Biotin and Related Studies

Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo

This paper introduces SeeID, a near-infrared light-controlled proximity labeling method for studying dynamic protein interactomes in vitro and in vivo, revealing proteasome association with Parkin during mitophagy.

Benchmarking of proximity-dependent biotinylation enzymes across cellular compartments and time windows

This study benchmarks ten proximity ligases across cellular compartments and time windows, finding variations in activity, background, and spatial specificity, with ultraID showing the best balance.

Investigating the Interactomic Landscape of Survival Motor Neurons (SMN) and the SMN Δ7 truncated protein

The paper combines TurboID and Co-IP to study protein interactions, showing how they complement each other in capturing transient and stable interactions in cell culture systems.

Directed evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy

This study evolves a laccase enzyme for cell surface labeling and EM, showing it can map T cell surface changes and visualize cell features without toxic H2O2.

Development of a cell-permeable Biotin-HaloTag ligand to explore functional differences between protein variants across cellular generations

This paper develops a cell-permeable Biotin-HaloTag ligand to enable sequential labeling and separation of distinct protein variants for functional studies.

Proximity Labeling of NIMA Kinase Complex Components in C. elegans

This study uses proximity labeling and DIA-MS to analyze NEKL-MLT kinase complex interactions in C. elegans, identifying known and novel interactors and validating their roles in membrane trafficking and cytoskeletal regulation.

Proximity labelling-based identification of vascular homing peptide receptors

The paper develops a proximity labeling method to identify vascular homing peptide receptors on live cells, demonstrating its effectiveness with RPARPAR and NRP-1.

LucID: A Self-Activating Bioluminescent Biotin Ligase for Light-Free Proximity Labeling in Deep Tissues

This paper introduces LucID, a light-free bioluminescent biotin ligase for proximity labeling in deep tissues, enabling spatially confined biotinylation without external light or reactive chemicals.

A novel tool for labeling intermediary proteins between two non-interacting proteins

The paper introduces STUPPIT, a tool to label intermediary proteins between non-interacting proteins, validated using proteomics to identify novel interactors in signaling pathways.

APPLE-MS: A affinity purification-mass spectrometry method assisted by PafA-mediated proximity labeling

APPLE-MS improves protein-protein interaction detection by combining proximity labeling with high-specificity enrichment, revealing novel interactions and dynamics in mitochondrial and membrane-associated contexts.

PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow.

PLAMseq identifies genomic loci and protein interactors in a single workflow, validated for RNA polymerase II and CTCF, and applied to study histone H1 SUMOylation.

Improved method for detecting protein-protein interactions using proximity ligation assay

The paper identifies false positives in proximity ligation assay for protein-protein interaction detection and suggests ways to improve specificity, particularly for membrane proteins.

Identification of the Staphylococcus aureus Endothelial Cell Surface Interactome by Proximity Labeling

This study identifies 306 endothelial cell surface proteins interacting with Staphylococcus aureus using a proximity labeling approach, revealing 89 validated receptor candidates with 53% known to interact with pathogens.

Spatiotemporally-resolved mapping of extracellular proteomes via in vivo-compatible TyroID

This paper introduces TyroID, an in vivo-compatible method for high-resolution mapping of extracellular proteomes, validated through applications in tumor xenografts and live mouse brains.

Mesoscale proximity labeling to study macro changes to chromatin occupancy

The paper introduces MesoMap, a mesoscale proximity labeling method to study chromatin occupancy changes, showing how HDAC inhibitors and the drug SR-1815 affect gene expression.

Coupling proximity biotinylation with genomic targeting to characterize locus-specific changes in chromatin environments

The paper develops and applies CasTurbo and CasUltra to profile locus-specific chromatin proteomes and study BET inhibitor effects on MYC promoter dynamics.

Quantification of subcellular RNA localization through direct detection of RNA oxidation

This paper introduces OINC-seq, a method to quantify subcellular RNA localization through direct oxidation detection, and demonstrates its application in various cellular compartments and live zebrafish.

Proximity labeling and orthogonal nanobody pulldown (ID-oPD) approaches to map the spinophilin interactome uncover a putative role for spinophilin in protein homeostasis.

The paper uses ID-oPD to map spinophilin's interactome, identifying proteins involved in mRNA processing and translation, and suggests a role in synaptic protein expression.

iAPEX: Improved APEX-based proximity labeling for subcellular proteomics using an enzymatic reaction cascade

The paper introduces iAPEX, an improved APEX-based proximity labeling method for live-cell proteomics, and applies it to study primary cilia in Xenopus laevis, identifying new ciliary proteins and validating existing ones.

Target protein identification in live cells and organisms with a non-diffusive proximity tagging system

The paper introduces POST-IT, a non-diffusive proximity tagging system for identifying target proteins in live cells and zebrafish embryos, and demonstrates its application in discovering new drug targets.

Painting cell-cell interactions by horseradish peroxidase and endogenously generated hydrogen peroxide

This study introduces HRP-TM, a membrane-localized horseradish peroxidase that uses endogenous H2O2 to label contacting cells, enabling physiological cell-cell interaction analysis without exogenous reagents.

Photoactivated SOPP3 enables APEX2-mediated proximity labeling with high spatio-temporal resolution in live cells

This paper introduces a new proximity labeling method using photoactivated SOPP3 and APEX2 to enable high spatio-temporal resolution in live cells without exogenous H2O2 or cytotoxicity.

Locus-specific chromatin proteomics using dCas-guided proximity labelling in Aspergillus nidulans.

This paper demonstrates locus-specific chromatin proteomics in Aspergillus nidulans using dCas9-BirA guided proximity labeling, identifying 32 chromatin-associated proteins at the nitrate locus after background reduction.

Characterization of BioID tagging systems in budding yeast and exploring the interactome of the Ccr4-Not complex.

The paper compares BioID variants in budding yeast, identifies TurboID as the most effective, and explores the Ccr4-Not complex interactome.

Proximity labeling defines the phagosome lumen proteome of murine and primary human macrophages

This study introduces PhagoID, a proximity-labeling method to analyze the phagosome lumen proteome in murine and human macrophages, revealing both conserved and species-specific proteins.

A proximity proteomics pipeline with improved reproducibility and throughput

This paper introduces a scalable proximity proteomics pipeline that improves reproducibility and throughput in biotinylation-based spatial proteomics.

In Vivo Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5

The paper uses proximity labeling to identify Pef1's role in DNA damage response and autophagy-related processes in S. pombe.

Activity-driven trafficking of endogenous synaptic proteins through proximity labeling

This paper introduces a method to capture and quantify activity-driven trafficking of endogenous synaptic proteins using proximity labeling, revealing new insights into synaptic translocation dynamics.

Workflow enhancement of TurboID-mediated proximity labeling for SPY signaling network mapping

The paper improves TurboID-mediated proximity labeling by optimizing enrichment and analysis methods, identifying 160 SPY interactors including 100 novel ones.

Immunoproximity biotinylation reveals the axon initial segment proteome

The paper defines the axon initial segment proteome using immunoproximity biotinylation and identifies SCRIB as a highly enriched AIS protein.