Visualizing ubiquitination in mammalian cells

Wijk, Sjoerd J. L. van; Fulda, Simone; Đikić, Ivan; Heilemann, Mike

doi:10.15252/embr.201846520

Cited by 94 publications

(78 citation statements)

References 156 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…[ 31 ] Ubiquitination plays an important role in protein localization, metabolism, function, regulation, and degradation. [ 32 ] At the same time, it is involved in the regulation of cell cycle, proliferation, apoptosis, differentiation, metastasis, gene expression, transcriptional regulation, signaling, inflammation, and immunity. Ubiquitination is closely related to the pathogenesis of tumors.…”

Section: Discussionmentioning

confidence: 99%

Hsa_circ_0002320: a novel clinical biomarker for colorectal cancer prognosis

Yang

Kong

et al. 2020

Medicine

View full text Add to dashboard Cite

A great many circular RNAs (circRNAs) exist in different types of mammalian cells. Previous studies have verified that a low level of hsa_circ_0002320 is present in gastric cancer and that it might represent a good prognostic indicator. However, its value in colorectal cancer (CRC) is unclear. The aim of this research was to explore the value of hsa_circ_0002320 as a potential diagnostic biomarker for CRC prognosis. Plasma samples, CRC tissues, and adjacent normal tissues were obtained from 50 patients with CRC, before any treatment, and 100 plasma samples were acquired from healthy individuals. Hsa_circ_0002320 levels in these samples were analyzed by reverse transcription-quantitative polymerase chain reaction. Correlations between hsa_circ_0002320, clinicopathological characteristics, and overall survival (OS) of CRC patients were also investigated. Receiver-operating characteristic (ROC) curve analysis was used to assess the value of hsa_circ_0002320 for CRC diagnosis. Finally, a bioinformatics analysis was performed to verify the effect of hsa_circ_0002320 on CRC prognosis. Expression levels of hsa_circ_0002320 were significantly decreased in CRC plasma ( P < .05). The expression level of hsa_circ_0002320 was significantly correlated with OS time ( P < .05). Higher hsa_circ_0002320 reflected significantly greater OS; the HR of high hsa_circ_0002320 was 0.161 (95% CI, 0.066–0.393; P = .000). The area under the ROC curve of hsa_circ_0002320 in CRC was 0.823, which was higher than for the carcinoembryogenic antigen (area under the curve = 0.764). Kaplan-Meier analysis showed that CRC patients with low expression of hsa_circ_0002320 exhibited poorer OS times than those with high expression. Hsa_circ_0002320 could be a novel, noninvasive diagnostic blood biomarker for CRC prognosis.

show abstract

Section: Discussionmentioning

confidence: 99%

Hsa_circ_0002320: a novel clinical biomarker for colorectal cancer prognosis

Yang

Kong

et al. 2020

Medicine

View full text Add to dashboard Cite

show abstract

“…The techniques and approaches for visualizing Ub signals have recently been reviewed in details by van Wijk et al (2019).…”

Section: Determination Of Cellular Localization Of Ubiquitin Modificamentioning

confidence: 99%

Resolving the Complexity of Ubiquitin Networks

Kliza

Husnjak

2020

Front. Mol. Biosci.

View full text Add to dashboard Cite

Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks.

show abstract

“…Imaging-based experiments using the Cy5-UbDha probe could allow the measurement of ubiquitination in cells [67]. However, these methods may affect ubiquitination and the signaling cascade, thus disrupting cell homeostasis [68].…”

Section: Delivery Of Abps To Cellsmentioning

confidence: 99%

Assay Systems for Profiling Deubiquitinating Activity

Cho

Park

Kim

et al. 2020

IJMS

View full text Add to dashboard Cite

Deubiquitinating enzymes regulate various cellular processes, particularly protein degradation, localization, and protein–protein interactions. The dysregulation of deubiquitinating enzyme (DUB) activity has been linked to several diseases; however, the function of many DUBs has not been identified. Therefore, the development of methods to assess DUB activity is important to identify novel DUBs, characterize DUB selectivity, and profile dynamic DUB substrates. Here, we review various methods of evaluating DUB activity using cell lysates or purified DUBs, as well as the types of probes used in these methods. In addition, we introduce some techniques that can deliver DUB probes into the cells and cell-permeable activity-based probes to directly visualize and quantify DUB activity in live cells. This review could contribute to the development of DUB inhibitors by providing important information on the characteristics and applications of various probes used to evaluate and detect DUB activity in vitro and in vivo.

show abstract

Visualizing ubiquitination in mammalian cells

Cited by 94 publications

References 156 publications

Hsa_circ_0002320: a novel clinical biomarker for colorectal cancer prognosis

Hsa_circ_0002320: a novel clinical biomarker for colorectal cancer prognosis

Resolving the Complexity of Ubiquitin Networks

Assay Systems for Profiling Deubiquitinating Activity

Contact Info

Product

Resources

About