ArticleRNA (New York, N.Y.)2020
RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
- Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity.PLoS computational biology · 2026Article
- Subcellular localization of human long non-coding RNAs is an isoform-resolved property masked by gene-level analysis.Molecular genetics and genomics : MGG · 2026Article
- APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.Nature protocols · 2026Review
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- mRNABench: A curated benchmark for mature mRNA property and function prediction.bioRxiv : the preprint server for biology · 2025Article
- Decoding subcellular RNA localization one molecule at a time.Genome biology · 2025Review
- RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization.Briefings in bioinformatics · 2023Article
- NN-RNALoc: Neural network-based model for prediction of mRNA sub-cellular localization using distance-based sub-sequence profiles.PloS one · 2023Article
- Prediction of Synaptically Localized RNAs in Human Neurons Using Developmental Brain Gene Expression Data.Genes · 2022Article
- Illuminating RNA biology through imaging.Nature cell biology · 2022Review
- Sequence determinants as key regulators in gene expression of T cells.Immunological reviews · 2021Review
- Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention.Nature communications · 2021Article
- Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Emerging Roles of Long Noncoding RNAs in the Cytoplasmic Milieu.Non-coding RNA · 2020Review
- Article
- RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus.bioRxiv : the preprint server for biology · 2020Article
- Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation.Cold Spring Harbor symposia on quantitative biology · 2019Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Subcellular localization is essential to RNA biogenesis, processing, and function across the gene expression life cycle. However, the specific nucleotide sequence motifs that direct RNA localization are incompletely understood. Fortunately, new sequencing technologies have provided transcriptome-wide atlases of RNA localization, creating an opportunity to leverage computational modeling. Here we present RNA-GPS, a new machine learning model that uses nucleotide-level features to predict RNA localization across eight different subcellular locations-the first to provide such a wide range of predictions. RNA-GPS's design enables high-throughput sequence ablation and feature importance analyses to probe the sequence motifs that drive localization prediction. We find localization informative motifs to be concentrated on 3'-UTRs and scattered along the coding sequence, and motifs related to splicing to be important drivers of predicted localization, even for cytotopic distinctions for membraneless bodies within the nucleus or for organelles within the cytoplasm. Overall, our results suggest transcript splicing is one of many elements influencing RNA subcellular localization.
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