ArticleNucleic acids research2022
A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 38 citations in OpenAlex.
- Promoter identity shapes splicing outcomes and fidelity.Nature communications · 2026Article
- NaP-TRAP: A Versatile and Accessible Workflow to Dissect Principles of Translational Regulation and mRNA Stability.Current protocols · 2026Article
- Robust mammalian RNA localization elements are complex and multipartite.bioRxiv : the preprint server for biology · 2026Article
- The choreography of development: RNA localization across time and space.Development (Cambridge, England) · 2026Review
- Cracking the (zip)code of dynein-dependent RNA localization.Nature structural & molecular biology · 2026Article
- In Vivo Massively Parallel Reporter Assay Reveals Sequence Determinants of mRNA Localization in Astrocytes.bioRxiv : the preprint server for biology · 2026Article
- NaP-TRAP: A versatile and accessible workflow to dissect principles of translational regulation and mRNA stability.bioRxiv : the preprint server for biology · 2026Article
- Disrupting USP14-mediated PARP1 dynamics reinstates MIC-A/B-driven antigen-independent CD8Science advances · 2026Article
- TDP-43 directly inhibits mRNA accumulation in neurites through modulation of mRNA stability.The EMBO journal · 2026Article
- Dysregulated neuronal mRNA transport and translation in FTD/ALS.NPJ dementia · 2026Review
- Review
- Systematic discovery of subcellular RNA patterns in the gut epithelium.Genome biology · 2025Article
- USP14 inhibits mitophagy and promotes tumorigenesis and chemosensitivity through deubiquitinating BAG4 in microsatellite instability-high colorectal cancer.Molecular medicine (Cambridge, Mass.) · 2025Article
- Decoding the complex journeys of RNAs along neurons.Nucleic acids research · 2025Article
- Article
- Axonal RNA localization is essential for long-term memory.Nature communications · 2025Article
- Decoding subcellular RNA localization one molecule at a time.Genome biology · 2025Review
- Quantification of subcellular RNA localization through direct detection of RNA oxidation.Nucleic acids research · 2025Article
- Quantification of subcellular RNA localization through direct detection of RNA oxidation.bioRxiv : the preprint server for biology · 2024Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Asymmetric subcellular mRNA localization allows spatial regulation of gene expression and functional compartmentalization. In neurons, localization of specific mRNAs to neurites is essential for cellular functioning. However, it is largely unknown how transcript sorting works in a sequence-specific manner. Here, we combined subcellular transcriptomics and massively parallel reporter assays and tested ∼50 000 sequences for their ability to localize to neurites. Mapping the localization potential of >300 genes revealed two ways neurite targeting can be achieved: focused localization motifs and broadly encoded localization potential. We characterized the interplay between RNA stability and localization and identified motifs able to bias localization towards neurite or soma as well as the trans-acting factors required for their action. Based on our data, we devised machine learning models that were able to predict the localization behavior of novel reporter sequences. Testing this predictor on native mRNA sequencing data showed good agreement between predicted and observed localization potential, suggesting that the rules uncovered by our MPRA also apply to the localization of native full-length transcripts.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.