Biotin and Related Studies

Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component

The paper introduces ecTurboID, a method to profile extracellular protein interactions, identifying LDLR as a new EGF-dependent EGFR partner.

Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies proteins that bind and control its translational efficiency in the cell cycle

The paper identifies proteins that bind the FAS1 mRNA in yeast during the cell cycle and shows Tdh3p's role in regulating its translation and cell cycle progression.

Phototriggered profiling of receptor-proximal proteins in vivo in minutes

This paper introduces PhoxID, a light-activated proximity labeling method to study receptor interactomes in live mice with minute-order temporal resolution.

Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells

This paper introduces LOV-Turbo, a light-regulated proximity labeling tool that enhances spatial and temporal control of proteomic mapping in living cells.

Specific Pupylation as IDEntity Reporter (SPIDER) for the identification of Protein-Biomolecule interactions

The paper introduces SPIDER, a method using pupylation and streptavidin-biotin to identify protein-biomolecule interactions, demonstrating its application in various biological contexts.

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines.

The paper uses TurboID-NES to profile proteomes of microglial and neuronal cell lines, showing it captures a significant portion of the proteome and responds to LPS treatment.

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.

The paper introduces O-MAP, a method for discovering RNA-interacting proteins, transcripts, and genomic loci in situ with high precision and without genetic manipulation.

A toolbox for systematic discovery of stable and transient protein interactors in baker's yeast

The paper develops ABOLISH, a method to reduce endogenous biotinylation in yeast, enabling more accurate detection of both stable and transient protein interactions using biotin ligases.

A new monoclonal antibody enables BAR analysis of subcellular importin β1 interactomes

This paper develops a novel anti-KPNB1 monoclonal antibody for BAR analysis, revealing new importin β1 interactors and expanding its known functions beyond nucleocytoplasmic transport.

Drug interaction mapping with proximity dependent enzyme recruiting chimeras

The paper introduces a method to identify small molecule protein targets using engineered biotin ligases and chimeric chemical probes, demonstrating its applicability with various inhibitors.

Molecular recording of calcium signaling via calcium-dependent protein proximity labeling

This paper introduces Cal-ID, a tool that records calcium signaling and neuronal activity by biotinylating nearby proteins, enabling high-resolution molecular mapping.

Monitoring Protein Import into the Endoplasmic Reticulum in Living Cells with Proximity Labeling

This study uses proximity labeling to monitor protein import into the endoplasmic reticulum in living cells and identifies factors influencing ER protein import.

Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR

The paper uses proximity labeling and mass spectrometry to identify proteins associated with internalized EGFR, revealing TFG's role in endosomal sorting.

Cell type-specific biotin labeling in vivo resolves regional neuronal proteomic differences in mouse brain

Physical and functional interactome atlas of human receptor tyrosine kinases

The paper maps the interactome and substrates of human receptor tyrosine kinases using AP-MS, BioID, and kinase assays, revealing interactions and functions of both well-known and understudied RTKs.

Subcellular proteomics of dopamine neurons in the mouse brain reveals axonal enrichment of proteins encoded by Parkinson's disease-linked genes

The paper uses subcellular proteomics to show Parkinson's disease-linked genes are enriched in axons of dopaminergic neurons in the mouse brain.

CLUH interactome reveals an association to SPAG5 and a proximity to the translation of mitochondrial protein

The paper identifies CLUH interactome in mammalian cells, revealing its association with SPAG5 and proximity to mitochondrial protein translation.

A chemical strategy to control protein networks in vivo

This paper introduces Mandi, a novel chemical inducer of protein proximity, and demonstrates its use in cell culture and living organisms for protein manipulation.

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

This study introduces Halo-seq, a method for quantifying subcellular RNA populations, and finds that AU-rich elements are enriched in the nucleus and their export depends on HuR.

Defining proximity proteomics of post-translationally modified proteins by antibody-mediated protein A-APEX2 labeling

The paper introduces AMAPEX, a method to label proximal proteins of post-translationally modified proteins using antibody-mediated protein A-APEX2 labeling, and validates it with histone modification profiling.

Functional proximity mapping of RNA binding proteins uncovers a mitochondrial mRNA anchor that promotes stress recovery

The paper introduces APEX-PS to map RNA binding proteins in cellular compartments, identifying SYNJ2BP as a mitochondrial mRNA anchor that aids stress recovery.

Cell type and subcellular compartment specific APEX2 proximity labeling proteomics in the mouse brain

The paper develops a method to profile cell-type specific subcellular proteomes in the mouse brain using APEX2 proximity labeling.

A proximity-dependent biotinylation map of a human cell: an interactive web resource

Profiling 192 subcellular markers by proximity-dependent biotinylation (BioID) in human HEK 293 cells maps 4,145 proteins across 32 compartments via 35,902 interactions, available with analysis tools at humancellmap.org.

CBRPP: a new RNA-centric method to study RNA-protein interactions

CBRPP identifies RNA-associated proteins in native cells without cross-linking or RNA manipulation.

A toolbox for efficient proximity-dependent biotinylation in zebrafish embryos

The paper develops and benchmarks in vivo TurboID and miniTurbo labeling in zebrafish embryos for proximity-dependent biotinylation, enabling protein discovery in living vertebrates.

Development and Comparative Evaluation of Endolysosomal Proximity Labeling-based Proteomic Methods in Human iPSC-derived Neurons

The paper develops and evaluates a proximity labeling method to study the endolysosomal proteome in human neurons, showing improved data normalization and complementary coverage compared to overexpression approaches.

Proximity-dependent proteomics reveals extensive interactions of Protocadherin-19 with regulators of Rho GTPases and the microtubule cytoskeleton

This study identifies the interactome of Protocadherin-19 using BioID and proximity-dependent biotinylation, revealing interactions with Rho GTPase regulators and microtubule proteins.

RNA-protein interaction mapping via MS2 or Cas13-based APEX targeting

This study maps RNA-protein interactions in living cells using MS2 and Cas13-based APEX2 targeting, identifying novel interactions like hTR and ALKBH5.

Proximity Labeling-assisted Identification of Endogenous Kinase Substrates

This study identifies endogenous kinase substrates using proximity labeling and phosphoproteomics, finding 33 CK2 and 52 PKA substrates and linking mutations to altered phosphorylation.

In vivo discovery of RNA proximal proteins in human cells via proximity-dependent biotinylation

This paper introduces RPL, a method to identify RNA-proximal proteins in human cells using CRISPR-Cas13b and APEX2, revealing new insights into RNA interactions and subcellular localization.