The PRIDE database and related tools and resources in 2019: improving support for quantification data. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Changing places: chromosomal passenger complex relocation in early anaphase. The CCAN complex: linking centromere specification to control of kinetochore-microtubule dynamics. Mis16 and Mis18 are required for CENP-A loading and histone deacetylation at centromeres. Structure of the MIS12 complex and molecular basis of its interaction with CENP-C at human kinetochores. CENP-C is a structural platform for kinetochore assembly. ![]() Structure of a survivin-borealin-INCENP core complex reveals how chromosomal passengers travel together. Proteome-wide identification of ubiquitin interactions using UbIA-MS. ChromID identifies the protein interactome at chromatin marks. Variability in streptavidin-sepharose matrix quality can significantly affect proximity-dependent biotinylation (BioID) data. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Defining proximity proteomics of histone modified proteins by antibody-mediated protein A-APEX2 labeling. Biotinylation by antibody recognition - a method for proximity labeling. Off-the-shelf proximity biotinylation for interaction proteomics. Chromatin proteomics to study epigenetics – challenges and opportunities. Localized protein biotinylation at dna damage sites identifies zpet, a repressor of homologous recombination. Proximity labeling: spatially resolved proteomic mapping for neurobiology. Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging. A proximity-dependent biotinylation map of a human cell. Efficient proximity labeling in living cells and organisms with TurboID. AirID, a novel proximity biotinylation enzyme, for analysis of protein–protein interactions. ultraID: a compact and efficient enzyme for proximity-dependent biotinylation in living cells. Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. Characterizing protein–protein interactions using mass spectrometry: challenges and opportunities. ![]() Mass spectrometry‐based protein–protein interaction networks for the study of human diseases. The protocol has been optimized for nuclear targets but may also be adapted to other subcellular regions of interest. Data analysis and data visualization are relatively straightforward and can be performed using any type of software that converts raw mass spectrometry spectra files into identified and quantified proteins. In principle, any scientist can perform this protocol within 3 days, although generating the proteomics data requires access to a high-end liquid chromatography–mass spectrometry setup. Finally, biotinylated proteins are enriched from crude lysates using streptavidin beads followed by mass spectrometry-based protein identification. Following incubation, during which ProteinA-Turbo antibody–antigen complexes are formed, unbound molecules are washed away, after which bait-proximal biotinylation is triggered by the addition of exogenous biotin. In this method, a bait-specific antibody and the ProteinA-Turbo enzyme are consecutively added to permeabilized fixed or unfixed cells. We recently developed an ‘off-the-shelf’ proximity biotinylation method that makes use of a recombinant enzyme consisting of the biotin ligase TurboID fused to the antibody-recognizing moiety Protein A. This technology typically relies on fusing a bait protein to a biotin ligase using overexpression or clustered regularly interspaced short palindromic repeats (CRISPR)-based tagging, thus prohibiting the use of such assays in cell types that are difficult to transfect or transduce. Proximity biotinylation is a commonly used method to identify the in vivo proximal proteome for proteins of interest.
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