ArticleGenome research2017
The identification and functional annotation of RNA structures conserved in vertebrates.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
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- Regulatory roles of LncRNAs in colorectal cancer immune evasion: current concepts and future perspectives.Discover oncology · 2025Review
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Computational discovery of conserved RNA structures and functional characterization of a structured lncRNA inNon-coding RNA research · 2025Article
- Identification of a conserved RNA structure in thebioRxiv : the preprint server for biology · 2025Article
- SMDesigner: a program to design sequence mutations to assess RNA structure.RNA (New York, N.Y.) · 2025Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Targeting and engineering long non-coding RNAs for cancer therapy.Nature reviews. Genetics · 2024Review
- RNAscape: geometric mapping and customizable visualization of RNA structure.Nucleic acids research · 2024Article
- Massively parallel dissection of RNA in RNA-protein interactions in vivo.Nucleic acids research · 2024Article
- Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA.Genome research · 2024Article
- Current concepts of the crosstalk between lncRNA and E2F1: shedding light on the cancer therapy.Frontiers in pharmacology · 2024Review
- GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins.Genome biology · 2023Article
- High-density lipoprotein regulates angiogenesis by long non-coding RNA HDRACA.Signal transduction and targeted therapy · 2023Article
- Tumour mutations in long noncoding RNAs enhance cell fitness.Nature communications · 2023Article
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
- Thirteen dubious ways to detect conserved structural RNAs.IUBMB life · 2023Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than sequence-based, alignments. After careful correction for sequence identity and GC content, we predict ∼516,000 human genomic regions containing CRSs. We find that a substantial fraction of human-mouse CRS regions (1) colocalize consistently with binding sites of the same RNA binding proteins (RBPs) or (2) are transcribed in corresponding tissues. Additionally, a CaptureSeq experiment revealed expression of many of our CRS regions in human fetal brain, including 662 novel ones. For selected human and mouse candidate pairs, qRT-PCR and in vitro RNA structure probing supported both shared expression and shared structure despite low abundance and low sequence identity. About 30,000 CRS regions are located near coding or long noncoding RNA genes or within enhancers. Structured (CRS overlapping) enhancer RNAs and extended 3' ends have significantly increased expression levels over their nonstructured counterparts. Our findings of transcribed uncharacterized regulatory regions that contain CRSs support their RNA-mediated functionality.
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