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A proxitome-RNA-capture approach reveals that processing bodies repress coregulated hub genes

https://doi.org/10.1093/plcell/koad288
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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RNA ‐protein interactions in an unstructured context
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Codon usage bias
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Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2
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Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates
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Atlas of Subcellular RNA Localization Revealed by APEX-Seq
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N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis
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Orchestration of Processing Body Dynamics and mRNA Decay in Arabidopsis Immunity
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Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons
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The AP2/ERF Transcription Factor WIND1 Controls Cell Dedifferentiation in Arabidopsis
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N6-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis
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Codon usage pattern and predicted gene expression in Arabidopsis thaliana
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AtXRN4 Degrades mRNA in Arabidopsis and Its Substrates Include Selected miRNA Targets
inferredcites →https://doi.org/10.1016/j.molcel.2017.09.003openalex-snapshot
P-Body Purification Reveals the Condensation of Repressed mRNA Regulons
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High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies
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Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality
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P-Bodies: Composition, Properties, and Functions
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DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs
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The LC3-conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles
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mRNA translation in stress granules is not uncommon
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Biomolecular condensates amplify mRNA decapping by biasing enzyme conformation
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It’s not just a phase: function and characteristics of RNA-binding proteins in phase separation
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Identification of MEDIATOR16 as the Arabidopsis COBRA suppressor MONGOOSE1
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Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy
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Processing bodies control the selective translation for optimal development of Arabidopsis young seedlings
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N6-methyladenosine–modified RNA acts as a molecular glue that drives liquid–liquid phase separation in plants
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IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
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Marking RNA: m6A writers, readers, and functions in Arabidopsis
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Role of Arabidopsis RAP2.4 in Regulating Light- and Ethylene-Mediated Developmental Processes and Drought Stress Tolerance
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The BioStudies database—one stop shop for all data supporting a life sciences study
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inferredcites →https://doi.org/10.1101/2022.10.05.510616openalex-snapshot
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Arabidopsis DCP2, DCP1, and VARICOSE Form a Decapping Complex Required for Postembryonic Development
inferredcites →https://doi.org/10.1105/tpc.106.047621openalex-snapshot
Components of the Arabidopsis mRNA Decapping Complex Are Required for Early Seedling Development
inferredcites →https://doi.org/10.1105/tpc.109.070078openalex-snapshot
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inferredcites →https://doi.org/10.1105/tpc.111.088823openalex-snapshot
SCAR Mediates Light-Induced Root Elongation inArabidopsisthrough Photoreceptors and Proteasomes
inferredcites →https://doi.org/10.1105/tpc.114.134494openalex-snapshot
Tudor Staphylococcal Nuclease Links Formation of Stress Granules and Processing Bodies with mRNA Catabolism in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.20.00235openalex-snapshot
Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems
inferredcites →https://doi.org/10.1126/sciadv.abm7863openalex-snapshot
Ethylene modulates translation dynamics in Arabidopsis under submergence via GCN2 and EIN2
inferredcites →https://doi.org/10.1126/science.1082320openalex-snapshot
Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies
inferredcites →https://doi.org/10.1126/science.aaw4951openalex-snapshot
Protein condensates as aging Maxwell fluids
inferredcites →https://doi.org/10.1126/science.aax4240openalex-snapshot
Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation
inferredcites →https://doi.org/10.1126/science.abj6647openalex-snapshot
LLPS of FXR1 drives spermiogenesis by activating translation of stored mRNAs
inferredcites →https://doi.org/10.1126/science.abo0904openalex-snapshot
Meiotic exit in Arabidopsis is driven by P-body–mediated inhibition of translation
inferredcites →https://doi.org/10.1146/annurev-arplant-070522-052132openalex-snapshot
Proximity Labeling in Plants
inferredcites →https://doi.org/10.1146/annurev-physchem-071819-113553openalex-snapshot
Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties
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Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7
inferredcites →https://doi.org/10.1186/s13059-023-02947-4openalex-snapshot
m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis
inferredcites →https://doi.org/10.1242/dev.127613openalex-snapshot
ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging
inferredcites →https://doi.org/10.1371/journal.pcbi.0010072openalex-snapshot
Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast
inferredcites →https://doi.org/10.1371/journal.pone.0071425openalex-snapshot
Analysis of Genome-Wide Changes in the Translatome of Arabidopsis Seedlings Subjected to Heat Stress
inferredcites →https://doi.org/10.1371/journal.pone.0113380openalex-snapshot
On the Normalization of the Minimum Free Energy of RNAs by Sequence Length
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The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
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Single‐cell damage elicits regional, nematode‐restricting ethylene responses in roots
inferredcites →https://doi.org/10.15252/embj.2020104416openalex-snapshot
Flavonol‐mediated stabilization of PIN efflux complexes regulates polar auxin transport
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An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome
inferredcites →https://doi.org/10.3389/fpls.2012.00048openalex-snapshot
Adenosine Methylation in Arabidopsis mRNA is Associated with the 3′ End and Reduced Levels Cause Developmental Defects
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Structural organization of the polysomes adjacent to mammalian processing bodies (P-bodies)
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Context-dependent deposition and regulation of mRNAs in P-bodies
inferredcites →https://doi.org/10.7554/elife.41300openalex-snapshot
Correction: Context-dependent deposition and regulation of mRNAs in P-bodies
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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Modulation of Stress Granule Dynamics by Phosphorylation and Ubiquitination in Plants
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Modulation of Stress Granule Dynamics by Phosphorylation and Ubiquitination in Plants
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Machine Learning for Precision Epigenetic Modification in Plants
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Coupling Affinity Purification with Proximity Labeling in Arabidopsis: The APEAL Approach
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A practical guide to investigating biomolecular condensates: a comment from the plant community
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Modulation of stress granule dynamics by phosphorylation and ubiquitination in plants
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Plant memory and communication of encounters
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Regulatory links between the circadian clock and stress-induced biomolecular condensates
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Interplay between membrane system and biomolecular condensates in plant
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Protein Detection and Localization in Plant Cells Using Spot‐Tagging
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Application of Proximity-Labeling Techniques in Plants: A Review of Successful Cases
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MO25 binds CBL-interacting protein kinases associated with ribonucleoprotein condensates and regulates meiotic exit
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