Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery

Deciphering molecular interactions by proximity labeling

(2021) Wei Qin et al.   NATURE METHODS

Proteomics of protein trafficking by in vivo tissue-specific labeling

(2021) Ilia A. Droujinine et al.   Nature Communications

Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches

(2020) Payman Samavarchi-Tehrani et al.   MOLECULAR & CELLULAR PROTEOMICS

How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms

(2020) Meredith Corley et al.   MOLECULAR CELL

Split-TurboID enables contact-dependent proximity labeling in cells

(2020) Kelvin F. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient recovery of the RNA-bound proteome and protein-bound transcriptome using phase separation (OOPS)

(2020) Eneko Villanueva et al.   Nature Protocols

Cell type-selective secretome profiling in vivo

(2020) Wei Wei et al.   Nature Chemical Biology

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

(2019) Rayner M. L. Queiroz et al.   NATURE BIOTECHNOLOGY

Spatial proteomics: a powerful discovery tool for cell biology

(2019) Emma Lundberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

(2019) Erika C. Urdaneta et al.   Nature Communications

Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells

(2019) Samuel A Myers et al.   MOLECULAR & CELLULAR PROTEOMICS

ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97

(2019) Bo Wang et al.   MOLECULAR CELL

The structure of human EXD2 reveals a chimeric 3′ to 5′ exonuclease domain that discriminates substrates via metal coordination

(2019) Jumi Park et al.   NUCLEIC ACIDS RESEARCH

Phase-to-Phase With Nucleoli – Stress Responses, Protein Aggregation and Novel Roles of RNA

(2019) Leena Latonen   Frontiers in Cellular Neuroscience

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

The nucleolus: a central response hub for the stressors that drive cancer progression

(2019) Shannon E. Weeks et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

CAPRI enables comparison of evolutionarily conserved RNA interacting regions

(2019) Amol Panhale et al.   Nature Communications

Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

(2019) Alejandro Padrón et al.   MOLECULAR CELL

Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling

(2019) Pengchong Wang et al.   Nature Chemical Biology

High-throughput approaches to profile RNA-protein interactions

(2019) Misha Nechay et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities

(2019) Laura J. Keller et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

A Proximity Labeling Strategy Provides Insights into the Composition and Dynamics of Lipid Droplet Proteomes

(2018) Kirill Bersuker et al.   DEVELOPMENTAL CELL

Biogenesis of the bc 1 Complex of the Mitochondrial Respiratory Chain

(2018) Mama Ndi et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic Characterization of Stress-Induced RNA Granulation

(2018) Sim Namkoong et al.   MOLECULAR CELL

How many human proteoforms are there?

(2018) Ruedi Aebersold et al.   Nature Chemical Biology

Capturing the interactome of newly transcribed RNA

(2018) Xichen Bao et al.   NATURE METHODS

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptome-wide discovery of coding and noncoding RNA-binding proteins

(2018) Rongbing Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mitochondrial outer-membrane location of the EXD2 exonuclease contradicts its direct role in nuclear DNA repair

(2018) Fenna Hensen et al.   Scientific Reports

Efficient proximity labeling in living cells and organisms with TurboID

(2018) Tess C Branon et al.   NATURE BIOTECHNOLOGY

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel et al.   CELL

Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles

(2018) Anne-Claude Gingras et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

DDX54 regulates transcriptome dynamics during DNA damage response

(2017) Miha Milek et al.   GENOME RESEARCH

Mutated PET117 causes complex IV deficiency and is associated with neurodevelopmental regression and medulla oblongata lesions

(2017) G. H. Renkema et al.   HUMAN GENETICS

The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review)

(2017) Fatima Ardito et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification

(2017) Meeli Mullari et al.   JOURNAL OF PROTEOME RESEARCH

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

(2017) Pornchai Kaewsapsak et al.   eLife

Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation

(2017) Victoria Hung et al.   eLife

A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

(2016) Jason D. Arroyo et al.   Cell Metabolism

Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins

(2016) Mahmoud-Reza Rafiee et al.   MOLECULAR CELL

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells

(2016) Chongsheng He et al.   MOLECULAR CELL

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2

(2016) Victoria Hung et al.   Nature Protocols

Serial interactome capture of the human cell nucleus

(2016) Thomas Conrad et al.   Nature Communications

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging

(2014) Victoria Hung et al.   MOLECULAR CELL

Directed evolution of APEX2 for electron microscopy and proximity labeling

(2014) Stephanie S Lam et al.   NATURE METHODS

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading

(2014) Keith T Gagnon et al.   Nature Protocols

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Free mRNA in excess upon polysome dissociation is a scaffold for protein multimerization to form stress granules

(2014) Ouissame Bounedjah et al.   NUCLEIC ACIDS RESEARCH

Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling

(2014) C. C. Williams et al.   SCIENCE

How cells get the message: dynamic assembly and function of mRNA–protein complexes

(2013) Michaela Müller-McNicoll et al.   NATURE REVIEWS GENETICS

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

(2013) H.-W. Rhee et al.   SCIENCE

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Phosphorylation meets nuclear import: a review

(2012) Jonathan D Nardozzi et al.   Cell Communication and Signaling

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR CELL

Quantitative phosphoproteomics to characterize signaling networks

(2012) Kristoffer T.G. Rigbolt et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease

(2011) Gerald W. Hart et al.   Annual Review of Biochemistry

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

The genomic binding sites of a noncoding RNA

(2011) M. D. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA

(2011) Nicholas J. Watkins et al.   Wiley Interdisciplinary Reviews-RNA

Nutrient-sensitized screening for drugs that shift energy metabolism from mitochondrial respiration to glycolysis

(2010) Vishal M Gohil et al.   NATURE BIOTECHNOLOGY

Purification of Proteins Associated with Specific Genomic Loci

(2009) Jérôme Déjardin et al.   CELL

Tom20 Mediates Localization of mRNAs to Mitochondria in a Translation-Dependent Manner

(2009) E. Eliyahu et al.   MOLECULAR AND CELLULAR BIOLOGY

RNA recognition motifs: boring? Not quite

(2008) Antoine Cléry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Identification and Characterization of a General Nuclear Translocation Signal in Signaling Proteins

(2008) Dana Chuderland et al.   MOLECULAR CELL

A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly

(2008) Takbum Ohn et al.   NATURE CELL BIOLOGY