, KLF4 and MYC. Although this cell fate transition is a slow and inefficient process, inhibiting several epigenetic barriers has shown to facilitate it. A previously employed epigenetic focused CRISPR-Cas9-mediated knockout screen during reprogramming uncovered novel human somatic cell reprogramming barriers. Here, I showed that USP22, target for gRNAs that were enriched in iPSCs from the screen, is a barrier for reprogramming and its loss is compatible with iPSC generation. Overexpressing wild-type or deubiquitinase mutant (C185A) USP22 in knockout background could rescue the phenotype. Additionally, knocking out other SAGA deubiquitinase subunits, ENY2 and ATXN7L3 did not increase the reprogramming efficiency. Mechanistically, we showed that USP22 loss upregulates an important pluripotency-related transcription factor, SOX2, expression even as early as 3 days after OSKM expression. We hypothesized that USP22 downregulates pluripotency-related gene expression during reprogramming independent from its SAGA integration and deubiquitinase activity. To address this, I will repeat rescuing USP22 knockout phenotype in reprogramming by overexpressing mutant versions of USP22 including K129R (acetyl inhibited) and HHAA (deubiqutinase). Additionally, I will check the expression of pluripotency-related genes at early time points of reprogramming upon USP22 knockout by transcriptome profiling. Lastly, I will generate USP22 knockout iPSC lines to force them to differentiation to observe if they have any problem with pluripotency exit. This work will establish a mechanistic understanding for the role USP22 play on both human somatic cell reprogramming, pluripotency and differentiation.

2023-07-31 | GSE225151 | GEO

USP22 controls necroptosis by regulating receptor interacting protein kinase 3 ubiquitination

Project description:Dynamic control of ubiquitination by deubiquitinating enzymes is essential for almost all biological processes. Ubiquitin-specific peptidase 22 (USP22) is part of the SAGA complex and catalyzes the removal of monoubiquitination from histone H2B, thereby regulating gene transcription. However, novel roles for USP22 have recently emerged, such as tumor development and cell death. Apart from apoptosis, the relevance of USP22 in other programmed cell death pathways still remains unclear. Here, we describe a novel role for USP22 in controlling necroptotic cell death in a variety of tumor cell lines. Loss of USP22 expression significantly delays TNF/Smac mimetic/zVAD.fmk (TBZ)-induced necroptosis, without affecting TNF-mediated NF-B activation or extrinsic apoptosis. Mass-spectrometric ubiquitin remnant profiling identified lysine 518 of Receptor-interacting protein kinase 3 (RIPK3) as USP22-dependent ubiquitination target during necroptosis induction. Mutation of K518 in RIPK3 reduced necroptosisassociated RIPK3 ubiquitination and amplified necrosome formation and necroptotic cell death. In conclusion, we identify a novel role of USP22 in necroptosis and further elucidate the relevance of ubiquitination as crucial regulator of necroptotic cell death.

2021-05-03 | PXD020909 | Pride

USP22 overexpression leads to aberrant signal transduction but is not sufficient to drive tumor formation in mice

Project description:USP22 overexpression is observed in several human cancers and is correlated with poor patient outcomes. The molecular basis underlying this correlation is not clear. USP22 is the catalytic subunit of the deubiquitylation module in the SAGA histone modifying complex, which regulates gene transcription. Our previous work demonstrated that loss of USP22 in mice leads to decreased expression of several components of receptor tyrosine kinase and TGFβ signaling pathways. To determine whether these pathways are upregulated when USP22 is overexpressed, we created a mouse model that expresses high levels of USP22 in all tissues. Phenotypic characterization of these mice revealed over branching of the mammary glands in females. Transcriptomic analyses indicate upregulation of key pathways involved in mammary gland branching in mammary epithelial cells derived from the USP22 overexpressing mice, including estrogen receptor, ERK/MAPK and TGFβ signaling. However, USP22 overexpression did not lead to increased tumorigenesis in any tissue. Our findings indicate that elevated levels of USP22 are not sufficient to induce tumors but it may enhance signaling abnormalities associated with oncogenesis.

2021-08-13 | GSE180005 | GEO

Usp22 controls multiple signaling pathways that are essential for vasculature formation in the mouse placenta

Project description:Usp22, a component of the SAGA complex, is over expressed in highly aggressive cancers, but the normal functions of this deubiquitinase are not well defined. We determined that loss of Usp22 in mice results in embryonic lethality due to defects in extra-embryonic placental tissues and failure to establish proper vascular interactions with the maternal circulatory system. These phenotypes arise from abnormal gene expression patterns that reflect defective kinase signaling, including TGFβ and several receptor tyrosine kinase (RTK) pathways. Usp22 deletion in endothelial cells and pericytes induced from embryonic stem cells also hinders these signaling cascades with detrimental effects on cell survival and differentiation as well as ability to form vessels. Our findings provide new insights to Usp22 functions during development that may offer clues to its role in disease states.

2019-02-04 | GSE126069 | GEO

Transcriptional profiling of Usp22-WT and Usp22-KO pancreatic tumor cells

Project description:RNA-seq analysis of sorted Usp22-WT and Usp22-KO tumor cells from subcutaneously implanted mouse pancreatic tumors

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Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [ChIP-Seq]

Project description:The deubiquitinating module (DUBm) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and ATXN7, ATXN7L3 and ENY2 adaptor proteins, which are all needed for the full activity of USP22 enzyme. In addition, ATXN7L3 is critical for directing the DUB module substrate specificity towards H2Bub1. We reported that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process. Global histone H2Bub1 levels were only slightly affected in Usp22 null embryos, while in contrast H2Bub1 levels were strongly increased in Atxn7l3 null mutants and derived cellular systems. Interestingly, the strong H2Bub1 increases observed in the Atxn7l3-/- mouse embryonic stem cells, or Atxn7l3-/- mouse embryonic fibroblasts, do not correlate with the modest genome-wide Pol II occupancy changes observed in the two knock-out cellular systems. Thus, histone H2Bub1 deubiquitylation does not directly regulate global RNA polymerase II transcription.

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Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [RNA-Seq]

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