PUB-MS: A Mass Spectrometry-based Method to Monitor Protein–Protein Proximity <i>in vivo</i>

Kulyyassov, Arman; Shoaib, Muhammad; Pichugin, Andrey; Kannouche, Patricia; Ramanculov, Erlan; Lipinski, Marc; Ogryzko, Vasily

doi:10.1021/pr200189p

Cited by 29 publications

(53 citation statements)

References 37 publications

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“…To confirm our previous findings (Kulyyassov et al 2011), we used immunofluorescence microscopy to monitor the distribution of biotinylated chromatin 6 h after its labeling by BirA-RAD18. Up until the biotin labeling, the cells were treated as in the previous section.…”

mentioning

confidence: 61%

“…1 in Kulyyassov et al 2011]). A similar method, although not designed for mass spectrometry analysis, was also developed in the laboratory of Dr. A.Y.…”

Section: Resultsmentioning

confidence: 99%

“…Ting (Fernandez-Suarez et al 2008). The general principle of the approach is based on coexpression of two proteins of interest fused to a biotin acceptor domain in one case and a biotin ligase enzyme (BirA) in the other (Kulyyassov et al 2011). The BAP domain was modified to weaken its affinity to BirA and thus to decrease the background biotinylation levels.…”

Section: Resultsmentioning

confidence: 99%

“…The vectors for expression of BAP-and BirA-fusions, as well as BirA-GFP, BirA-RAD18, BAP-H2A, BAP-macroH2A2, and BAP-H2AFB3 expression vectors have been described elsewhere (Kulyyassov et al 2011). The H2AZ and H3.1 ORFs were subcloned from pOZ.FHH vectors (Saade et al 2009), whereas the POLH ORFs (wild type and mutant) were amplified by PCR and inserted into the BirA-fusion vector using XhoI and NotI restriction sites.…”

Section: Recombinant Dnamentioning

confidence: 99%

“…The distinctive feature of the PUB-NChIP method is that chromatin in proximity to the BirA-fusion is left with a permanent molecular mark (i.e., biotin), which can persist after the proximity between BAP-and BirA-fusions has been lost (Kulyyassov et al 2011). We decided to take advantage of this property to ask what happens to the histone PTMs in the RAD18-labeled chromatin at a specified time after the biotinylation.…”

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confidence: 99%

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PUB-NChIP—“in vivo biotinylation” approach to study chromatin in proximity to a protein of interest

et al. 2012

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We have developed an approach termed PUB-NChIP (proximity utilizing biotinylation with native ChIP) to purify and study the protein composition of chromatin in proximity to a nuclear protein of interest. It is based on coexpression of (1) a protein of interest, fused with the bacterial biotin ligase BirA, together with (2) a histone fused to a biotin acceptor peptide (BAP), which is specifically biotinylated by BirA-fusion in the proximity of the protein of interest. Using the RAD18 protein as a model, we demonstrate that the RAD18-proximal chromatin is enriched in some H4 acetylated species. Moreover, the RAD18-proximal chromatin containing a replacement histone H2AZ has a different pattern of H4 acetylation. Finally, biotin pulse-chase experiments show that the H4 acetylation pattern starts to resemble the acetylation pattern of total H4 after the proximity of chromatin to RAD18 has been lost.

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mentioning

confidence: 61%

“…1 in Kulyyassov et al 2011]). A similar method, although not designed for mass spectrometry analysis, was also developed in the laboratory of Dr. A.Y.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Recombinant Dnamentioning

confidence: 99%

mentioning

confidence: 99%

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PUB-NChIP—“in vivo biotinylation” approach to study chromatin in proximity to a protein of interest

et al. 2012

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Discovering cellular protein‐protein interactions: Technological strategies and opportunities

Titeca

Lemmens

Tavernier

et al. 2018

Mass Spectrometry Reviews

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The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.

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Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

Wang

et al. 2017

Proteomics

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Proteins perform biochemical functions by forming complexes, or protein-protein interactions (PPIs). Many different approaches such as phage display, yeast hybridization, etc. were developed to illustrate the PPIs, and disclose the composition and organization of protein complexes. However, none of these approaches are based on the real-time and in vivo PPI analysis. Proximity-dependent labeling (PDL) of interacting proteins has recently been proposed by taking advantage of several enzymes, which are capable of attaching the known reactive groups to the nearby proteins covalently. Among the PDL methods, BioID is the earliest and the most widely used one and has been upgraded from its prototype, making it an extremely convenient research tool. In this review, we describe the BioID technology development, its potential applications according to the nature of the target protein, and some recent efforts to circumvent the technical limitations. Moreover, some comparable PDL methods are introduced, including selective proteomic proximity labeling assay using tyramide, enzyme-mediated activation of radical sources, Proximity Labeling with Ascorbate Peroxidase, in vivo proximal labeling, etc., and we propose that systematic comparison of the working radius of these methods may be helpful to develop a tool box, from which the right method can be selected for a given target protein for PPI research.

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PUB-MS: A Mass Spectrometry-based Method to Monitor Protein–Protein Proximity in vivo

Cited by 29 publications

References 37 publications

PUB-NChIP—“in vivo biotinylation” approach to study chromatin in proximity to a protein of interest

PUB-NChIP—“in vivo biotinylation” approach to study chromatin in proximity to a protein of interest

Discovering cellular protein‐protein interactions: Technological strategies and opportunities

Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool

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