ArticleRNA (New York, N.Y.)2019
Predictive models of subcellular localization of long RNAs.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Subcellular localization of human long non-coding RNAs is an isoform-resolved property masked by gene-level analysis.Molecular genetics and genomics : MGG · 2026Article
- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- Exon junction complex and nuclear pore complex components preferentially govern the nuclear export of spliced lncRNAs.Cell death discovery · 2026Article
- Intron Retention Controls Localization of lncRNAsbioRxiv : the preprint server for biology · 2026Article
- Chromatin-associated circRNA ciCRLF3(2) regulates cell differentiation blockage via activating non-homologous end joining-based DNA repair.Cell death and differentiation · 2026Article
- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- A comprehensive review on RNA subcellular localization prediction.Briefings in functional genomics · 2026Review
- High-throughput Screening of Sequence Elements Associated with RNA Localization.Computational and structural biotechnology journal · 2026Article
- LncRNA Subcellular Localization Across Diverse Cell Lines: An Exploration Using Deep Learning with InexactNon-coding RNA · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Studying relative RNA localization from nucleus to the cytosol.NAR genomics and bioinformatics · 2025Article
- An Emphasis on the Role of Long Non-Coding RNAs in Viral Gene Expression, Pathogenesis, and Innate Immunity in Viral Chicken Diseases.Non-coding RNA · 2025Review
- Involvement of lncRNAs NEAT1 and ZBTB11-AS1 in Active and Persistent HIV-1 Infection in C20 Human Microglial Cell Line.International journal of molecular sciences · 2025Article
- Decoding subcellular RNA localization one molecule at a time.Genome biology · 2025Review
- Deciphering the mechanisms of long non-coding RNAs in ferroptosis: insights into its clinical significance in cancer progression and immunology.Cell death discovery · 2025Review
- Review
- LINC01271 promotes fracture healing via regulating miR-19a-3p/PIK3CA axis.Journal of orthopaedic surgery and research · 2025Article
- Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves.BMC genomics · 2025Article
- Construction of an lncRNA-mediated ceRNA network to investigate the inflammatory regulatory mechanisms of ischemic stroke.PloS one · 2025Article
- Evaluation of machine learning models that predict lncRNA subcellular localization.NAR genomics and bioinformatics · 2024Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Export to the cytoplasm is a key regulatory junction for both protein-coding mRNAs and long noncoding RNAs (lncRNAs), and cytoplasmic enrichment varies dramatically both within and between those groups. We used a new computational approach and RNA-seq data from human and mouse cells to quantify the genome-wide association between cytoplasmic/nuclear ratios of both gene groups and various factors, including expression levels, splicing efficiency, gene architecture, chromatin marks, and sequence elements. Splicing efficiency emerged as the main predictive factor, explaining up to a third of the variability in localization. Combination with other features allowed predictive models that could explain up to 45% of the variance for protein-coding genes and up to 34% for lncRNAs. Factors associated with localization were similar between lncRNAs and mRNAs with some important differences. Readily accessible features can thus be used to predict RNA localization.
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Registered trials
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.