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Profiling HeLa cell ubiquitylome with OtUBD and FK2

ABSTRACT: This project compares the novel ubiquitin affinity reagent OtUBD with a monoclonal ubiquitin antibody FK2 in their abilities to facilitae the profiling of the ubiquitylated proteome of HeLa cells. Enrichments were done side by side using a semi-denaturing condition.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Mengwen Zhang

LAB HEAD: Mark Hochstrasser

PROVIDER: PXD032675 | Pride | 2022-05-30

REPOSITORIES: Pride

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			Action	DRS
	F525644.mgf	Mgf
	F525644.xml	Xml
	F525645.mgf	Mgf
	F525645.xml	Xml
	F525646.mgf	Mgf

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Profiling yeast ubiquitylome with OtUBD pulldowns

Project description:This project includes two separate experiments where the ubiquitylated proteome of the budding yeast Saccharomyces cerevisiae was enriched from whole cell lysate by affinity purification using a novel OtUBD affinity resin. In the first experiment, two distinct experimental conditions (native, denaturing) were used to compare the proteins enriched by OtUBD affinity resin and the negative control resin. In the second experiment, the ubiquitylation profile of proteins were compared among wildtype yeast cells and yeasts lacking certain E3 ligase enzymes.

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Alterations in proteome and proteostasis networks during replicative senescence

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Profiling linkage-specific ubiquitin chain functions reveals a key role of K29-linked ubiquitylation in epigenome maintenance

Project description:Linkage-specific ubiquitin (Ub) chains dictate the functional outcome of many critical Ub-dependent signaling processes. However, the functions and targets of several poly-Ub topologies remain poorly understood due to a lack of tools for their specific detection and manipulation. To remedy this knowledge gap, we applied a cell-based Ub replacement strategy enabling specific, conditional abrogation of each of the seven lysine-based Ub chain types in human cells to comprehensively profile global ubiquitylation changes resulting from disabling formation of individual Ub chain types. Focusing on K29-linked ubiquitylation, we found that this linkage type is enriched among chromatin-associated proteins, and that the H3K9me3 methyltransferase SUV39H1 is a prominent cellular target of this modification. We demonstrate that K29-linked ubiquitylation is essential for the proteasomal degradation of SUV39H1 despite its extensive modification by K48-linked ubiquitylation, and that K29-linked ubiquitylation of SUV39H1 is catalyzed and reversed by TRIP12 and TRABID, respectively. Importantly, preventing K29-linked ubiquitylation of SUV39H1 markedly increases H3K9me3 levels, but not other histone marks. Collectively, our Ub replacement cell line panel and datasets provide valuable resources for illuminating cellular functions of linkage-specific ubiquitylation processes and reveal a key role for K29-linked ubiquitylation in epigenome maintenance.

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