Dataset Information

UIM domain interacting proteins

ABSTRACT: we identified the UIM domain interacting protein though IP-MS, and quantified the related ubiquitin chains

ORGANISM(S): Saccharomyces Cerevisiae

SUBMITTER: Ping Xu

PROVIDER: PXD024048 | iProX | Sun Feb 07 00:00:00 GMT 2021

REPOSITORIES: iProX

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Publications

The Ubiquitin Interacting Motif-Like Domain of Met4 Selectively Binds K48 Polyubiquitin Chains.

Villamil Mark M Xiao Weidi W Yu Clinton C Huang Lan L Xu Ping P Kaiser Peter P

Molecular & cellular proteomics : MCP 20211109 1

Protein ubiquitylation is an important posttranslational modification that governs most cellular processes. Signaling functions of ubiquitylation are very diverse and involve proteolytic as well as nonproteolytic events, such as localization, regulation of protein interactions, and control of protein activity. The intricacy of ubiquitin signaling is further complicated by several different polyubiquitin chain types that are likely recognized and interpreted by different protein readers. For exam ...[more]

PMID: 34763062

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Project description:A variety of self-interacting domains, defined at different levels of resolution, have been described in mammalian genomes. These include Chromatin Compartments (A and B), Topologically Associated Domains (TADs), contact domains, sub-TADs, insulated neighborhoods and frequently interacting regions (FIREs). Whereas many studies have found the organisation of self-interacting domains to be conserved across cell types, some do form in a lineage-specific manner. However, it is not clear to what degree such tissue-specific structures result from processes related to gene activity such as enhancer-promoter interactions or whether they form earlier during lineage commitment and are therefore likely to be prerequisite for promoting gene expression. To examine these models of genome organisation in detail, we used a combination of high-resolution chromosome conformation capture, a newly-developed form of quantitative fluorescence in-situ hybridisation and super-resolution imaging to study a 70 kb self-interacting domain containing the mouse alpha-globin locus. To understand how this self-interacting domain is established, we studied this structure when the genes are inactive and during erythroid differentiation when the genes are progressively switched on. In contrast to many current models of long-range gene regulation, we show that an erythroid-specific, decompacted self-interacting domain, delimited by convergent CTCF/cohesin binding sites, forms prior to the onset of robust gene expression. Using previously established mouse models we also show that formation of the self-interacting domain does not rely on interactions between the alpha-globin genes and their enhancers or on tissue-specific changes in CTCF binding. Rather, formation of the domain simply depends on the presence of activated lineage-specific cis-elements driving a transcription-independent mechanism for opening chromatin throughout the 70 kb region to create a permissive environment for gene expression. These findings are consistent with a model of loop-extrusion in which all segments of chromatin within a region delimited by CTCF boundary elements contact each other. Our findings suggest that activation of tissue-specific element(s) within such a self-interacting region is sufficient to influence all chromatin within such a domain.

Dataset Information

UIM domain interacting proteins

Publications

The Ubiquitin Interacting Motif-Like Domain of Met4 Selectively Binds K48 Polyubiquitin Chains.

Similar Datasets

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