ArticleNature genetics2024
Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 44 citations in OpenAlex.
- Uncovering essential RNA components of fusion oncoprotein condensates using bicon-seq.The EMBO journal · 2026Article
- Exploring the Effect of Whole-Genome Duplication on Salmonid LincRNA Repertoire.International journal of molecular sciences · 2026Article
- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- Heart rate control by listening to light.Nature communications · 2026Article
- An integrative workflow for lncRNA orthology detection and its application to 13 evolutionarily diverse species.Nucleic acids research · 2026Article
- Long Non-coding RNA TLX1NB Regulates Inflammatory Response in Periodontitis by Interacting With Matrix Metalloproteinase 8.Inflammation · 2026Article
- Review
- GAS5 mediates notch signaling to exacerbate calcium oxalate-induced renal injury through the NF-κB/NLRP3 axis by promoting macrophage polarization.Cellular and molecular life sciences : CMLS · 2026Article
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- Article
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
- CIRCpedia v3: an interactive database for circular RNA characterization and functional exploration.Nucleic acids research · 2026Article
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The syntenic long non-coding RNA DANCR is an essential regulator of zebrafish development and a human melanoma oncogene.PLoS genetics · 2025Article
- Computational identification and validation of non-coding rna biomarkers in gastrointestinal cancer.Functional & integrative genomics · 2025Review
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Computational discovery of conserved RNA structures and functional characterization of a structured lncRNA inNon-coding RNA research · 2025Article
- The functionally conserved human lncRNA motif GULF lowers glucose and lipid levels in obese mice.The Journal of clinical investigation · 2025Article
- Article
- Review
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
Abstract
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects, which were subsequently rescued by predicted zebrafish homologs. Knocking down coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Furthermore, we verified that human, mouse and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved functions relying on specific RBP-binding sites. Overall, our study demonstrates a comprehensive approach for studying the functional conservation of lncRNAs and implicates numerous lncRNAs in regulating vertebrate physiology.
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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.